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Sample records for fractal structure filaments

  1. 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.}

  2. Fractal structure of asphaltene aggregates.

    PubMed

    Rahmani, Nazmul H G; Dabros, Tadeusz; Masliyah, Jacob H

    2005-05-15

    A photographic technique coupled with image analysis was used to measure the size and fractal dimension of asphaltene aggregates formed in toluene-heptane solvent mixtures. First, asphaltene aggregates were examined in a Couette device and the fractal-like aggregate structures were quantified using boundary fractal dimension. The evolution of the floc structure with time was monitored. The relative rates of shear-induced aggregation and fragmentation/restructuring determine the steady-state floc structure. The average floc structure became more compact or more organized as the floc size distribution attained steady state. Moreover, the higher the shear rate is, the more compact the floc structure is at steady state. Second, the fractal dimensions of asphaltene aggregates were also determined in a free-settling test. The experimentally determined terminal settling velocities and characteristic lengths of the aggregates were utilized to estimate the 2D and 3D fractal dimensions. The size-density fractal dimension (D(3)) of the asphaltene aggregates was estimated to be in the range from 1.06 to 1.41. This relatively low fractal dimension suggests that the asphaltene aggregates are highly porous and very tenuous. The aggregates have a structure with extremely low space-filling capacity.

  3. Backbone fractal dimension and fractal hybrid orbital of protein structure

    NASA Astrophysics Data System (ADS)

    Peng, Xin; Qi, Wei; Wang, Mengfan; Su, Rongxin; He, Zhimin

    2013-12-01

    Fractal geometry analysis provides a useful and desirable tool to characterize the configuration and structure of proteins. In this paper we examined the fractal properties of 750 folded proteins from four different structural classes, namely (1) the α-class (dominated by α-helices), (2) the β-class (dominated by β-pleated sheets), (3) the (α/β)-class (α-helices and β-sheets alternately mixed) and (4) the (α + β)-class (α-helices and β-sheets largely segregated) by using two fractal dimension methods, i.e. "the local fractal dimension" and "the backbone fractal dimension" (a new and useful quantitative parameter). The results showed that the protein molecules exhibit a fractal behavior in the range of 1 ⩽ N ⩽ 15 (N is the number of the interval between two adjacent amino acid residues), and the value of backbone fractal dimension is distinctly greater than that of local fractal dimension for the same protein. The average value of two fractal dimensions decreased in order of α > α/β > α + β > β. Moreover, the mathematical formula for the hybrid orbital model of protein based on the concept of backbone fractal dimension is in good coincidence with that of the similarity dimension. So it is a very accurate and simple method to analyze the hybrid orbital model of protein by using the backbone fractal dimension.

  4. Fractal structures in nonlinear dynamics

    NASA Astrophysics Data System (ADS)

    Aguirre, Jacobo; Viana, Ricardo L.; Sanjuán, Miguel A. F.

    2009-01-01

    In addition to the striking beauty inherent in their complex nature, fractals have become a fundamental ingredient of nonlinear dynamics and chaos theory since they were defined in the 1970s. Moreover, fractals have been detected in nature and in most fields of science, with even a certain influence in the arts. Fractal structures appear naturally in dynamical systems, in particular associated with the phase space. The analysis of these structures is especially useful for obtaining information about the future behavior of complex systems, since they provide fundamental knowledge about the relation between these systems and uncertainty and indeterminism. Dynamical systems are divided into two main groups: Hamiltonian and dissipative systems. The concepts of the attractor and basin of attraction are related to dissipative systems. In the case of open Hamiltonian systems, there are no attractors, but the analogous concepts of the exit and exit basin exist. Therefore basins formed by initial conditions can be computed in both Hamiltonian and dissipative systems, some of them being smooth and some fractal. This fact has fundamental consequences for predicting the future of the system. The existence of this deterministic unpredictability, usually known as final state sensitivity, is typical of chaotic systems, and makes deterministic systems become, in practice, random processes where only a probabilistic approach is possible. The main types of fractal basin, their nature, and the numerical and experimental techniques used to obtain them from both mathematical models and real phenomena are described here, with special attention to their ubiquity in different fields of physics.

  5. 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.

  6. Fragmentation of Fractal Random Structures

    NASA Astrophysics Data System (ADS)

    Elçi, Eren Metin; Weigel, Martin; Fytas, Nikolaos G.

    2015-03-01

    We analyze the fragmentation behavior of random clusters on the lattice under a process where bonds between neighboring sites are successively broken. Modeling such structures by configurations of a generalized Potts or random-cluster model allows us to discuss a wide range of systems with fractal properties including trees as well as dense clusters. We present exact results for the densities of fragmenting edges and the distribution of fragment sizes for critical clusters in two dimensions. Dynamical fragmentation with a size cutoff leads to broad distributions of fragment sizes. The resulting power laws are shown to encode characteristic fingerprints of the fragmented objects.

  7. Segmentation of histological structures for fractal analysis

    NASA Astrophysics Data System (ADS)

    Dixon, Vanessa; Kouznetsov, Alexei; Tambasco, Mauro

    2009-02-01

    Pathologists examine histology sections to make diagnostic and prognostic assessments regarding cancer based on deviations in cellular and/or glandular structures. However, these assessments are subjective and exhibit some degree of observer variability. Recent studies have shown that fractal dimension (a quantitative measure of structural complexity) has proven useful for characterizing structural deviations and exhibits great potential for automated cancer diagnosis and prognosis. Computing fractal dimension relies on accurate image segmentation to capture the architectural complexity of the histology specimen. For this purpose, previous studies have used techniques such as intensity histogram analysis and edge detection algorithms. However, care must be taken when segmenting pathologically relevant structures since improper edge detection can result in an inaccurate estimation of fractal dimension. In this study, we established a reliable method for segmenting edges from grayscale images. We used a Koch snowflake, an object of known fractal dimension, to investigate the accuracy of various edge detection algorithms and selected the most appropriate algorithm to extract the outline structures. Next, we created validation objects ranging in fractal dimension from 1.3 to 1.9 imitating the size, structural complexity, and spatial pixel intensity distribution of stained histology section images. We applied increasing intensity thresholds to the validation objects to extract the outline structures and observe the effects on the corresponding segmentation and fractal dimension. The intensity threshold yielding the maximum fractal dimension provided the most accurate fractal dimension and segmentation, indicating that this quantitative method could be used in an automated classification system for histology specimens.

  8. Fractal structures in nonlinear plasma physics.

    PubMed

    Viana, R L; da Silva, E C; Kroetz, T; Caldas, I L; Roberto, M; Sanjuán, M A F

    2011-01-28

    Fractal structures appear in many situations related to the dynamics of conservative as well as dissipative dynamical systems, being a manifestation of chaotic behaviour. In open area-preserving discrete dynamical systems we can find fractal structures in the form of fractal boundaries, associated to escape basins, and even possessing the more general property of Wada. Such systems appear in certain applications in plasma physics, like the magnetic field line behaviour in tokamaks with ergodic limiters. The main purpose of this paper is to show how such fractal structures have observable consequences in terms of the transport properties in the plasma edge of tokamaks, some of which have been experimentally verified. We emphasize the role of the fractal structures in the understanding of mesoscale phenomena in plasmas, such as electromagnetic turbulence.

  9. 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

  10. [Molecular structure and fractal analysis of oligosaccharide].

    PubMed

    Liu, Wen-long; Wang, Lu-man; He, Dong-qi; Zhang, Tian-lan; Gou, Bao-di; Li, Qing

    2014-10-18

    To propose a calculation method of oligosaccharides' fractal dimension, and to provide a new approach to studying the drug molecular design and activity. By using the principle of energy optimization and computer simulation technology, the steady structures of oligosaccharides were found, and an effective way of oligosaccharides fractal dimension's calculation was further established by applying the theory of box dimension to the chemical compounds. By using the proposed method, 22 oligosaccharides' fractal dimensions were calculated, with the mean 1.518 8 ± 0.107 2; in addition, the fractal dimensions of the two activity multivalent oligosaccharides which were confirmed by experiments, An-2 and Gu-4, were about 1.478 8 and 1.516 0 respectively, while C-type lectin-like receptor Dectin-1's fractal dimension was about 1.541 2. The experimental and computational results were expected to help to find a class of glycoside drugs whose target receptor was Dectin-1. Fractal dimension, differing from other known macro parameters, is a useful tool to characterize the compound molecules' microscopic structure and function, which may play an important role in the molecular design and biological activity study. In the process of oligosaccharides drug screening, the fractal dimension of receptor and designed oligosaccharides or glycoclusters can be calculated respectively. The oligosaccharides with fractal dimension close to that of target receptor should then take priority compared with others, to get the drug molecules with latent activity.

  11. Fractal structures and fractal functions as disease indicators

    USGS Publications Warehouse

    Escos, J.M; Alados, C.L.; Emlen, J.M.

    1995-01-01

    Developmental instability is an early indicator of stress, and has been used to monitor the impacts of human disturbance on natural ecosystems. Here we investigate the use of different measures of developmental instability on two species, green peppers (Capsicum annuum), a plant, and Spanish ibex (Capra pyrenaica), an animal. For green peppers we compared the variance in allometric relationship between control plants, and a treatment group infected with the tomato spotted wilt virus. The results show that infected plants have a greater variance about the allometric regression line than the control plants. We also observed a reduction in complexity of branch structure in green pepper with a viral infection. Box-counting fractal dimension of branch architecture declined under stress infection. We also tested the reduction in complexity of behavioral patterns under stress situations in Spanish ibex (Capra pyrenaica). Fractal dimension of head-lift frequency distribution measures predator detection efficiency. This dimension decreased under stressful conditions, such as advanced pregnancy and parasitic infection. Feeding distribution activities reflect food searching efficiency. Power spectral analysis proves to be the most powerful tool for character- izing fractal behavior, revealing a reduction in complexity of time distribution activity under parasitic infection.

  12. Filament Winding Of Carbon/Carbon Structures

    NASA Technical Reports Server (NTRS)

    Jacoy, Paul J.; Schmitigal, Wesley P.; Phillips, Wayne M.

    1991-01-01

    Improved method of winding carbon filaments for carbon/carbon composite structures less costly and labor-intensive, also produces more consistent results. Involves use of roller squeegee to ensure filaments continuously wet with resin during winding. Also involves control of spacing and resin contents of plies to obtain strong bonds between carbon filaments and carbon matrices. Lends itself to full automation and involves use of filaments and matrix-precursor resins in their simplest forms, thereby reducing costs.

  13. Dynamic structure factor of vibrating fractals.

    PubMed

    Reuveni, Shlomi; Klafter, Joseph; Granek, Rony

    2012-02-10

    Motivated by novel experimental work and the lack of an adequate theory, we study the dynamic structure factor S(k,t) of large vibrating fractal networks at large wave numbers k. We show that the decay of S(k,t) is dominated by the spatially averaged mean square displacement of a network node, which evolves subdiffusively in time, ((u[over →](i)(t)-u[over →](i)(0))(2))∼t(ν), where ν depends on the spectral dimension d(s) and fractal dimension d(f). As a result, S(k,t) decays as a stretched exponential S(k,t)≈S(k)e(-(Γ(k)t)(ν)) with Γ(k)∼k(2/ν). Applications to a variety of fractal-like systems are elucidated.

  14. Intermediate Filaments: Structure and Assembly.

    PubMed

    Herrmann, Harald; Aebi, Ueli

    2016-11-01

    Proteins of the intermediate filament (IF) supergene family are ubiquitous structural components that comprise, in a cell type-specific manner, the cytoskeleton proper in animal tissues. All IF proteins show a distinctly organized, extended α-helical conformation prone to form two-stranded coiled coils, which are the basic building blocks of these highly flexible, stress-resistant cytoskeletal filaments. IF proteins are highly charged, thus representing versatile polyampholytes with multiple functions. Taking vimentin, keratins, and the nuclear lamins as our prime examples, we present an overview of their molecular and structural parameters. These, in turn, document the ability of IF proteins to form distinct, highly diverse supramolecular assemblies and biomaterials found, for example, at the inner nuclear membrane, throughout the cytoplasm, and in highly complex extracellular appendages, such as hair and nails, of vertebrate organisms. Ultimately, our aim is to set the stage for a more rational understanding of the immediate effects that missense mutations in IF genes have on cellular functions and for their far-reaching impact on the development of the numerous IF diseases caused by them.

  15. Fractality in selfsimilar minimal mass structures

    NASA Astrophysics Data System (ADS)

    De Tommasi, D.; Maddalena, F.; Puglisi, G.; Trentadue, F.

    2017-10-01

    In this paper we study the diffusely observed occurrence of Fractality and Self-organized Criticality in mechanical systems. We analytically show, based on a prototypical compressed tensegrity structure, that these phenomena can be viewed as the result of the contemporary attainment of mass minimization and global stability in elastic systems.

  16. Fractal structures in centrifugal flywheel governor system

    NASA Astrophysics Data System (ADS)

    Rao, Xiao-Bo; Chu, Yan-Dong; Lu-Xu; Chang, Ying-Xiang; Zhang, Jian-Gang

    2017-09-01

    The global structure of nonlinear response of mechanical centrifugal governor, forming in two-dimensional parameter space, is studied in this paper. By using three kinds of phases, we describe how responses of periodicity, quasi-periodicity and chaos organize some self-similarity structures with parameters varying. For several parameter combinations, the regular vibration shows fractal characteristic, that is, the comb-shaped self-similarity structure is generated by alternating periodic response with intermittent chaos, and Arnold's tongues embedded in quasi-periodic response are organized according to Stern-Brocot tree. In particular, a new type of mixed-mode oscillations (MMOs) is found in the periodic response. These unique structures reveal the natural connection of various responses between part and part, part and the whole in parameter space based on self-similarity of fractal. Meanwhile, the remarkable and unexpected results are to contribute a valid dynamic reference for practical applications with respect to mechanical centrifugal governor.

  17. Myosin filament structure in vertebrate smooth muscle

    PubMed Central

    1996-01-01

    The in vivo structure of the myosin filaments in vertebrate smooth muscle is unknown. Evidence from purified smooth muscle myosin and from some studies of intact smooth muscle suggests that they may have a nonhelical, side-polar arrangement of crossbridges. However, the bipolar, helical structure characteristic of myosin filaments in striated muscle has not been disproved for smooth muscle. We have used EM to investigate this question in a functionally diverse group of smooth muscles (from the vascular, gastrointestinal, reproductive, and visual systems) from mammalian, amphibian, and avian species. Intact muscle under physiological conditions, rapidly frozen and then freeze substituted, shows many myosin filaments with a square backbone in transverse profile. Transverse sections of fixed, chemically skinned muscles also show square backbones and, in addition, reveal projections (crossbridges) on only two opposite sides of the square. Filaments gently isolated from skinned smooth muscles and observed by negative staining show crossbridges with a 14.5-nm repeat projecting in opposite directions on opposite sides of the filament. Such filaments subjected to low ionic strength conditions show bare filament ends and an antiparallel arrangement of myosin tails along the length of the filament. All of these observations are consistent with a side-polar structure and argue against a bipolar, helical crossbridge arrangement. We conclude that myosin filaments in all smooth muscles, regardless of function, are likely to be side-polar. Such a structure could be an important factor in the ability of smooth muscles to contract by large amounts. PMID:8698822

  18. Evaluation of 3D Printer Accuracy in Producing Fractal Structure.

    PubMed

    Kikegawa, Kana; Takamatsu, Kyuuichirou; Kawakami, Masaru; Furukawa, Hidemitsu; Mayama, Hiroyuki; Nonomura, Yoshimune

    2017-01-01

    Hierarchical structures, also known as fractal structures, exhibit advantageous material properties, such as water- and oil-repellency as well as other useful optical characteristics, owing to its self-similarity. Various methods have been developed for producing hierarchical geometrical structures. Recently, fractal structures have been manufactured using a 3D printing technique that involves computer-aided design data. In this study, we confirmed the accuracy of geometrical structures when Koch curve-like fractal structures with zero to three generations were printed using a 3D printer. The fractal dimension was analyzed using a box-counting method. This analysis indicated that the fractal dimension of the third generation hierarchical structure was approximately the same as that of the ideal Koch curve. These findings demonstrate that the design and production of fractal structures can be controlled using a 3D printer. Although the interior angle deviated from the ideal value, the side length could be precisely controlled.

  19. 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.

  20. After notes on self-similarity exponent for fractal structures

    NASA Astrophysics Data System (ADS)

    Fernández-Martínez, Manuel; Caravaca Garratón, Manuel

    2017-06-01

    Previous works have highlighted the suitability of the concept of fractal structure, which derives from asymmetric topology, to propound generalized definitions of fractal dimension. The aim of the present article is to collect some results and approaches allowing to connect the self-similarity index and the fractal dimension of a broad spectrum of random processes. To tackle with, we shall use the concept of induced fractal structure on the image set of a sample curve. The main result in this paper states that given a sample function of a random process endowed with the induced fractal structure on its image, it holds that the self-similarity index of that function equals the inverse of its fractal dimension.

  1. Paradigms of Complexity: Fractals and Structures in the Sciences

    NASA Astrophysics Data System (ADS)

    Novak, Miroslav M.

    The Table of Contents for the book is as follows: * Preface * The Origin of Complexity (invited talk) * On the Existence of Spatially Uniform Scaling Laws in the Climate System * Multispectral Backscattering: A Fractal-Structure Probe * Small-Angle Multiple Scattering on a Fractal System of Point Scatterers * Symmetric Fractals Generated by Cellular Automata * Bispectra and Phase Correlations for Chaotic Dynamical Systems * Self-Organized Criticality Models of Neural Development * Altered Fractal and Irregular Heart Rate Behavior in Sick Fetuses * Extract Multiple Scaling in Long-Term Heart Rate Variability * A Semi-Continous Box Counting Method for Fractal Dimension Measurement of Short Single Dimension Temporal Signals - Preliminary Study * A Fractional Brownian Motion Model of Cracking * Self-Affine Scaling Studies on Fractography * Coarsening of Fractal Interfaces * A Fractal Model of Ocean Surface Superdiffusion * Stochastic Subsurface Flow and Transport in Fractal Fractal Conductivity Fields * Rendering Through Iterated Function Systems * The σ-Hull - The Hull Where Fractals Live - Calculating a Hull Bounded by Log Spirals to Solve the Inverse IFS-Problem by the Detected Orbits * On the Multifractal Properties of Passively Convected Scalar Fields * New Statistical Textural Transforms for Non-Stationary Signals: Application to Generalized Mutlifractal Analysis * Laplacian Growth of Parallel Needles: Their Mullins-Sekerka Instability * Entropy Dynamics Associated with Self-Organization * Fractal Properties in Economics (invited talk) * Fractal Approach to the Regional Seismic Event Discrimination Problem * Fractal and Topological Complexity of Radioactive Contamination * Pattern Selection: Nonsingular Saffman-Taylor Finger and Its Dynamic Evolution with Zero Surface Tension * A Family of Complex Wavelets for the Characterization of Singularities * Stabilization of Chaotic Amplitude Fluctuations in Multimode, Intracavity-Doubled Solid-State Lasers * Chaotic

  2. SANS spectra of the fractal supernucleosomal chromatin structure models

    NASA Astrophysics Data System (ADS)

    Ilatovskiy, Andrey V.; Lebedev, Dmitry V.; Filatov, Michael V.; Petukhov, Michael G.; Isaev-Ivanov, Vladimir V.

    2012-03-01

    The eukaryotic genome consists of chromatin—a nucleoprotein complex with hierarchical architecture based on nucleosomes, the organization of higher-order chromatin structures still remains unknown. Available experimental data, including SANS spectra we had obtained for whole nuclei, suggested fractal nature of chromatin. Previously we had built random-walk supernucleosomal models (up to 106 nucleosomes) to interpret our SANS spectra. Here we report a new method to build fractal supernucleosomal structure of a given fractal dimension or two different dimensions. Agreement between calculated and experimental SANS spectra was significantly improved, especially for model with two fractal dimensions—3 and 2.

  3. Structure of flexible filamentous plant viruses.

    PubMed

    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

    2008-10-01

    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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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)

  9. 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)

  10. Modeling of Aperiodic Fractal Waveguide Structures for Multifrequency Light Transport

    NASA Astrophysics Data System (ADS)

    Hiltunen, Marianne; Dal Negro, Luca; Feng, Ning-Ning; Kimerling, Lionel C.; Michel, Jurgen

    2007-07-01

    In this paper, we present the design of a novel waveguide structure capable of multifrequency transmission bands with strongly enhanced electric field states. The concept of the structure is based on aperiodic and quasi-periodic fractal ordering of scattering subunits combined within a traditional channel-waveguide scheme. The resulting 3-D fractal waveguides are characterized by complex transmission spectra and sustain quasi-localized field modes with strong enhancement effects due to the lack of translational symmetry. In this paper, we will describe how it is possible to accurately model these complex waveguide structures within a simple 1-D model. We will explore the formation of photonic band gaps and the character of the quasi-localized states in fractal waveguide structures generated according to different deterministic rules, such as Fibonacci, Thue Morse, and Rudin Shapiro sequences. Furthermore, we will qualitatively compare the characteristics of the optical gaps and field states in periodic, fractal, and aperiodic waveguides. The results of our comparative study will show that fractal waveguides based on aperiodic order exhibit the richest transmission spectra with field-enhancement effects occurring at multiple frequencies. The proposed fractal waveguide design can provide an attractive route toward the fabrication of optically active devices for multiwavelength operation.

  11. 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.

  12. Fractal analysis of the role of the rough interface between Bi2Sr2CaCu2Ox filaments and the Ag matrix in the mechanical behavior of composite round wires

    NASA Astrophysics Data System (ADS)

    Gou, Xiaofan; Schwartz, Justin

    2013-05-01

    Multifilamentary round wires (RWs) of Bi2Sr2CaCu2Ox (Bi2212) superconductor in a Ag/AgMg matrix have complex microstructures that strongly influence their electrical and mechanical behavior. The Bi2212/Ag interfaces, which in some locations are characterized by Bi2212 growths into the Ag matrix that result in rough, jagged interfaces, and in other locations are characterized by Bi2212 growths that bridge and connect to neighboring Bi2212 filaments, are believed to be amongst the most important microstructural features; yet their role is not well understood. In this work, a fractal-based framework is created in an effort to understand the role of the structure of individual filaments and the Bi2212/Ag interfaces in determining the macroscopic electromechanical behavior of Bi2212 RW. Scanning electron micrographs of an individual Bi2212 filament extracted from a Bi2212 RW are used to analyze the rough Bi2212/Ag interface and develop a fractal model using the Weierstrass-Mandelbrot (W-M) fractal function. The W-M fractal function is then used to generate simulated Bi2212/Ag microstructures. Finally, the mechanical behavior of the microstructures is investigated. It is found that the interfilamentary bridges which play a significant role in Bi2212 transport are not likely to be the cause of electromechanical degradation and failure. Instead, large stress concentrations are identified at the concave tips that occur along the jagged Bi2212/Ag interface. In particular, locations where the concave tips are within the Bi2212 filament are the likely initiation points of failure in Bi2212 RWs.

  13. 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.

  14. 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

  15. 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.

  16. Enhanced Fluorescent Immunoassays on Silver Fractal-like Structures

    PubMed Central

    Shtoyko, Tanya; Matveeva, Evgenia G.; Chang, I-Fen; Gryczynski, Zygmunt; Goldys, Ewa; Gryczynski, Ignacy

    2009-01-01

    Using the effect of the fluorescence enhancement in close proximity to metal nanostructures, we have been able to demonstrate ultrasensitive immunoassays suitable for the detection of biomarkers. Silver fractal-like structures have been grown by electrochemical reduction of silver on the surface of glass slides. A model immunoassay was performed on the slide surface with rabbit IgG (antigen) non-covalently immobilized on the slide, and Rhodamine Red-X labeled anti-rabbit IgG conjugate subsequently bound to the immobilized antigen. The fluorescence signal was measured from the glass-fractals surface using a confocal microscope, and the images were compared to the images from the same surface not coated with fractals. Our results showed significant enhancement (more than 100-fold) of the signal detected on fractals compared to bare glass. We thus demonstrate that such fractal-like structures can assist in improving the signals from assays used in medical diagnostics, especially those for analytes with molecular weight under 100 kD. PMID:18288816

  17. Chaotic transients and fractal structures governing coupled swing dynamics

    SciTech Connect

    Ueda, Y.; Enomoto, T. ); Stewart, H.B. )

    1990-01-01

    Numerical simulations are used to study coupled swing equations modeling the dynamics of two electric generators connected to an infinite bus by a simple transmission network. In particular, the effect of varying parameters corresponding to the input power supplied to each generator is studied. In addition to stable steady operating conditions, which should correspond to synchronized, normal operation, the coupled swing model has other stable states of large amplitude oscillations which, if realized, would represent non-synchronized motions: the phase space boundary separating their basins of attraction is fractal, corresponding to chaotic transient motions. These fractal structures in phase space and the associated fractal structures in parameter space will be of primary concern to engineers in predicting system behavior.

  18. 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.

  19. Fractal structure of the liver: effect on drug elimination.

    PubMed

    Weiss, Michael

    2013-02-01

    Liver modeling in pharmacokinetics has been based on outflow curves of extracellular tracers obtained in single-pass perfused rat livers. These reference curves represent the hepatic transit time densities (TTD) of tracers. Since the fractal structure of the sinusoidal network implies a TTD with power-law tail, the question is whether the use of conventional empirical TTDs with exponential tail may lead to biased estimates of hepatic clearance. A simulation study using a novel TTD model that accounts for fractal heterogeneity of hepatic flow shows that the bias is less than about 5%. Using this approach to determine the influence of hepatic flow dispersion on drug extraction, only a minor effect was found. The results demonstrate that there is no need for specific fractal models of hepatic drug elimination.

  20. 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

  1. 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.

  2. Excitation of Terahertz Charge Transfer Plasmons in Metallic Fractal Structures

    NASA Astrophysics Data System (ADS)

    Ahmadivand, Arash; Gerislioglu, Burak; Sinha, Raju; Vabbina, Phani Kiran; Karabiyik, Mustafa; Pala, Nezih

    2017-08-01

    There have been extensive researches on terahertz (THz) plasmonic structures supporting resonant modes to demonstrate nano and microscale devices with high efficiency and responsivity as well as frequency selectivity. Here, using antisymmetric plasmonic fractal Y-shaped (FYS) structures as building blocks, we introduce a highly tunable four-member fractal assembly to support charge transfer plasmons (CTPs) and classical dipolar resonant modes with significant absorption cross section in the THz domain. We first present that the unique geometrical nature of the FYS system and corresponding spectral response allow for supporting intensified dipolar plasmonic modes under polarised light exposure in a standalone structure. In addition to classical dipolar mode, for the very first time, we demonstrated CTPs in the THz domain due to the direct shuttling of the charges across the metallic fractal microantenna which led to sharp resonant absorption peaks. Using both numerical and experimental studies, we have investigated and confirmed the excitation of the CTP modes and highly tunable spectral response of the proposed plasmonic fractal structure. This understanding opens new and promising horizons for tightly integrated THz devices with high efficiency and functionality.

  3. The structures, mass motions and footpoints of solar filaments

    NASA Astrophysics Data System (ADS)

    Venkataramanasastry, Aparna

    This thesis focuses on identifying the mechanism by which solar filaments acquire mass. Some of the speculations for how a filament gets its mass are 1) injection of mass from the chromosphere into the filament structure, and 2) condensation of mass from the corona into the region of the filament channel. Mass motion at the footpoints of the filaments is studied to detect mass entering and leaving the filament body. The magnetic properties of the footpoints of the filaments are also studied. Recommendations are drawn by comparing observational properties obtained in this study with the features used in some of the previously developed models. The datasets used for this study are high-resolution image sets of centerline and Doppler wings of Halpha, obtained using the Dutch Open Telescope (DOT). The data were obtained on Oct 30, 2010. The data set contains three filaments in an active region in the northern hemisphere of the Sun. The images in each wavelength are aligned and made into movies to find the footpoints of the filaments through which the mass goes into and comes out of the filaments from and to the chromosphere, respectively. The magnetic properties of the footpoints are studied by overlaying the magnetogram images with the DOT images by using full-disk Halpha images for matching the features in the two. Of the three filaments, one of the filaments is observed to be stable throughout the duration of the observations; another filament erupts after about two hours of the beginning of observations; and the third filament is in its early stages of formation. The ends of the stable filament are clearly observed whereas the ends of the erupting filament and the forming filament are observed clearly intermittently during the duration of the observations. The animations of the region near the ends of filament 1 reveal definite injection and draining of mass via the footpoints into and out of the filament. The mass motion into and out of the filaments are observed

  4. Kinetic signature of fractal-like filament networks formed by orientational linear epitaxy.

    PubMed

    Hwang, Wonmuk; Eryilmaz, Esma

    2014-07-11

    We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scale-free behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.

  5. Kinetic Signature of Fractal-like Filament Networks Formed by Orientational Linear Epitaxy

    NASA Astrophysics Data System (ADS)

    Hwang, Wonmuk; Eryilmaz, Esma

    2014-07-01

    We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scale-free behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.

  6. Not just fractal surfaces, but surface fractal aggregates: Derivation of the expression for the structure factor and its applications

    NASA Astrophysics Data System (ADS)

    Besselink, R.; Stawski, T. M.; Van Driessche, A. E. S.; Benning, L. G.

    2016-12-01

    Densely packed surface fractal aggregates form in systems with high local volume fractions of particles with very short diffusion lengths, which effectively means that particles have little space to move. However, there are no prior mathematical models, which would describe scattering from such surface fractal aggregates and which would allow the subdivision between inter- and intraparticle interferences of such aggregates. Here, we show that by including a form factor function of the primary particles building the aggregate, a finite size of the surface fractal interfacial sub-surfaces can be derived from a structure factor term. This formalism allows us to define both a finite specific surface area for fractal aggregates and the fraction of particle interfacial sub-surfaces at the perimeter of an aggregate. The derived surface fractal model is validated by comparing it with an ab initio approach that involves the generation of a "brick-in-a-wall" von Koch type contour fractals. Moreover, we show that this approach explains observed scattering intensities from in situ experiments that followed gypsum (CaSO4 ṡ 2H2O) precipitation from highly supersaturated solutions. Our model of densely packed "brick-in-a-wall" surface fractal aggregates may well be the key precursor step in the formation of several types of mosaic- and meso-crystals.

  7. Topologiacl Models of 2D Fractal Cellular Structures

    NASA Astrophysics Data System (ADS)

    Le Caër, G.; Delannay, R.

    1995-11-01

    In space-filling 2D cellular structures with trivalent vertices and in which each cell is constrained to share at most one side with any cell and no side with itself, the maximum fraction of three-sided cells is produced by a decoration of vertices of any initial structure by three-sided cells. Fractal cellular structures are obtained if the latter decoration process is iterated indefinitely. Other methods of constructions of fractal structures are also described. The probability distribution P(n) of the number n of cell sides and some two-cell topological properties of a 2D fractal cellular structure constructed from the triangular Sierpinski gasket are investigated. On the whole, the repartition of cells in 2D structures with n geq 3 and P(3) ne 0 evolve regularly when topological disorder, conveniently measured by the variance μ2 of P(n), increases. The strong correlations which exist among cells, in particular in natural structures (μ2lesssim 5), decrease progressively when μ2 increases, a cell repartition close to a random one being reached for μ2sim 12. We argue that the structures finally evolve to fractal structures (for which μ2 is infinite) but we have not characterized the latter transition. Dans des structures cellulaires 2D à sommets trivalents qui remplissent l'espace et dans lesquelles une cellule partage au plus un côté avec toute autre cellule et aucun avec elle-même, la proportion maximum admissible de cellules à trois côtés est obtenue par une décoration de tous les sommets d'une structure initiale quelconque par des cellules à trois côtés. Des structures cellulaires “fractales” 2D sont ainsi engendrées si le processus précédent est répété à l'infini. D'autres méthodes de constructions de structures fractales sont également décrites. La distribution de probabilité P(n) du nombre n de côtés des cellules ainsi que des corrélations de paires sont étudiées pour une structure cellulaire fractale construite à partir

  8. Ubiquitination and filamentous structure of cytidine triphosphate synthase

    PubMed Central

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

    2016-01-01

    ABSTRACT 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

  9. 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.

  10. Filament shape versus coronal potential magnetic field structure

    NASA Astrophysics Data System (ADS)

    Filippov, B.

    2016-01-01

    Solar filament shape in projection on disc depends on the structure of the coronal magnetic field. We calculate the position of polarity inversion lines (PILs) of coronal potential magnetic field at different heights above the photosphere, which compose the magnetic neutral surface, and compare with them the distribution of the filament material in Hα chromospheric images. We found that the most of the filament material is enclosed between two PILs, one at a lower height close to the chromosphere and one at a higher level, which can be considered as a height of the filament spine. Observations of the same filament on the limb by the Solar Terrestrial Relations Observatory spacecraft confirm that the height of the spine is really very close to the value obtained from the PIL and filament border matching. Such matching can be used for filament height estimations in on-disc observations. Filament barbs are housed within protruding sections of the low-level PIL. On the base of simple model, we show that the similarity of the neutral surfaces in potential and non-potential fields with the same sub-photospheric sources is the reason for the found tendency for the filament material to gather near the potential-field neutral surface.

  11. Structural parameters of young star clusters: fractal analysis

    NASA Astrophysics Data System (ADS)

    Hetem, A.

    2017-07-01

    A unified view of star formation in the Universe demand detailed and in-depth studies of young star clusters. This work is related to our previous study of fractal statistics estimated for a sample of young stellar clusters (Gregorio-Hetem et al. 2015, MNRAS 448, 2504). The structural properties can lead to significant conclusions about the early stages of cluster formation: 1) virial conditions can be used to distinguish warm collapsed; 2) bound or unbound behaviour can lead to conclusions about expansion; and 3) fractal statistics are correlated to the dynamical evolution and age. The technique of error bars estimation most used in the literature is to adopt inferential methods (like bootstrap) to estimate deviation and variance, which are valid only for an artificially generated cluster. In this paper, we expanded the number of studied clusters, in order to enhance the investigation of the cluster properties and dynamic evolution. The structural parameters were compared with fractal statistics and reveal that the clusters radial density profile show a tendency of the mean separation of the stars increase with the average surface density. The sample can be divided into two groups showing different dynamic behaviour, but they have the same dynamic evolution, since the entire sample was revealed as being expanding objects, for which the substructures do not seem to have been completely erased. These results are in agreement with the simulations adopting low surface densities and supervirial conditions.

  12. 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

  13. Fractal analysis illuminates the form of connectionist structural gradualness.

    PubMed

    Tabor, Whitney; Cho, Pyeong Whan; Szkudlarek, Emily

    2013-07-01

    We examine two connectionist networks-a fractal learning neural network (FLNN) and a Simple Recurrent Network (SRN)-that are trained to process center-embedded symbol sequences. Previous work provides evidence that connectionist networks trained on infinite-state languages tend to form fractal encodings. Most such work focuses on simple counting recursion cases (e.g., anbn), which are not comparable to the complex recursive patterns seen in natural language syntax. Here, we consider exponential state growth cases (including mirror recursion), describe a new training scheme that seems to facilitate learning, and note that the connectionist learning of these cases has a continuous metamorphosis property that looks very different from what is achievable with symbolic encodings. We identify a property-ragged progressive generalization-which helps make this difference clearer. We suggest two conclusions. First, the fractal analysis of these more complex learning cases reveals the possibility of comparing connectionist networks and symbolic models of grammatical structure in a principled way-this helps remove the black box character of connectionist networks and indicates how the theory they support is different from symbolic approaches. Second, the findings indicate the value of future, linked mathematical and empirical work on these models-something that is more possible now than it was 10 years ago.

  14. 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.

  15. Structure and assembly of calf hoof keratin filaments.

    PubMed

    Sayers, Z; Michon, A M; Sicre, P; Koch, M H

    1990-05-01

    Keratin filament polypeptides were purified from calf hoof stratum corneum with the aim of studying the in vitro assembly process and determining structural parameters of reconstituted filaments. Anion exchange chromatography was used to obtain the most complete fractionation and identification of the acidic and basic components in the purified polypeptide mixture to date. The reassembly products of the fractionated components were investigated by electron microscopy. Fully reconstituted filaments yield homogeneous solutions, and values of 9.8 nm for the filament diameter and 25 kDa/nm for the mass per unit length (M/L) were obtained by X-ray solution scattering. The structures formed in solution at various stages of filament assembly were not sufficiently homogeneous to be studied by this technique. X-ray diffraction patterns from native stratum corneum display strong maxima at 3.6 and 5.4 nm. Contrary to previous reports, these maxima do not appear to be due to lipids since they are also observed with delipidated rehydrated specimens. A series of weak maxima is also detected in the patterns of dry tissue. The absence of these features in the patterns of reconstituted filaments suggests that, in contrast to some electron microscopic observations, there are no prominent regularities in the structure of calf hoof keratin filaments.

  16. Fractal parameterization analysis of ferroelectric domain structure evolution induced by electron beam irradiation

    NASA Astrophysics Data System (ADS)

    Maslovskaya, A. G.; Barabash, T. K.

    2017-01-01

    The article presents some results of fractal analysis of ferroelectric domain structure images visualized with scanning electron microscope (SEM) techniques. The fractal and multifractal characteristics were estimated to demonstrate self-similar organization of ferroelectric domain structure registered with static and dynamic contrast modes of SEM. Fractal methods as sensitive analytical tools were used to indicate degree of domain structure and domain boundary imperfections. The electron irradiation-induced erosion effect of ferroelectric domain boundaries in electron beam-stimulated polarization current mode of SEM is characterized by considerable raising of fractal dimension. For dynamic contrast mode of SEM there was revealed that complication of domain structure during its dynamics is specified by increase in fractal dimension of images and slight raising of boundary fractal dimension.

  17. 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.

  18. Fractal structure of films deposited in a tokamak

    SciTech Connect

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

    2007-04-15

    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 {mu}m 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.

  19. Chaotic dynamics and fractal structures in experiments with cold atoms

    NASA Astrophysics Data System (ADS)

    Daza, Alvar; Georgeot, Bertrand; Guéry-Odelin, David; Wagemakers, Alexandre; Sanjuán, Miguel A. F.

    2017-01-01

    We use tools from nonlinear dynamics for the detailed analysis of cold-atom experiments. A powerful example is provided by the recent concept of basin entropy, which allows us to quantify the final-state unpredictability that results from the complexity of the phase-space geometry. We show here that this enables one to reliably infer the presence of fractal structures in phase space from direct measurements. We illustrate the method with numerical simulations in an experimental configuration made of two crossing laser guides that can be used as a matter-wave splitter.

  20. Structural changes accompanying phosphorylation of tarantula muscle myosin filaments

    PubMed Central

    1987-01-01

    Electron microscopy has been used to study the structural changes that occur in the myosin filaments of tarantula striated muscle when they are phosphorylated. Myosin filaments in muscle homogenates maintained in relaxing conditions (ATP, EGTA) are found to have nonphosphorylated regulatory light chains as shown by urea/glycerol gel electrophoresis and [32P]phosphate autoradiography. Negative staining reveals an ordered, helical arrangement of crossbridges in these filaments, in which the heads from axially neighboring myosin molecules appear to interact with each other. When the free Ca2+ concentration in a homogenate is raised to 10(-4) M, or when a Ca2+-insensitive myosin light chain kinase is added at low Ca2+ (10(-8) M), the regulatory light chains of myosin become rapidly phosphorylated. Phosphorylation is accompanied by potentiation of the actin activation of the myosin Mg- ATPase activity and by loss of order of the helical crossbridge arrangement characteristic of the relaxed filament. We suggest that in the relaxed state, when the regulatory light chains are not phosphorylated, the myosin heads are held down on the filament backbone by head-head interactions or by interactions of the heads with the filament backbone. Phosphorylation of the light chains may alter these interactions so that the crossbridges become more loosely associated with the filament backbone giving rise to the observed changes and facilitating crossbridge interaction with actin. PMID:2958483

  1. [Power-law species richness accumulation as manifestation of the fractal community structure].

    PubMed

    Gelashvili, D B; Iudin, D I; Rozenberg, G S; Iakimov, N V

    2007-01-01

    Applications of the fractal to describing the species structure of communities are discussed. Fundamental notions of fractal geometry are explained in the first part. The problem of applying the concept of fractal to describe the spatial allocation of particular species and of community as a whole is reviewed in the second part. In the final part, the usage of the selfsimirity principle for analyzing community organization is substantiated, and evidence of the fractal structure of biocenoses is presented according to Whittaker's concept of alpha diversity. It is shown that community is characterized, as a fractal object, by scale invariance, by power function relationship between the number of structural elements of the community (individuals, populations, species) and the scale (sampling effort), and, finally, by fractional value of the power (fractal dimension). Power function is the formula the takes into account the share of rare species, or species represented by a single individual. providing for no saturation of the function f(x). This formula also does not contradict the A.P. Levich's "rule of ecological non-additivity" and, lastly, allows the application of fractal formalism to characterize the species structure of a community. It is concluded that the mathematical image of species richness is a monofractal, i.e., a set characterised by only one parameter, fractal dimension. Thus, the species structure of a community (as well as the pattern of its spatial allocation) displays self-similarity and is a fractal.

  2. Magnetic Structure of a Filament during its Phase of Activity

    NASA Astrophysics Data System (ADS)

    Sasso, C.; Lagg, A.; Solanki, S. K.

    2008-09-01

    We analyze and interpret spectropolarimetric observations of an active region filament located close to the solar disc center, during its phase of activity. The observations are obtained in the chromospheric He I lines at 1083.0 nm. We provide novel observational results on the magnetic field measurements in solar filaments to give constraints to the theoretical models of their support in the solar corona. Our main goal is to interpret the behavior of the atmospheric parameters retrieved from the spectropolarimetric data to give a picture of the magnetic structure of the observed filament. The analysis of the observed polarization of the He I 1083.0 nm multiplet in the filament, carried out by inverting the Stokes profiles, reveals the presence of different unresolved atmospheric components of the He lines, coexisting within the resolution element (1.2 arcsec). The different components, belonging to different magnetic field lines, show supersonic up- and downflows, sometimes within the same resolution element. The He blueshifted components belong to mostly transversal field lines in the body of the filament. These field lines are found to be curving upwards on both sides. This picture suggests the presence of dipped field lines that are moving upward, carrying with them the filament material. During this movement, we also observe filament material flowing down along field lines having the same polarity as the photospheric field (i.e. they have the opposite inclination with respect to the dipped field lines). These downflows are faster at the filament end points and can reach values close to 10 times the speed of sound. The field lines are found to be almost parallel to the filament axis in the plane perpendicular to the line of sight. We use the two main theoretical models of prominence support (dip or flux rope models) to interpret the results obtained.

  3. Myosin and Actin Filaments in Muscle: Structures and Interactions.

    PubMed

    Squire, John M; Paul, Danielle M; Morris, Edward P

    2017-01-01

    In the last decade, improvements in electron microscopy and image processing have permitted significantly higher resolutions to be achieved (sometimes <1 nm) when studying isolated actin and myosin filaments. In the case of actin filaments the changing structure when troponin binds calcium ions can be followed using electron microscopy and single particle analysis to reveal what happens on each of the seven non-equivalent pseudo-repeats of the tropomyosin α-helical coiled-coil. In the case of the known family of myosin filaments not only are the myosin head arrangements under relaxing conditions being defined, but the latest analysis, also using single particle methods, is starting to reveal the way that the α-helical coiled-coil myosin rods are packed to give the filament backbones.

  4. 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.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Acharya, Raj S.; LeBlanc, Adrian; Shackelford, Linda; Swarnakar, Vivek; Krishnamurthy, Ram; Hausman, E.; Lin, Chin-Shoou

    1995-05-01

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

  7. 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.

  8. 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.

  9. 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.

  10. Multi-fractal structure in Arctic sea ice satellite data

    NASA Astrophysics Data System (ADS)

    Moon, W.; Wettlaufer, J. S.

    2011-12-01

    Since 21th century, Arctic sea ice has shown significant decrease especially during summer season. These decline has been considered by climate scientists as a critical sign of the effect of global warming. Especially, IPCC global climate models confirmed the recent decline of Arctic sea ice and predict the more decline in the near future. Even with rather significant amount of inter-model variability in climate models, satellite data during around 30 years support the results of climate models. However, the decline of Arctic sea ice is confirmed based on monthly averaged data and linear regression after erasing seasonal cycle. Even with strong conjecture of the real decline of Arctic sea ice, we cannot exclude one part of natural oscillations affecting Arctic sea ice physics due to strong non-stationarity. It is also possible not to make any conclusive statements using the monthly averaged data due to a lack of data or multi-fractal structure of data excluded in the data. Here, we will use MF-DFA (Multi-Fractal Detrended Fluctuation Analysis) to determine the multi-scale structure of Arctic sea ice area and albedo using AVHRR Polar Pathfinder Twice-Daily 5km EASE-grid composites, which is expected to decide whether the decline shown in the linear regression of the monthly averaged data can be considered as the real decline caused by global warming or not. Also, the multi-scale structure information drawn from this analysis is expected to give us the guideline for selecting significant physics for low-order Arctic sea ice

  11. An improvement of the fractal theory and its application in pore structure evaluation and permeability estimation

    NASA Astrophysics Data System (ADS)

    Ge, Xinmin; Fan, Yiren; Deng, Shaogui; Han, Yujiao; Liu, Jiaxiong

    2016-09-01

    We present an improved fractal model for pore structure evaluation and permeability estimation based on the high pressure mercury porosimetry data. An accumulative fractal equation is introduced to characterize the piecewise nature of the capillary pressure and the mercury saturation. The iterative truncated singular value decomposition algorithm is developed to solve the accumulative fractal equation and obtain the fractal dimension distributions. Furthermore, the fractal dimension distributions and relevant parameters are used to characterize the pore structure and permeability. The results demonstrate that the proposed model provides better characterization of the mercury injection capillary pressure than conventional monofractal theory. In addition, there is a direct relationship between the pore structure types and the fractal dimension spectrums. What is more, the permeability is strongly correlated with the geometric and the arithmetic mean values of fractal dimensions, and the permeability estimated using these new fractal dimension parameters achieve excellent result. The improved model and solution give a fresh perspective of the conventional monofractal theory, which may be applied in many geological and geophysical fields.

  12. Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography

    PubMed Central

    Loss, Leandro A.; Bebis, George; Chang, Hang; Auer, Manfred; Sarkar, Purbasha; Parvin, Bahram

    2016-01-01

    Electron tomography is a promising technology for imaging ultrastructures at nanoscale resolutions. However, image and quantitative analyses are often hindered by high levels of noise, staining heterogeneity, and material damage either as a result of the electron beam or sample preparation. We have developed and built a framework that allows for automatic segmentation and quantification of filamentous objects in 3D electron tomography. Our approach consists of three steps: (i) local enhancement of filaments by Hessian filtering; (ii) detection and completion (e.g., gap filling) of filamentous structures through tensor voting; and (iii) delineation of the filamentous networks. Our approach allows for quantification of filamentous networks in terms of their compositional and morphological features. We first validate our approach using a set of specifically designed synthetic data. We then apply our segmentation framework to tomograms of plant cell walls that have undergone different chemical treatments for polysaccharide extraction. The subsequent compositional and morphological analyses of the plant cell walls reveal their organizational characteristics and the effects of the different chemical protocols on specific polysaccharides. PMID:28090597

  13. Fractal astronomy.

    NASA Astrophysics Data System (ADS)

    Beech, M.

    1989-02-01

    The author discusses some of the more recent research on fractal astronomy and results presented in several astronomical studies. First, the large-scale structure of the universe is considered, while in another section one drops in scale to examine some of the smallest bodies in our solar system; the comets and meteoroids. The final section presents some thoughts on what influence the fractal ideology might have on astronomy, focusing particularly on the question recently raised by Kadanoff, "Fractals: where's the physics?"

  14. 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.

  15. Particle accelerations and current structures of Weibel and Filamentation instabilities

    NASA Astrophysics Data System (ADS)

    Ryu, C. M.; Huynh, C. T.

    2015-12-01

    Particle accelerations of the Wibel instability (WI) and the Filamentation instability(FI) are studied by using PIC simuations, comparing them side-by-side. Although two instabilities are almost identical in the linear growth phase, significant differences are found in the nonlinear phase in their particle accelerations and current structures. The FI shows enhanced electron acceleration, whereas particle acceleration is almost absent in the WI. The different particle accelerations between the FI and the WI seem to be associated with their different current structures; a hollow electron current structure for the FI and a center filled current structure for that of the WI. Different electron distributions seem to bring in different current filament structures, eventually leading to different magnetic characteristics.

  16. 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.

  17. 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

  18. Porous AlMg-SiC Composites Structure Modeling By Means of Fractal Analysis

    NASA Astrophysics Data System (ADS)

    Rusu, O.; Rusu, I.

    2017-06-01

    This work is a continuation of the authors research in the field of ultralight metallic composite materials, based on AlMg10 alloy and SiC particles and obtained by salt dissolution method. We used for the fractal analysis the fractal geometry modeling by means of fractal dimension types of composites obtained from performed experiments. We achieved the following fractal dimensions for the samples: 1.37 (for 5% SiC sample), 1.41 (for 10% SiC sample) and 1.45 (for 15% SiC sample). Fractal analysis indicated that all the obtained samples have cells with a statistically regular form. We conclude that this kind of composite materials can be included in ultralights porous metal composite materials, with a tendency to a metal foam structure.

  19. 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

  20. The intermediate-sized filaments in rat kangaroo PtK2 cells. II. Structure and composition of isolated filaments.

    PubMed

    Franke, W W; Schmid, E; Osborn, M; Weber, K

    1978-08-01

    When cultured cells of the rat kangaroo cell line PtK2 grown on plastic or glass surfaces are lysed and extracted with combinations of low and high salt buffers and the non-ionic detergent Triton X-100 cytoskeletal preparations are obtained that show an enrichment of 6 to 11 nm thick filaments. The arrays of these filaments have been examined by various light and electron microscopic techniques, including ultrathin sectioning, whole mount transmission electron microscopy, negative staining, and indirect immunofluorescence microscopy. In addition, 6 to 11 nm filaments isolated from these cells with similar extraction procedures and with centrifugation techniques have been examined by electron microscopy. The arrays of these isolated intermediate-sized filaments, their ultrastructure and their specific decoration by certain antibodies present in normal rabbit sera as well as by guinea pig antibodies against purified bovine prekeratin is demonstrated. When preparations enriched in these intermediate-sized filaments are examined by SDS-polyacrylamide gel electrophoresis a corresponding enrichment of three polypeptide bands with apparent molecular weights of about 45 000, 52 000 and 58 000 (the latter component sometimes appears split into two bands) is observed, besides some residual actin and a few high molecular weight bands. The morphology of the isolated filaments, their immunological reaction with antibodies decorating prekeratin-containing structures, and the sizes of their constitutive polypeptides suggest that these filaments are closely related to prekeratin-containing filaments observed in a variety of epithelial cells.

  1. 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.

  2. Structural characterization of chaos game fractals using small-angle scattering analysis.

    PubMed

    Anitas, Eugen Mircea; Slyamov, Azat

    2017-01-01

    Small-angle scattering (SAS) technique is applied to study the nano and microstructural properties of spatial patterns generated from chaos game representation (CGR). Using a simplified version of Debye formula, we calculate and analyze in momentum space, the monodisperse scattering structure factor from a system of randomly oriented and non-interacting 2D Sierpinski gaskets (SG). We show that within CGR approach, the main geometrical and fractal properties, such as the overall size, scaling factor, minimal distance between scattering units, fractal dimension and the number of units composing the SG, can be recovered. We confirm the numerical results, by developing a theoretical model which describes analytically the structure factor of SG. We apply our findings to scattering from single scale mass fractals, and respectively to a multiscale fractal representing DNA sequences, and for which an analytic description of the structure factor is not known a priori.

  3. Structural characterization of chaos game fractals using small-angle scattering analysis

    PubMed Central

    Slyamov, Azat

    2017-01-01

    Small-angle scattering (SAS) technique is applied to study the nano and microstructural properties of spatial patterns generated from chaos game representation (CGR). Using a simplified version of Debye formula, we calculate and analyze in momentum space, the monodisperse scattering structure factor from a system of randomly oriented and non-interacting 2D Sierpinski gaskets (SG). We show that within CGR approach, the main geometrical and fractal properties, such as the overall size, scaling factor, minimal distance between scattering units, fractal dimension and the number of units composing the SG, can be recovered. We confirm the numerical results, by developing a theoretical model which describes analytically the structure factor of SG. We apply our findings to scattering from single scale mass fractals, and respectively to a multiscale fractal representing DNA sequences, and for which an analytic description of the structure factor is not known a priori. PMID:28704515

  4. 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.

  5. 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.

  6. Fractal analysis of radiographs: assessment of trabecular bone structure and prediction of elastic modulus and strength.

    PubMed

    Majumdar, S; Lin, J; Link, T; Millard, J; Augat, P; Ouyang, X; Newitt, D; Gould, R; Kothari, M; Genant, H

    1999-07-01

    The purpose of this study was to determine whether fractal dimension of radiographs provide measures of trabecular bone structure which correlate with bone mineral density (BMD) and bone biomechanics, and whether these relationships depend on the technique used to calculate the fractal dimension. Eighty seven cubic specimen of human trabecular bone were obtained from the vertebrae and femur. The cubes were radiographed along all three orientations--superior-inferior (SI), medial-lateral (ML), and anterior-posterior (AP), digitized, corrected for background variations, and fractal based techniques were applied to quantify trabecular structure. Three different techniques namely, semivariance, surface area, and power spectral methods were used. The specimens were tested in compression along three orientations and the Young's modulus (YM) was determined. Compressive strength was measured along the SI direction. Quantitative computed tomography was used to measure trabecular BMD. High-resolution magnetic-resonance images were used to obtain three-dimensional measures of trabecular architecture such as the apparent bone volume fraction, trabecular thickness, spacing, and number. The measures of trabecular structure computed in the different directions showed significant differences (p<0.05). The correlation between BMD, YM, strength, and the fractal dimension were direction and technique dependent. The trends of variation of the fractal dimension with BMD and biomechanical properties also depended on the technique and the range of resolutions over which the data was analyzed. The fractal dimension showed varying trends with bone mineral density changes, and these trends also depended on the range of frequencies over which the fractal dimension was measured. For example, using the power spectral method the fractal dimension increased with BMD when computed over a lower range of spatial frequencies and decreased for higher ranges. However, for the surface area technique

  7. Fractal structures and their computer simulation in rapidly quenched Ai-Mn alloys

    NASA Astrophysics Data System (ADS)

    Zhang, Meng; Hong, Chunyong; Dai, Hong; Yang, Pinsheng; Tan, Yuxi

    1999-02-01

    The microstructure of rapidly quenched A1-Mn alloys were studied by TEM and SEM. The icosahedral phase in AI-Mn alloys was observed to show various types of fractal morphologies, which may be classified into four kinds: 1) dendritic shape, 2) flower-like shape, 3) granular shape and 4) grain-oscillation shape. After being digitized by a computer, the fractal dimensions (D) of these morphologies were calculated. Based on the traditional diffusion limited aggregation (DLA) model computer simulations were made with two-seeded and many-seeded clusters, which reflect the growing mechanism of some fractal structures in A1-Mn alloys. It is suggested that these fractal structures are formed by many icosahedral particles about 20 nm in size aggregating during the rapid quenching process.

  8. Evaporation-induced formation of fractal-like structures from nanofluids.

    PubMed

    Crivoi, Alexandru; Duan, Fei

    2012-01-28

    After the nanofluids are fully dried, the self-assembled nanoparticles can form various structures on the substrate. The fractal-like patterns are among them. The two-dimensional Kinetic Monte Carlo model is developed to predict the drying patterns of the nanofluids in an open domain, where the dewetting front shrinks from the edge toward the center. The simulation reveals that the initially dispersed particles can be deposited into an isotropic branched structure which remains frozen after full evaporation of the base fluid. The well-developed fractal-like particle aggregates are different from the fractal cavities obtained in the previous closed domain simulation. The present prediction of the fractal particle aggregation is verified by the experiments with the water-based nanofluids. The images taken using a scanning electron microscope prove that the evaporation-induced branched microstructures are formed by the nanoparticles as the water is totally dried.

  9. Fractal structure of sequential behaviour patterns: an indicator of stress

    USGS Publications Warehouse

    Alados, C.L.; Escos, J.M; Emlen, J.M.

    1996-01-01

    The detection of stress arising from parasitic infection bySarcoptes scabieisand from pregnancy is explored, using a fractal analysis of head lifting behaviour and feeding–non-feeding activity sequences in female Spanish ibex,Capra pyrenaica, under natural conditions. Because organisms under stress increase their metabolic rate and, in consequence, energy consumption, it follows that stress will, generally, lead to a reduction in complexity (fractal dimension) of exploratory behaviour. In the present study the fractal dimension of the three measures of complexity used declined with stress, both from pregnancy and from parasitic infection. This observation provides a new and effective way to assess the general state of animals’ health in the field, without the need for capture and handling.

  10. 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.

  11. Novel Actin-like Filament Structure from Clostridium tetani*

    PubMed Central

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

    2012-01-01

    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

  12. 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.

  13. 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.

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

    PubMed Central

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

    1999-01-01

    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

  15. Method of incorporating prior information on the structure of random fractal surfaces

    NASA Astrophysics Data System (ADS)

    Blackledge, J. M.

    1990-08-01

    Random fractal surfaces (Mandeibrot surfaces) are finding more and more applications in computer graphics, image analysis and the simulation of naturally occurring topologies. A random fractal as a fractional geometry whose statistical properties are scale invarient. In other words, the object looks similar (statistically) at all magnifications. The generation of a random fractal surface involves the user having to input two essential parameters: (i) the Fractal Dimension (a decimal number D where 2 < D < 3) which controls the surface roughness and (ii) the seed of a random number generator which determines the structure of the surface. By changing the seed, the user can generate different surfaces and by increasing the fractal dimension the surface roughness can be increased. In practice, algorithms of this type do not allow the user to construct a random fractal with specific topological features. Hence, in respect of the surface obtained, the user is ultimately at the mercy of a random number generator. In this paper, we address the problem of how to incorporate a priori information into a Mandelbrot surface in such a way that the end product is still fractal. A solution is provided to this problem which provides the user with control over the general topology of the surface. We demonstrate its application for incorporating low resolution data obtained from geographical/geological survey maps on the topology of a given area. Also, we show how the method can be used to generate synthetic terrain databases for the validation of certain surveying algorithms. The technique employs the Fourier Synthesis Method for generating Mandelbrot surfaces and is based on transmitting a predetermined proportion of the complex Fourier coefficients used to describe a given topology. In addition to its use as a complex terrain modeller, it is also shown how the same technique can be used for data compression of general topologies. The idea here is to describe a surface in terms of

  16. Structural Modeling and Molecular Dynamics Simulation of the Actin Filament

    SciTech Connect

    Splettstoesser, Thomas; Holmes, Kenneth; Noe, Frank; Smith, Jeremy C

    2011-01-01

    Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.

  17. Towards a molecular description of intermediate filament structure and assembly

    SciTech Connect

    Parry, David A.D.; Strelkov, Sergei V.; Burkhard, Peter; Aebi, Ueli; Herrmann, Harald . E-mail: h.herrmann@dkfz.de

    2007-06-10

    Intermediate filaments (IFs) represent one of the prominent cytoskeletal elements of metazoan cells. Their constituent proteins are coded by a multigene family, whose members are expressed in complex patterns that are controlled by developmental programs of differentiation. Hence, IF proteins found in epidermis differ significantly from those in muscle or neuronal tissues. Due to their fibrous nature, which stems from a fairly conserved central {alpha}-helical coiled-coil rod domain, IF proteins have long resisted crystallization and thus determination of their atomic structure. Since they represent the primary structural elements that determine the shape of the nucleus and the cell more generally, a major challenge is to arrive at a more rational understanding of how their nanomechanical properties effect the stability and plasticity of cells and tissues. Here, we review recent structural results of the coiled-coil dimer, assembly intermediates and growing filaments that have been obtained by a hybrid methods approach involving a rigorous combination of X-ray crystallography, small angle X-ray scattering, cryo-electron tomography, computational analysis and molecular modeling.

  18. Quantification of structural changes in acute inflammation by fractal dimension, angular second moment and correlation.

    PubMed

    Stankovic, Marija; Pantic, Igor; De Luka, Silvio R; Puskas, Nela; Zaletel, Ivan; Milutinovic-Smiljanic, Sanja; Pantic, Senka; Trbovich, Alexander M

    2016-03-01

    The aim of the study was to examine alteration and possible application of fractal dimension, angular second moment, and correlation for quantification of structural changes in acutely inflamed tissue. Acute inflammation was induced by injection of turpentine oil into the right and left hind limb muscles of mice, whereas control animals received intramuscular saline injection. After 12 h, animals were anesthetised and treated muscles collected. The tissue was stained by hematoxylin and eosin, digital micrographs produced, enabling determination of fractal dimension of the cells, angular second moment and correlation of studied tissue. Histopathological analysis showed presence of inflammatory infiltrate and tissue damage in inflammatory group, whereas tissue structure in control group was preserved, devoid of inflammatory infiltrate. Fractal dimension of the cells, angular second moment and correlation of treated tissue in inflammatory group decreased in comparison to the control group. In this study, we were first to observe and report that fractal dimension of the cells, angular second moment, and correlation were reduced in acutely inflamed tissue, indicating loss of overall complexity of the cells in the tissue, the tissue uniformity and structure regularity. Fractal dimension, angular second moment and correlation could be useful methods for quantification of structural changes in acute inflammation. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  19. 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.

  20. Negative Stains Containing Trehalose: Application to Tubular and Filamentous Structures

    NASA Astrophysics Data System (ADS)

    Harris, J. Robin; Gerber, Max; Gebauer, Wolfgang; Wernicke, Wolfgang; Markl, Jürgen

    1996-02-01

    Several examples are presented that show the successful application of uranyl acetate and ammonium molybdate negative staining in the presence of trehalose for TEM studies of filamentous and tubular structures. The principal benefit to be gained from the inclusion of trehalose stems from the considerably reduced flattening of the large tubular structures and the greater orientational freedom of single molecules due to an increased depth of the negative stain in the presence of trehalose. Trehalose is likely to provide considerable protection to protein molecules and their assemblies during the drying of negatively stained specimens. Some reduction in the excessive density imparted by uranyl acetate around large assemblies is also achieved. Nevertheless, in the presence of 1% (w/v) trehalose, it is desirable to increase the concentration of negative stain to 5% (w/v) for ammonium molybdate and to 4% for uranyl acetate to produce satisfactory image contrast. In general, the ammonium molybdate-trehalose negative stain is more satisfactory than the uranyl acetate-trehalose combination, because of the greater electron beam sensitivity of the uranyl negative stain. Reassembled taxol-stabilized pig brain microtubules, together with collagen fibrils, sperm tails, helical filaments, and reassociated hemocyanin (KLH2), all from the giant keyhole limpet Megathura crenulata, have been studied by negative staining in the presence of trehalose. In all cases satisfactory TEM imaging conditions were readily obtained on the specimens, as long as regions of excessively deep stain were avoided.

  1. Addition of electrophilic lipids to actin alters filament structure

    SciTech Connect

    Gayarre, Javier; Sanchez, David; Sanchez-Gomez, Francisco J.; Terron, Maria C.; Llorca, Oscar; Perez-Sala, Dolores . E-mail: dperezsala@cib.csic.es

    2006-11-03

    Pathophysiological processes associated with oxidative stress lead to the generation of reactive lipid species. Among them, lipids bearing unsaturated aldehyde or ketone moieties can form covalent adducts with cysteine residues and modulate protein function. Through proteomic techniques we have identified actin as a target for the addition of biotinylated analogs of the cyclopentenone prostaglandins 15-deoxy-{delta}{sup 12,14}-PGJ{sub 2} (15d-PGJ{sub 2}) and PGA{sub 1} in NIH-3T3 fibroblasts. This modification could take place in vitro and mapped to the protein C-terminal end. Other electrophilic lipids, like the isoprostane 8-iso-PGA{sub 1} and 4-hydroxy-2-nonenal, also bound to actin. The C-terminal region of actin is important for monomer-monomer interactions and polymerization. Electron microscopy showed that actin treated with 15d-PGJ{sub 2} or 4-hydroxy-2-nonenal formed filaments which were less abundant and displayed shorter length and altered structure. Streptavidin-gold staining allowed mapping of biotinylated 15d-PGJ{sub 2} at sites of filament disruption. These results shed light on the structural implications of actin modification by lipid electrophiles.

  2. Addition of electrophilic lipids to actin alters filament structure.

    PubMed

    Gayarre, Javier; Sánchez, David; Sánchez-Gómez, Francisco J; Terrón, María C; Llorca, Oscar; Pérez-Sala, Dolores

    2006-11-03

    Pathophysiological processes associated with oxidative stress lead to the generation of reactive lipid species. Among them, lipids bearing unsaturated aldehyde or ketone moieties can form covalent adducts with cysteine residues and modulate protein function. Through proteomic techniques we have identified actin as a target for the addition of biotinylated analogs of the cyclopentenone prostaglandins 15-deoxy-Delta(12,14)-PGJ(2) (15d-PGJ(2)) and PGA(1) in NIH-3T3 fibroblasts. This modification could take place in vitro and mapped to the protein C-terminal end. Other electrophilic lipids, like the isoprostane 8-iso-PGA(1) and 4-hydroxy-2-nonenal, also bound to actin. The C-terminal region of actin is important for monomer-monomer interactions and polymerization. Electron microscopy showed that actin treated with 15d-PGJ(2) or 4-hydroxy-2-nonenal formed filaments which were less abundant and displayed shorter length and altered structure. Streptavidin-gold staining allowed mapping of biotinylated 15d-PGJ(2) at sites of filament disruption. These results shed light on the structural implications of actin modification by lipid electrophiles.

  3. 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.

  4. Critical behavior of the ferromagnetic q -state Potts model in fractal dimensions: Monte Carlo simulations on Sierpinski and Menger fractal structures

    NASA Astrophysics Data System (ADS)

    Monceau, Pascal

    2006-09-01

    The extension of the phase diagram of the q -state Potts model to noninteger dimension is investigated by means of Monte Carlo simulations on Sierpinski and Menger fractal structures. Both multicanonical and canonical simulations have been carried out with the help of the Wang-Landau and the Wolff cluster algorithms. Lower bounds are provided for the critical values qc of q where a first-order transition is expected in the cases of two structures whose fractal dimension is smaller than 2: The transitions associated with the seven-state and ten-state Potts models on Sierpinski carpets with fractal dimensions df≃1.8928 and df≃1.7925 , respectively, are shown to be second-order ones, the renormalization eigenvalue exponents yh are calculated, and bounds are provided for the renormalization eigenvalue exponents yt and the critical temperatures. Moreover, the results suggest that second-order transitions are expected to occur for very large values of q when the fractal dimension is lowered below 2—that is, in the case of hierarchically weakly connected systems with an infinite ramification order. At last, the transition associated with the four-state Potts model on a fractal structure with a dimension df≃2.631 is shown to be a weakly first-order one.

  5. Dynamics of fractal networks

    NASA Astrophysics Data System (ADS)

    Orbach, R.

    1986-02-01

    Random structures often exhibit fractal geometry, defined in terms of the mass scaling exponent, D, the fractal dimension. The vibrational dynamics of fractal networks are expressed in terms of the exponent d double bar, the fracton dimensionality. The eigenstates on a fractal network are spatially localized for d double bar less than or equal to 2. The implications of fractal geometry are discussed for thermal transport on fractal networks. The electron-fracton interaction is developed, with a brief outline given for the time dependence of the electronic relaxation on fractal networks. It is suggested that amorphous or glassy materials may exhibit fractal properties at short length scales or, equivalently, at high energies. The calculations of physical properties can be used to test the fractal character of the vibrational excitations in these materials.

  6. Paramyosin structures in the thick filaments of the anterior byssus retractor muscle of Mytilus edulis.

    PubMed

    Heumann, H G

    1980-10-01

    Freeze-substituted cells of the anterior byssus retractor muscle of Mytilus edulis contain paramyosin filaments which exhibit a characteristic fine structure. Longitudinally sectioned filaments show a variety of band patterns, those occurring most frequently being cross, oblique or double oblique striations. The periodic spacings within one pattern are precise as can be demonstrated by Markham analysis and optical diffractometry. The patterns arise from structures in the interior of the filament since they persist in serially sectioned filaments and a layered structure is visible in cross-sectioned filaments. The different patterns are found to be convertible by rotating the grid around the filament axis. The observations led to the conclusion that the paramyosin core has some kind of helical arrangement. A model is proposed which consists of concentric layers of parallel paramyosin molecules which are displaced along the molecular axis in such a way that the characteristic Bear-Selby net structure results.

  7. Structure and fractal dimension of protein-detergent complexes

    NASA Astrophysics Data System (ADS)

    Chen, Sow-Hsin; Teixeira, José

    1986-11-01

    Small-angle neutron-scattering experiments were made on bovine serum albumin (BSA)-lithium dodecyl sulfate (LDS) complexes in buffer solutions. As increasing amounts of LDS are added, the scattering data indicate that BSA molecules are successively transformed into random coil conformations with LDS forming globular micelles randomly decorating the polypeptide backbones. A cross-section formula is developed which successfully fits small-angle neutron-scattering spectra over the entire Q range. The fractal dimension, the micellar size, and the extent of the denatured protein are simultaneously extracted.

  8. Significant performance enhancement in continuous wave terahertz photomixers based on fractal structures

    NASA Astrophysics Data System (ADS)

    Jafari, H.; Heidarzadeh, H.; Rostami, A.; Rostami, G.; Dolatyari, M.

    2017-01-01

    A photoconductive fractal antenna significantly improves the performance of photomixing-based continuous wave (CW) terahertz (THz) systems. An analysis has been carried out for the generation of CW-THz radiation by photomixer photoconductive antenna technique. To increase the active area for generation and hence the THz radiation power we used interdigitated electrodes that are coupled with a fractal tree antenna. In this paper, both semiconductor and electromagnetic problems are considered. Here, photomixer devices with Thue-Morse fractal tree antennas in two configurations (narrow and wide) are discussed. This new approach gives better performance, especially in the increasing of THz output power of photomixer devices, when compared with the conventional structures. In addition, applying the interdigitated electrodes improved THz photocurrent, considerably. It produces THz radiation power several times higher than the photomixers with simple gap.

  9. Laser-based equipment for investigating fractal structure of dental tissue

    NASA Astrophysics Data System (ADS)

    Zinchik, Alexander A.; Sharikova, Anna; Stafeev, Sergey C.

    1997-04-01

    The description of experimental installation for investigation fractal structure of dental tissues light scattering is presented. The installation includes light source (He-Ne laser), beam transformer based on microlens array, light polarization control unit and registrating device (which represented computer interfaced CCD-camera). The experimental installation provides the estimation of different kinds of light scattering in the enamel and dentin. The joint computer processing of images corresponding to different states light polarization allows us to separate the effects of light scattering caused by different scattering object as well as by relief junctions. The results of research may be useful for dental restorations, because fractal dimension defined adhesion properties of dentin.

  10. 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.

  11. 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

  12. 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.

  13. Near-atomic structure of jasplakinolide-stabilized malaria parasite F-actin reveals the structural basis of filament instability.

    PubMed

    Pospich, Sabrina; Kumpula, Esa-Pekka; von der Ecken, Julian; Vahokoski, Juha; Kursula, Inari; Raunser, Stefan

    2017-09-18

    During their life cycle, apicomplexan parasites, such as the malaria parasite Plasmodium falciparum, use actomyosin-driven gliding motility to move and invade host cells. For this process, actin filament length and stability are temporally and spatially controlled. In contrast to canonical actin, P. falciparum actin 1 (PfAct1) does not readily polymerize into long, stable filaments. The structural basis of filament instability, which plays a pivotal role in host cell invasion, and thus infectivity, is poorly understood, largely because high-resolution structures of PfAct1 filaments were missing. Here, we report the near-atomic structure of jasplakinolide (JAS)-stabilized PfAct1 filaments determined by electron cryomicroscopy. The general filament architecture is similar to that of mammalian F-actin. The high resolution of the structure allowed us to identify small but important differences at inter- and intrastrand contact sites, explaining the inherent instability of apicomplexan actin filaments. JAS binds at regular intervals inside the filament to three adjacent actin subunits, reinforcing filament stability by hydrophobic interactions. Our study reveals the high-resolution structure of a small molecule bound to F-actin, highlighting the potential of electron cryomicroscopy for structure-based drug design. Furthermore, our work serves as a strong foundation for understanding the structural design and evolution of actin filaments and their function in motility and host cell invasion of apicomplexan parasites.

  14. Magnetism of internal surfaces in a fractal structure

    NASA Astrophysics Data System (ADS)

    Branco, N. S.; Chame, Anna

    1993-09-01

    We study the inhomogeneous magnetization behavior of an Ising ferromagnet in Sierpiński pastry shells, using a real-space renormalization group approach. Two qualitatively different regions on the fractal are distinguished: the bulk and the set of internal surfaces which border the eliminated portions. We obtain the spontaneous mean magnetizations for these regions as a function of the temperature for different values of α = JS/ JB (J S and J B are the internal surface and bulk coupling constants respectively) and different geometrical parameters b and l. The critical β exponents are obtained for the several transitions. We obtain different universality classes for the bulk transitions, depending on what occurs at the surfaces, and a step-like behavior of the magnetization as a function of the temperature of some values of b and l.

  15. Development of epoxy matrices for filament-wound graphite structures

    SciTech Connect

    Morgan, R.J.; Walkup, C.M.; Kong, F.M.; Mones, E.T.

    1984-11-27

    This paper reviews our program to develop epoxy matrix systems for filament-wound graphite structures. The criteria for this matrix development program requires that the epoxide and amine components are processible and non-toxic; and the corresponding matrix itself is tough, possesses a Tg > 120/sup 0/C and does not lose its mechanical-thermal properties upon exposure to service environment conditions. We report our data on processible, hindered amine cured-epoxide matrices such as menthane or 2,5 dimethyl 2,5 hexane diamine cured bis-phenol-A-diglycidyl ether (DGEBA) epoxide systems in the presence of viscosity-lowering diluents. To produce tough, processible matrices that do not deteriorate upon exposure to service environment conditions requires a knowledge of the network structure formed and how such structure may deteriorate under molecular flow associated with the shear-band toughening mechanisms. For amine-cured DGEBA matrices we report deterioration in the mechanical response and Tg after plastic flow has occurred in such glasses. Permanent chemical changes that occur during this flow induced degradation process were monitored by stress-Fourier transform infrared spectroscopy. The ability to eliminate the aging of tough, cross-linked composite matrices upon molecular flow is discussed in terms of networks with segments of equal extensibility. 15 references, 4 figures, 2 tables.

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

    SciTech Connect

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

    2016-01-25

    Here, 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.

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

    DOE PAGES

    Kang, Hyunook; Weiss, Thomas M.; Bang, Injin; ...

    2016-01-25

    Here, 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 themore » 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.« less

  18. Fabrication of Multscale Fractal-Like Structures by Controlling Fluid Interface Instability

    NASA Astrophysics Data System (ADS)

    Islam, Tanveer Ul; Gandhi, Prasanna S.

    2016-11-01

    Nature, in quest for the best designs has shaped its vital systems into fractal geometries. Effectual way of spontaneous fabrication of scalable, ordered fractal-like structures by controlling Saffman-Taylor instability in a lifted Hele-Shaw cell is deployed here. In lifted Hele-Shaw cell uncontrolled penetration of low-viscosity fluid into its high-viscosity counterpart is known to develop irregular, non-repeatable, normally short-lived, branched patterns. We propose and characterize experimentally anisotropies in a form of spatially distributed pits on the cell plates to control initiation and further penetration of non-splitting fingers. The proposed control over shielding mechanism yields recipes for fabrication of families of ordered fractal-like patterns of multiple generations. As an example, we demonstrate and characterize fabrication of a Cayley tree fractal-like pattern. The patterns, in addition, are retained permanently by employing UV/thermally curable fluids. The proposed technique thus establishes solid foundation for bio-mimicking natural structures spanning multiple-scales for scientific and engineering use.

  19. Fabrication of Multscale Fractal-Like Structures by Controlling Fluid Interface Instability

    PubMed Central

    Islam, Tanveer ul; Gandhi, Prasanna S.

    2016-01-01

    Nature, in quest for the best designs has shaped its vital systems into fractal geometries. Effectual way of spontaneous fabrication of scalable, ordered fractal-like structures by controlling Saffman-Taylor instability in a lifted Hele-Shaw cell is deployed here. In lifted Hele-Shaw cell uncontrolled penetration of low-viscosity fluid into its high-viscosity counterpart is known to develop irregular, non-repeatable, normally short-lived, branched patterns. We propose and characterize experimentally anisotropies in a form of spatially distributed pits on the cell plates to control initiation and further penetration of non-splitting fingers. The proposed control over shielding mechanism yields recipes for fabrication of families of ordered fractal-like patterns of multiple generations. As an example, we demonstrate and characterize fabrication of a Cayley tree fractal-like pattern. The patterns, in addition, are retained permanently by employing UV/thermally curable fluids. The proposed technique thus establishes solid foundation for bio-mimicking natural structures spanning multiple-scales for scientific and engineering use. PMID:27849003

  20. Fractal nematic colloids

    PubMed Central

    Hashemi, S. M.; Jagodič, U.; Mozaffari, M. R.; Ejtehadi, M. R.; Muševič, I.; Ravnik, M.

    2017-01-01

    Fractals are remarkable examples of self-similarity where a structure or dynamic pattern is repeated over multiple spatial or time scales. However, little is known about how fractal stimuli such as fractal surfaces interact with their local environment if it exhibits order. Here we show geometry-induced formation of fractal defect states in Koch nematic colloids, exhibiting fractal self-similarity better than 90% over three orders of magnitude in the length scales, from micrometers to nanometres. We produce polymer Koch-shaped hollow colloidal prisms of three successive fractal iterations by direct laser writing, and characterize their coupling with the nematic by polarization microscopy and numerical modelling. Explicit generation of topological defect pairs is found, with the number of defects following exponential-law dependence and reaching few 100 already at fractal iteration four. This work demonstrates a route for generation of fractal topological defect states in responsive soft matter. PMID:28117325

  1. Fractal nematic colloids.

    PubMed

    Hashemi, S M; Jagodič, U; Mozaffari, M R; Ejtehadi, M R; Muševič, I; Ravnik, M

    2017-01-24

    Fractals are remarkable examples of self-similarity where a structure or dynamic pattern is repeated over multiple spatial or time scales. However, little is known about how fractal stimuli such as fractal surfaces interact with their local environment if it exhibits order. Here we show geometry-induced formation of fractal defect states in Koch nematic colloids, exhibiting fractal self-similarity better than 90% over three orders of magnitude in the length scales, from micrometers to nanometres. We produce polymer Koch-shaped hollow colloidal prisms of three successive fractal iterations by direct laser writing, and characterize their coupling with the nematic by polarization microscopy and numerical modelling. Explicit generation of topological defect pairs is found, with the number of defects following exponential-law dependence and reaching few 100 already at fractal iteration four. This work demonstrates a route for generation of fractal topological defect states in responsive soft matter.

  2. Fractal nematic colloids

    NASA Astrophysics Data System (ADS)

    Hashemi, S. M.; Jagodič, U.; Mozaffari, M. R.; Ejtehadi, M. R.; Muševič, I.; Ravnik, M.

    2017-01-01

    Fractals are remarkable examples of self-similarity where a structure or dynamic pattern is repeated over multiple spatial or time scales. However, little is known about how fractal stimuli such as fractal surfaces interact with their local environment if it exhibits order. Here we show geometry-induced formation of fractal defect states in Koch nematic colloids, exhibiting fractal self-similarity better than 90% over three orders of magnitude in the length scales, from micrometers to nanometres. We produce polymer Koch-shaped hollow colloidal prisms of three successive fractal iterations by direct laser writing, and characterize their coupling with the nematic by polarization microscopy and numerical modelling. Explicit generation of topological defect pairs is found, with the number of defects following exponential-law dependence and reaching few 100 already at fractal iteration four. This work demonstrates a route for generation of fractal topological defect states in responsive soft matter.

  3. 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

  4. Structural complexity of filaments formed from the actin and tubulin folds

    PubMed Central

    Jiang, Shimin; Ghoshdastider, Umesh; Narita, Akihiro; Popp, David

    2016-01-01

    ABSTRACT From yeast to man, an evolutionary distance of 1.3 billion years, the F-actin filament structure has been conserved largely in line with the 94% sequence identity. The situation is entirely different in bacteria. In comparison to eukaryotic actins, the bacterial actin-like proteins (ALPs) show medium to low levels of sequence identity. This is extreme in the case of the ParM family of proteins, which often display less than 20% identity. ParMs are plasmid segregation proteins that form the polymerizing motors that propel pairs of plasmids to the extremities of a cell prior to cell division, ensuring faithful inheritance of the plasmid. Recently, exotic ParM filament structures have been elucidated that show ParM filament geometries are not limited to the standard polar pair of strands typified by actin. Four-stranded non-polar ParM filaments existing as open or closed nanotubules are found in Clostridium tetani and Bacillus thuringiensis, respectively. These diverse architectures indicate that the actin fold is capable of forming a large variety of filament morphologies, and that the conception of the “actin” filament has been heavily influenced by its conservation in eukaryotes. Here, we review the history of the structure determination of the eukaryotic actin filament to give a sense of context for the discovery of the new ParM filament structures. We describe the novel ParM geometries and predict that even more complex actin-like filaments may exist in bacteria. Finally, we compare the architectures of filaments arising from the actin and tubulin folds and conclude that the basic units possess similar properties that can each form a range of structures. Thus, the use of the actin fold in microfilaments and the tubulin fold for microtubules likely arose from a wider range of filament possibilities, but became entrenched as those architectures in early eukaryotes. PMID:28042378

  5. Ultrasonic analysis of Kevlar-epoxy filament wound structures

    SciTech Connect

    Brosey, W.D.

    1985-07-16

    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.

  6. 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.

  7. Hexatic and fat-fractal structures for water droplets condensing on oil

    NASA Astrophysics Data System (ADS)

    Steyer, A.; Guenoun, P.; Beysens, D.

    1993-07-01

    Experiments on water droplets condensing on a liquid substrate (breath figures) are reported. Attractive capillary interactions between drops lead to the formation of particular two-dimensional structures. An hexatic order with exponent η~=0.9 is observed over a small length scale. At larger length scales the defects in the structure exhibit a fat-fractal distribution with exponent β~=3.3.

  8. 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.

  9. Large-scale coherent structures in fractal-generated, axisymmetric wakes

    NASA Astrophysics Data System (ADS)

    Nedic, Jovan; Supponen, Outi; Ganapathisubramani, Bharathram; Vassilicos, John Christos

    2013-11-01

    The coherence and energy of large-scale structures in turbulent axisymmetric wakes are known to play a role on the drag coefficient of the body. Specifically, there is an expectation that drag can be reduced by reducing the energy of the vortex shedding. We use fractal plates which have been shown to have higher drag coefficients than square plates and disks with the same frontal area (Nedic, Ganapathisubramani & Vassilicos FDR 2013), yet show that the energy of the large-scale vortices shed from these plates is reduced by 15% to 60% compared to non-fractal plates. Fractal plates can reduce wake size and alter dissipation scalings [see DFD13-2013-000126] and the relation CD =CVCɛ between the drag coefficient and coefficients of wake volume and average turbulent dissipation rate can be used to explore consequences on drag. Furthermore, the azimuthal mode associated with the vortex shedding (m = 1) is still found to be dominant for all plates, however its coherence is slightly altered by the fractals, whilst mode m = 2 has been dramatically altered.

  10. 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.

  11. 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.

  12. Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles.

    PubMed

    Bharat, Tanmay A M; Murshudov, Garib N; Sachse, Carsten; Löwe, Jan

    2015-07-02

    Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with centromeric parC plasmid DNA, while facilitating the addition of subunits to ParM filaments. Growing ParMRC spindles push sister plasmids to the cell poles. Here, using modern electron cryomicroscopy methods, we investigate the structures and arrangements of ParM filaments in vitro and in cells, revealing at near-atomic resolution how subunits and filaments come together to produce the simplest known mitotic machinery. To understand the mechanism of dynamic instability, we determine structures of ParM filaments in different nucleotide states. The structure of filaments bound to the ATP analogue AMPPNP is determined at 4.3 Å resolution and refined. The ParM filament structure shows strong longitudinal interfaces and weaker lateral interactions. Also using electron cryomicroscopy, we reconstruct ParM doublets forming antiparallel spindles. Finally, with whole-cell electron cryotomography, we show that doublets are abundant in bacterial cells containing low-copy-number plasmids with the ParMRC locus, leading to an asynchronous model of R1 plasmid segregation.

  13. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Spontaneous formation of fractal structures on triglyceride surfaces with reference to their super water-repellent properties.

    PubMed

    Fang, Wenjun; Mayama, Hiroyuki; Tsujii, Kaoru

    2007-01-25

    Alkylketene dimer (AKD), a kind of wax, has been known to form fractal surfaces spontaneously and show super water-repellency. Such formation of water-repellent and fractal surfaces was also found in this work for triglycerides. Since the crystal phase transitions of these waxes were well studied, we studied the formation of their fractal surfaces through contact angle measurements, differential scanning calorimetry (DSC), and X-ray diffraction (XRD). From time-dependent contact angle measurements, it was found that the formation of super water-repellent surfaces with fractal structures occurred spontaneously also on the triglyceride surfaces at different temperatures. The freshly solidified triglyceride surfaces were almost transparent, and their initial contact angles of water were close to 110 degrees. The surfaces then became rough and clouded after being incubated for a certain time at a specified temperature. The super water-repellent surfaces were quite rough and showed fractal structures with the dimension of ca. 2.2 calculated from the scanning electron microscopic (SEM) images by the box-counting method. The phase transformation from a metastable state to a stable cystalline one after the solidification from the melt of triglycerides was clearly observed by DSC and XRD measurements. The fractal crystalline structures and the super water-repellency resulted from this phase transformation and the crystal growth. Ensuring the initial sample solidified into the metastable state and curing the surface at an appropriate temperature are key factors for the successful preparation of fractal triglyceride surfaces by the solidification method.

  15. Structural transition of actin filament in a cell-sized water droplet with a phospholipid membrane

    NASA Astrophysics Data System (ADS)

    Hase, M.; Yoshikawa, K.

    2006-03-01

    Actin filament, F-actin, is a semiflexible polymer with a negative charge, and is one of the main constituents of cell membranes. To clarify the effect of cross talk between a phospholipid membrane and actin filaments in cells, we conducted microscopic observations on the structural changes in actin filaments in a cell-sized (several tens of micrometers in diameter) water droplet coated with a phospholipid membrane such as phosphatidylserine (PS; negatively charged head group) or phosphatidylethanolamine (PE; neutral head group) as a simple model of a living cell membrane. With PS, actin filaments are distributed uniformly in the water phase without adsorption onto the membrane surface between 2 and 6mM Mg2+, while between 6 and 12mM Mg2+, actin filaments are adsorbed onto the inner membrane surface. With PE, the actin filaments are uniformly adsorbed onto the inner membrane surface between 2 and 12mM Mg2+. With both PS and PE membranes, at Mg2+ concentrations higher than 12mM, thick bundles are formed in the bulk water droplet accompanied by the dissolution of actin filaments from the membrane surface. The attraction between actin filaments and membrane is attributable to an increase in the translational entropy of counterions accompanied by the adsorption of actin filaments onto the membrane surface. These results suggest that a microscopic water droplet coated with phospholipid can serve as an easy-to-handle model of cell membranes.

  16. Fractal antenna and fractal resonator primer

    NASA Astrophysics Data System (ADS)

    Cohen, Nathan

    2015-03-01

    Self-similarity and fractals have opened new and important avenues for antenna and electronic solutions over the last 25 years. This primer provides an introduction to the benefits provided by fractal geometry in antennas, resonators, and related structures. Such benefits include, among many, wider bandwidths, smaller sizes, part-less electronic components, and better performance. Fractals also provide a new generation of optimized design tools, first used successfully in antennas but applicable in a general fashion.

  17. Growing gold fractal nano-structures and studying changes in their morphology as a function of film growth rate

    NASA Astrophysics Data System (ADS)

    Banerjee, Amit; Banerjee, S. S.

    2016-10-01

    We investigate the formation of fractal like nano-structures on free standing gold films grown via surfactant mediated thin film growth process. We determine these structures to be confined within the first few monolayers of the thin film. Their chemical composition is identical to that of the Au film, although their density is different from the surrounding film. We observe changes in the morphology of these fractal structures by controlling the film growth rate, which spans across three orders of magnitude. From our study, we quantify the morphological changes in the fractal structure via a roundness parameter and we suggest an empirical relation between the roundness parameter and the growth rate. The study shows an inverse relationship between the roundness parameter and the growth rate and also that the fractal to compact morphological transition is continuous.

  18. Critical behavior of the quantum Ising model on a fractal structure.

    PubMed

    Yi, Hangmo

    2013-07-01

    We study the critical behavior of the transverse-field quantum Ising model on a fractal structure, namely the Sierpinski carpet. When a magnetic field Δ is applied perpendicular to the Ising spin direction, quantum fluctuations affect the transition between the ferromagnetic and the paramagnetic phases. Employing the continuous-time quantum Monte Carlo simulation method and the finite-size scaling analysis, we investigate the interplay between the quantum fluctuations and the exotic dimensionality of the fractal structure and its effect on the critical behavior. As the transverse magnetic field increases, the critical temperature monotonically decreases until it apparently vanishes at a critical field Δ(c), beyond which the system becomes paramagnetic at all temperatures. However, the critical exponents are independent of Δ and remain the same as in the purely classical(Δ=0) case.

  19. Changes in fractal structure of heart rate variability during a nap in one case.

    PubMed

    Shono, H; Shono, M; Takasaki, M; Iwasaka, T; Sugimori, H

    2001-06-01

    The objective of the present study was to analyze fractal structures of adult heart rate (HR) variability during a nap. Fractal analysis was carried out in one case over consecutive 10-min time series of HR, which were simultaneously recorded with electroencephalogram. Scaling relationships showed cross-over patterns characterized by alphas and alphal (i.e. slopes above and below a cross-over point). The alphas and alphal were black and white noise at Stage 4 of NREM sleep, and black and 1/f noise in REM sleep. Cross-over points changed from the first to second sleep cycle. We demonstrate the multifractal structures of HR variability during a nap in the present case.

  20. 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.

  1. 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

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

    PubMed

    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.

  3. [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

  4. Structural five-fold symmetry in the fractal morphology of diffusion-limited aggregates

    NASA Astrophysics Data System (ADS)

    Arneodo, A.; Argoul, F.; Muzy, J. F.; Tabard, M.

    1992-09-01

    The statistical self-similarity of the geometry of diffusion-limited aggregates and the multifractal nature of the growth probability distribution on the surface of the growing clusters are investigated using the wavelet transform. This study reveals the existence of a predominant structural five-fold symmetry in the internal frozen region as well as in the active outer region of the interface. This observation is corroborated by a statistical analysis of the screening effects that govern diffusion-limited aggregation (DLA) growth in linear and sector-shaped cells. The existence of this symmetry is likely to be a clue to a hierarchichal fractal ordering. We report on the discovery of Fibonacci sequences in the inner extinct region of large mass off-lattice DLA clusters, with a branching ratio which converges asymptotically to the golden mean. We suggest an interpretation of the DLA morphology as a “quasifractal” counterpart of the well-ordered snowflake fractal architecture.

  5. Respiratory Syncytial Virus Assembles into Structured Filamentous Virion Particles Independently of Host Cytoskeleton and Related Proteins

    PubMed Central

    Shaikh, Fyza Y.; Utley, Thomas J.; Craven, Ryan E.; Rogers, Meredith C.; Lapierre, Lynne A.; Goldenring, James R.; Crowe, James E.

    2012-01-01

    Respiratory syncytial virus (RSV) is a single-stranded RNA virus that assembles into viral filaments at the cell surface. Virus assembly often depends on the ability of a virus to use host proteins to accomplish viral tasks. Since the fusion protein cytoplasmic tail (FCT) is critical for viral filamentous assembly, we hypothesized that host proteins important for viral assembly may be recruited by the FCT. Using a yeast two-hybrid screen, we found that filamin A interacted with FCT, and mammalian cell experiments showed it localized to viral filaments but did not affect viral replication. Furthermore, we found that a number of actin-associated proteins also were excluded from viral filaments. Actin or tubulin cytoskeletal rearrangement was not necessary for F trafficking to the cell surface or for viral assembly into filaments, but was necessary for optimal viral replication and may be important for anchoring viral filaments. These findings suggest that RSV assembly into filaments occurs independently of actin polymerization and that viral proteins are the principal drivers for the mechanical tasks involved with formation of complex, structured RSV filaments at the host cell plasma membrane. PMID:22808269

  6. Facile and fast synthesis of single-crystalline fractal zinc structures through a solution phase reaction and their conversion to zinc oxide.

    PubMed

    Cho, Seungho; Kim, Semi; Kim, Hye-Jin; Lee, Bo Ram; Lee, Kun-Hong

    2009-09-01

    We report a novel method for the synthesis of fractal Zn structures through a solution phase reaction. An Al-film-deposited substrate was immersed in an aqueous ammonia solution containing Zn ions and maintained at 95 degrees C for 5 min. After the reaction, the Al-deposited side of the substrate was found to be covered with fractal Zn structures. These Zn structures are highly oriented, and the Zn(002) planes are parallel to the substrate. They are single-crystalline and the average thickness of the plates is approximately 50 nm. On the basis of our results, we propose a mechanism for the spontaneous growth of such fractal Zn structures. Single-crystalline fractal ZnO structures can also be obtained by calcination of the as-synthesized fractal Zn crystals at 500 degrees C for 5 h in air. These fractal ZnO structures are highly oriented and inherit their morphologies from the Zn structures.

  7. Ag fractal structures in electroless metal deposition systems with and without magnetic field

    NASA Astrophysics Data System (ADS)

    Ibrahim, Huria; Farah, Hiba; Zein Eddin, Amal; Isber, Samih; Sultan, Rabih

    2017-08-01

    Metal electrodeposition systems display tree-like structures with extensive ramification and a fractal character. Electrolysis is not a necessary route for the growth of such dendritic metal deposits. We can grow beautiful ramification patterns via a simple redox reaction. We present here a study of silver (Ag) deposits from the reduction of Ag+ in (AgNO3) solution by metallic copper. The experiments are carried out in discotic geometry, in a Petri dish hosting a thin AgNO3 solution film. A variety of deposited structures and patterns is obtained at different Ag+ concentrations, yet with essentially the same fractal dimension averaged at 1.64, typical of diffusion-limited aggregation (DLA). A linear magnetic field of low induction (0.50-1.0 T) applied across the medium causes a notable transformation in the morphology of the deposits. In both the field off and the field on cases, the effect of vertical (hence 3D) heaving seems to be dominant, perhaps explaining the nearly constant fractal dimension.

  8. Microelectronics and nanotechnology, and the fractal-like structure of information, knowledge, and science

    NASA Astrophysics Data System (ADS)

    Nutu, Catalin Silviu; Axinte, Tiberiu

    2016-12-01

    The article is centralizing and is concentrating the information from a considerable amount of papers related to the field of microelectronics and nanotechnology and also provides an approach to science and to the future evolution of science, based on the theory of the fractals. The new science of microelectronics and nanotechnology is one of the best examples of how the science of future will look like, namely at the confluence of increasingly more other sciences, where increasingly more sciences are to be added in the structure of the new science and the role of the multidisciplinary and interdisciplinary is becoming more and more important. Although not giving explicit details (e.g. specific formulas) the theory of fractals is used in the paper to explain the way of generation of new science for the specific case of microelectronics and nanotechnology, but is also used in the paper to outline a different way to approach new science and eventually to approach new sciences to come. There are mainly two motivations for the present article, namely: on the one hand, the position of the microelectronics and nanotechnologies in the fractal-like structure of science, and, on the other hand, that much of the communication, information, knowledge and science transfer, dissemination and advancement in sciences are taking place using the new technologies related to microelectronics and nanotechnologies.

  9. 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.

  10. 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

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

    SciTech Connect

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

    2015-08-15

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

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

    NASA Astrophysics Data System (ADS)

    Nakouzi, Elias; Sultan, Rabih

    2011-12-01

    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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Thin Filament Structure and the Steric Blocking Model.

    PubMed

    Lehman, William

    2016-03-15

    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. Copyright © 2016 John Wiley & Sons, Inc.

  18. Thermal vacuum, cosmic microwave radiation, neutrino masses and fractal-like self-similar structure

    NASA Astrophysics Data System (ADS)

    Capolupo, Antonio; Lambiase, Gaetano; Vitiello, Giuseppe

    2017-08-01

    The behavior of thermal vacuum condensates of scalar and fermion fields is analyzed and it is shown that the condensate of Maxwell fields reproduces the characteristics of the cosmic microwave radiation. By studying fermion thermal states with the temperature of the cosmic neutrino background, we derive a value of the sum of the active neutrino masses which is compatible with its estimated lower bound. Moreover, we reveal the fractal self-similar structure of the thermal radiation and we relate it to the coherent structure of the thermal vacuum.

  19. Consequences of the fractal architecture of trees on their structural measures.

    PubMed

    Pluciński, Mateusz; Pluciński, Szymon; Rodríguez-Iturbe, Ignacio

    2008-03-07

    While the mechanics of trees are well known, a systematic and comprehensive study of the mechanical consequences of a tree's fractal structure has been lacking. Here, we analyze the structure of botanical trees using computer modeling and show that many relevant measures of support throughout all the branches of a tree follow specific patterns which can be described by characteristic probability distributions and well-defined spatial relationships. Most notably, moments, forces, and axial and shear stresses throughout the different branches all exhibit power-law distributions. These results suggest a new approach to the study of the mechanics of trees, one accounting for the implications of the above results.

  20. Rift Valley fever phlebovirus NSs protein core domain structure suggests molecular basis for nuclear filaments.

    PubMed

    Barski, Michal; Brennan, Benjamin; Miller, Ona K; Potter, Jane A; Vijayakrishnan, Swetha; Bhella, David; Naismith, James H; Elliott, Richard M; Schwarz-Linek, Ulrich

    2017-09-15

    Rift Valley fever phlebovirus (RVFV) is a clinically and economically important pathogen increasingly likely to cause widespread epidemics. RVFV virulence depends on the interferon antagonist non-structural protein (NSs), which remains poorly characterized. We identified a stable core domain of RVFV NSs (residues 83-248), and solved its crystal structure, a novel all-helical fold organized into highly ordered fibrils. A hallmark of RVFV pathology is NSs filament formation in infected cell nuclei. Recombinant virus encoding the NSs core domain induced intranuclear filaments, suggesting it contains all essential determinants for nuclear translocation and filament formation. Mutations of key crystal fibril interface residues in viruses encoding full-length NSs completely abrogated intranuclear filament formation in infected cells. We propose the fibrillar arrangement of the NSs core domain in crystals reveals the molecular basis of assembly of this key virulence factor in cell nuclei. Our findings have important implications for fundamental understanding of RVFV virulence.

  1. Fractal structures in the chaotic motion of charged particles in a magnetized plasma under the influence of drift waves

    NASA Astrophysics Data System (ADS)

    Mathias, A. C.; Viana, R. L.; Kroetz, T.; Caldas, I. L.

    2017-03-01

    Chaotic dynamics in open Hamiltonian dynamical systems typically presents a number of fractal structures in phase space derived from the interwoven structure of invariant manifolds and the corresponding chaotic saddle. These structures are thought to play an important role in the transport properties related to the chaotic motion. Such properties can explain some aspects of the non-uniform nature of the anomalous transport observed in magnetically confined plasmas. Accordingly we consider a theoretical model for the interaction of charged test particles with drift waves. We describe the exit basin structure of the corresponding chaotic orbit in phase space and interpret it in terms of the invariant manifold structure underlying chaotic dynamics. As a result, the exit basin boundary is shown to be a fractal curve, by direct calculation of its box-counting dimension. Moreover, when there are more than two basins, we verify the existence of the Wada property, an extreme form of fractality.

  2. Structural architecture of the CARMA1/Bcl10/MALT1 signalosome: nucleation-induced filamentous assembly.

    PubMed

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

    2013-09-26

    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.

  3. 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

  4. Robust estimation of fractal measures for characterizing the structural complexity of the human brain: optimization and reproducibility.

    PubMed

    Goñi, Joaquín; Sporns, Olaf; Cheng, Hu; Aznárez-Sanado, Maite; Wang, Yang; Josa, Santiago; Arrondo, Gonzalo; Mathews, Vincent P; Hummer, Tom A; Kronenberger, William G; Avena-Koenigsberger, Andrea; Saykin, Andrew J; Pastor, María A

    2013-12-01

    High-resolution isotropic three-dimensional reconstructions of human brain gray and white matter structures can be characterized to quantify aspects of their shape, volume and topological complexity. In particular, methods based on fractal analysis have been applied in neuroimaging studies to quantify the structural complexity of the brain in both healthy and impaired conditions. The usefulness of such measures for characterizing individual differences in brain structure critically depends on their within-subject reproducibility in order to allow the robust detection of between-subject differences. This study analyzes key analytic parameters of three fractal-based methods that rely on the box-counting algorithm with the aim to maximize within-subject reproducibility of the fractal characterizations of different brain objects, including the pial surface, the cortical ribbon volume, the white matter volume and the gray matter/white matter boundary. Two separate datasets originating from different imaging centers were analyzed, comprising 50 subjects with three and 24 subjects with four successive scanning sessions per subject, respectively. The reproducibility of fractal measures was statistically assessed by computing their intra-class correlations. Results reveal differences between different fractal estimators and allow the identification of several parameters that are critical for high reproducibility. Highest reproducibility with intra-class correlations in the range of 0.9-0.95 is achieved with the correlation dimension. Further analyses of the fractal dimensions of parcellated cortical and subcortical gray matter regions suggest robustly estimated and region-specific patterns of individual variability. These results are valuable for defining appropriate parameter configurations when studying changes in fractal descriptors of human brain structure, for instance in studies of neurological diseases that do not allow repeated measurements or for disease

  5. Robust estimation of fractal measures for characterizing the structural complexity of the human brain: optimization and reproducibility

    PubMed Central

    Goñi, Joaquín; Sporns, Olaf; Cheng, Hu; Aznárez-Sanado, Maite; Wang, Yang; Josa, Santiago; Arrondo, Gonzalo; Mathews, Vincent P; Hummer, Tom A; Kronenberger, William G; Avena-Koenigsberger, Andrea; Saykin, Andrew J.; Pastor, María A.

    2013-01-01

    High-resolution isotropic three-dimensional reconstructions of human brain gray and white matter structures can be characterized to quantify aspects of their shape, volume and topological complexity. In particular, methods based on fractal analysis have been applied in neuroimaging studies to quantify the structural complexity of the brain in both healthy and impaired conditions. The usefulness of such measures for characterizing individual differences in brain structure critically depends on their within-subject reproducibility in order to allow the robust detection of between-subject differences. This study analyzes key analytic parameters of three fractal-based methods that rely on the box-counting algorithm with the aim to maximize within-subject reproducibility of the fractal characterizations of different brain objects, including the pial surface, the cortical ribbon volume, the white matter volume and the grey matter/white matter boundary. Two separate datasets originating from different imaging centers were analyzed, comprising, 50 subjects with three and 24 subjects with four successive scanning sessions per subject, respectively. The reproducibility of fractal measures was statistically assessed by computing their intra-class correlations. Results reveal differences between different fractal estimators and allow the identification of several parameters that are critical for high reproducibility. Highest reproducibility with intra-class correlations in the range of 0.9–0.95 is achieved with the correlation dimension. Further analyses of the fractal dimensions of parcellated cortical and subcortical gray matter regions suggest robustly estimated and region-specific patterns of individual variability. These results are valuable for defining appropriate parameter configurations when studying changes in fractal descriptors of human brain structure, for instance in studies of neurological diseases that do not allow repeated measurements or for disease

  6. Multiple crystal structures of actin dimers and their implications for interactions in the actin filament

    PubMed Central

    Sawaya, Michael R.; Kudryashov, D. S.; Pashkov, Inna; Adisetiyo, Helty; Reisler, Emil; Yeates, Todd O.

    2008-01-01

    The structure of actin in its monomeric form is known at high resolution, while the structure of filamentous F-actin is only understood at considerably lower resolution. Knowing pre­cisely how the monomers of actin fit together would lead to a deeper understanding of the dynamic behavior of the actin filament. Here, a series of crystal structures of actin dimers are reported which were prepared by cross-linking in either the longitudinal or the lateral direction in the filament state. Laterally cross-linked dimers, comprised of monomers belonging to different protofilaments, are found to adopt configurations in crystals that are not related to the native structure of filamentous actin. In contrast, multiple structures of longitudinal dimers consistently reveal the same interface between monomers within a single protofilament. The re­appearance of the same longitudinal interface in multiple crystal structures adds weight to arguments that the interface visualized is similar to that in actin filaments. Highly conserved atomic interactions involving residues 199–205 and 287–291 are highlighted. PMID:18391412

  7. 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.

  8. X-ray structures associated with disappearing H-alpha filaments in active regions

    NASA Technical Reports Server (NTRS)

    Kahler, S. W.

    1980-01-01

    The paper examines the relationship between active region disappearing H-alpha filaments and the associated coronal X-ray structures observed both before the disappearance event and afterwards. The events chosen for the study were selected from a list of active region X-ray transients observed in the images from the X-ray telescope on Skylab and from a list compiled by Webb (1976) of sudden disappearances of filaments during the Skylab period. Results indicate no distinction between the disappearing and the remaining active region filaments in terms of their pre-event associated X-ray emission features. However, X-ray brightenings were associated in a nearly one-to-one correspondence with disappearing portions of the filaments.

  9. 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

  10. 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

  11. Sarcomere-length dependence of myosin filament structure in skeletal muscle fibres of the frog.

    PubMed

    Reconditi, Massimo; Brunello, Elisabetta; Fusi, Luca; Linari, Marco; Martinez, Manuel Fernandez; Lombardi, Vincenzo; Irving, Malcolm; Piazzesi, Gabriella

    2014-03-01

    X-ray diffraction patterns were recorded at beamline ID02 of the European Synchrotron Radiation Facility from small bundles of skeletal muscle fibres from Rana esculenta at sarcomere lengths between 2.1 and 3.5 μm at 4°C. The intensities of the X-ray reflections from resting fibres associated with the quasi-helical order of the myosin heads and myosin binding protein C (MyBP-C) decreased in the sarcomere length range 2.6-3.0 μm but were constant outside it, suggesting that an OFF conformation of the thick filament is maintained by an interaction between MyBP-C and the thin filaments. During active isometric contraction the intensity of the M3 reflection from the regular repeat of the myosin heads along the filaments decreased in proportion to the overlap between thick and thin filaments, with no change in its interference fine structure. Thus, myosin heads in the regions of the thick filaments that do not overlap with thin filaments are highly disordered during isometric contraction, in contrast to their quasi-helical order at rest. Heads in the overlap region that belong to two-headed myosin molecules that are fully detached from actin are also highly disordered, in contrast to the detached partners of actin-attached heads. These results provide strong support for the concept of a regulatory structural transition in the thick filament involving changes in both the organisation of the myosin heads on its surface and the axial periodicity of the myosin tails in its backbone, mediated by an interaction between MyBP-C and the thin filaments.

  12. 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.

  13. Effects of humic acid on recoverability and fractal structure of alum-kaolin flocs.

    PubMed

    Zhong, Runsheng; Zhang, Xihui; Xiao, Feng; Li, Xiaoyan

    2011-01-01

    Particle surface characteristics, floc recoverability and fractal structure of alum-kaolin flocs were investigated using in situ particle image velocimetry (PIV) and microbalance with or without humic acid. Experimental results indicated that the zeta potential of kaolin particle surface after adsorption of humic acid was related with humic acid concentration and its acid-base buffering capacity. Adsorption of humic acid resulted in more negative electrophoresis on the particle surface. Coagulant dosages for particles to form flocs would increase with increasing humic concentration. PIV was used to evaluate floc structural fragmentation, floc surface erosion as well as recoverability after high shear. It was found that the floc size during the steady phase of growth was small, while the regrowing capability decreased in the presence of humic acid. The recoverability was closely related with floc breakage modes including floc structural fragmentation and floc surface erosion. The fractal dimensions of alum-kaolin flocs by mass-size method based on microbalance would decrease with increasing humic concentration. This study proved that humic acid had adverse influences on the performance of coagulation process.

  14. Defect modes properties in self-similar fractal multilayer structures containing lossless single negative metamaterials

    NASA Astrophysics Data System (ADS)

    Rahimi, H.; Rezaei, M.

    2013-08-01

    Transfer matrix method is used to investigate the electromagnetic transmission spectra of a one-dimensional photonic fractal multilayer structure composed of single-negative metamaterial when common positive dielectric defect layers of are introduced. It is found that the frequency of the resonance defect modes can be tuned independently by varying the defect layer thicknesses. It is also found that by increasing the value of refractive index of defect layers and the number of periods, the full width half maximum of defect modes will be narrowed and shifted to lower frequencies. Also, our investigations show that for both TE and TM polarizations moving away from normal incidence to oblique incidence shows that the defect modes shift to upper frequencies. In other words, the defect modes inside the band gap depend on the incident angle and polarization. More interesting, for angles of incidence greater than 55° the defect modes for TE polarization (unlike to TM polarization) are eliminated. Moreover, the electromagnetic fields in the defect layers are strongly localized, and they can be excite independently. We believe that the proposed fractal structures can be useful in designing tunable independently high-Q filters with specific channels by adjusting their structural parameters.

  15. CONDENSED MATTER: STRUCTURE, MECHANICAL AND THERMAL PROPERTIES: A Model for Fractal Dimension of Rough Surfaces

    NASA Astrophysics Data System (ADS)

    Li, Jian-Hua; Yu, Bo-Ming; Zou, Ming-Qing

    2009-11-01

    We report a model for the fractal dimension Ds of rough surfaces based on the fractal distribution of roughness elements on surfaces and the fractal character of surface profiles. The proposed model for the fractal dimension Ds is expressed as a function of the fractal dimensions D for conic roughness diameter/height and Dp for surface profile, maximum roughness base diameter λmax, the ratio β of conic roughness height to its base radius as well as the ratio λminλmax of the minimum to the maximal base diameter.

  16. 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

  17. 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

  18. The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression

    PubMed Central

    Almassalha, L. M.; Tiwari, A.; Ruhoff, P. T.; Stypula-Cyrus, Y.; Cherkezyan, L.; Matsuda, H.; Dela Cruz, M. A.; Chandler, J. E.; White, C.; Maneval, C.; Subramanian, H.; Szleifer, I.; Roy, H. K.; Backman, V.

    2017-01-01

    Most of what we know about gene transcription comes from the view of cells as molecular machines: focusing on the role of molecular modifications to the proteins carrying out transcriptional reactions at a loci-by-loci basis. This view ignores a critical reality: biological reactions do not happen in an empty space, but in a highly complex, interrelated, and dense nanoenvironment that profoundly influences chemical interactions. We explored the relationship between the physical nanoenvironment of chromatin and gene transcription in vitro. We analytically show that changes in the fractal dimension, D, of chromatin correspond to simultaneous increases in chromatin accessibility and compaction heterogeneity. Using these predictions, we demonstrate experimentally that nanoscopic changes to chromatin D within thirty minutes correlate with concomitant enhancement and suppression of transcription. Further, we show that the increased heterogeneity of physical structure of chromatin due to increase in fractal dimension correlates with increased heterogeneity of gene networks. These findings indicate that the higher order folding of chromatin topology may act as a molecular-pathway independent code regulating global patterns of gene expression. Since physical organization of chromatin is frequently altered in oncogenesis, this work provides evidence pairing molecular function to physical structure for processes frequently altered during tumorigenesis. PMID:28117353

  19. The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression.

    PubMed

    Almassalha, L M; Tiwari, A; Ruhoff, P T; Stypula-Cyrus, Y; Cherkezyan, L; Matsuda, H; Dela Cruz, M A; Chandler, J E; White, C; Maneval, C; Subramanian, H; Szleifer, I; Roy, H K; Backman, V

    2017-01-24

    Most of what we know about gene transcription comes from the view of cells as molecular machines: focusing on the role of molecular modifications to the proteins carrying out transcriptional reactions at a loci-by-loci basis. This view ignores a critical reality: biological reactions do not happen in an empty space, but in a highly complex, interrelated, and dense nanoenvironment that profoundly influences chemical interactions. We explored the relationship between the physical nanoenvironment of chromatin and gene transcription in vitro. We analytically show that changes in the fractal dimension, D, of chromatin correspond to simultaneous increases in chromatin accessibility and compaction heterogeneity. Using these predictions, we demonstrate experimentally that nanoscopic changes to chromatin D within thirty minutes correlate with concomitant enhancement and suppression of transcription. Further, we show that the increased heterogeneity of physical structure of chromatin due to increase in fractal dimension correlates with increased heterogeneity of gene networks. These findings indicate that the higher order folding of chromatin topology may act as a molecular-pathway independent code regulating global patterns of gene expression. Since physical organization of chromatin is frequently altered in oncogenesis, this work provides evidence pairing molecular function to physical structure for processes frequently altered during tumorigenesis.

  20. Myosin filament sliding through the Z-disc relates striated muscle fibre structure to function.

    PubMed

    Rode, Christian; Siebert, Tobias; Tomalka, Andre; Blickhan, Reinhard

    2016-03-16

    Striated muscle contraction requires intricate interactions of microstructures. The classic textbook assumption that myosin filaments are compressed at the meshed Z-disc during striated muscle fibre contraction conflicts with experimental evidence. For example, myosin filaments are too stiff to be compressed sufficiently by the muscular force, and, unlike compressed springs, the muscle fibres do not restore their resting length after contractions to short lengths. Further, the dependence of a fibre's maximum contraction velocity on sarcomere length is unexplained to date. In this paper, we present a structurally consistent model of sarcomere contraction that reconciles these findings with the well-accepted sliding filament and crossbridge theories. The few required model parameters are taken from the literature or obtained from reasoning based on structural arguments. In our model, the transition from hexagonal to tetragonal actin filament arrangement near the Z-disc together with a thoughtful titin arrangement enables myosin filament sliding through the Z-disc. This sliding leads to swivelled crossbridges in the adjacent half-sarcomere that dampen contraction. With no fitting of parameters required, the model predicts straightforwardly the fibre's entire force-length behaviour and the dependence of the maximum contraction velocity on sarcomere length. Our model enables a structurally and functionally consistent view of the contractile machinery of the striated fibre with possible implications for muscle diseases and evolution. © 2016 The Author(s).

  1. 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.

  2. DARK RIBBONS PROPAGATING AND SWEEPING ACROSS EXTREME ULTRAVIOLET STRUCTURES AFTER FILAMENT ERUPTIONS

    SciTech Connect

    Xiao, Junmin; Zhang, Jun; Li, Ting; Yang, Shuhong E-mail: zjun@nao.cas.cn E-mail: shuhongyang@nao.cas.cn

    2015-05-20

    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{sup −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.

  3. 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.

  4. Fractal radar scattering from soil.

    PubMed

    Oleschko, Klaudia; Korvin, Gabor; Figueroa, Benjamin; Vuelvas, Marco Antonio; Balankin, Alexander S; Flores, Lourdes; Carreón, Dora

    2003-04-01

    A general technique is developed to retrieve the fractal dimension of self-similar soils through microwave (radar) scattering. The technique is based on a mathematical model relating the fractal dimensions of the georadargram to that of the scattering structure. Clear and different fractal signatures have been observed over four geosystems (soils and sediments) compared in this work.

  5. 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.

  6. Assembly and exchange of intermediate filament proteins of neurons: neurofilaments are dynamic structures

    PubMed Central

    1989-01-01

    We have explored the dynamics of intermediate filament assembly and subunit exchange using fluorescently labeled neurofilament proteins and a fluorescence resonance energy transfer assay. Neurofilaments (NFs) are assembled from three highly phosphorylated proteins with molecular masses of 180 (NF-H), 130 (NF-M), and 66 kD (NF-L) of which NF-L forms the structural core. The core component, NF-L, was stoichiometrically labeled at cysteine 321 with fluorescein, coumarin, or biotin-maleimide to produce assembly-competent fluorescent or biotinylated derivatives, respectively. Using coumarin-labeled NF-L as fluorescence donor and fluorescein-labeled NF-L as the fluorescence acceptor, assembly of NF filaments was induced by rapidly raising the NaCl concentration to 170 mM, and the kinetics was followed by the decrease in the donor fluorescence. Assembly of NF-L subunits into filaments does not require nucleotide binding or hydrolysis but is strongly dependent on ionic strength, pH, and temperature. The critical concentration of NF-L, that concentration that remains unassembled at equilibrium with fully formed filaments, is 38 micrograms/ml or 0.6 microM. Under physiological salt conditions NF-L filaments also undergo extensive subunit exchange. Kinetic analysis and evaluation of several possible mechanisms indicate that subunit exchange is preceded by dissociation of subunits from the filament and generation of a kinetically active pool of soluble subunits. Given the concentration of NF-L found in nerve cells and the possibility of regulating this pool, these results provide the first information that intermediate filaments are dynamic structures and that NF-L within the NF complex is in dynamic equilibrium with a small but kinetically active pool of unassembled NF-L units. PMID:2925792

  7. 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.

  8. Structure of a longitudinal actin dimer assembled by tandem w domains: implications for actin filament nucleation.

    PubMed

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

    2010-10-15

    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 β4. 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 β4 to tandem W domains can change their activity from actin filament nucleation to monomer sequestration.

  9. Fractal Stiffening

    NASA Technical Reports Server (NTRS)

    Harper, David William (Inventor)

    2017-01-01

    A structural support having fractal-stiffening and method of fabricating the support is presented where an optimized location of at least three nodes is predetermined prior to fabricating the structural support where a first set of webs is formed on one side of the support and joined to the nodes to form a first pocket region. A second set of webs is formed within the first pocket region forming a second pocket region where the height of the first set of webs extending orthogonally from the side of the support is greater than the second set of webs extending orthogonally from the support.

  10. The biology of desmin filaments: how do mutations affect their structure, assembly, and organisation?

    PubMed

    Bär, Harald; Strelkov, Sergei V; Sjöberg, Gunnar; Aebi, Ueli; Herrmann, Harald

    2004-11-01

    Desmin, the major intermediate filament (IF) protein of muscle, is evolutionarily highly conserved from shark to man. Recently, an increasing number of mutations of the desmin gene has been described to be associated with human diseases such as certain skeletal and cardiac myopathies. These diseases are histologically characterised by intracellular aggregates containing desmin and various associated proteins. Although there is progress regarding our knowledge on the cellular function of desmin within the cytoskeleton, the impact of each distinct mutation is currently not understood at all. In order to get insight into how such mutations affect filament assembly and their integration into the cytoskeleton we need to establish IF structure at atomic detail. Recent progress in determining the dimer structure of the desmin-related IF-protein vimentin allows us to assess how such mutations may affect desmin filament architecture.

  11. 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

  12. Non-equilibrium microscale thermomechanical modeling of bimetallic particulate fractal structures during ball milling fabrication

    NASA Astrophysics Data System (ADS)

    Aureli, Matteo; Doumanidis, Constantine C.; Gunduz, I. E.; Hussien, Aseel Gamal Suliman; Liao, Yiliang; Jaffar, Syed Murtaza; Rebholz, Claus; Doumanidis, Charalabos C.

    2017-07-01

    Nanostructured bimetallic reactive multilayers can be conveniently produced by ball milling of elemental powders. This research explores the non-equilibrium microscale conductive thermal transport in ball-milled particulate fractal structures during fabrication, arising from heat dissipation by bulk plastic deformation and surface friction. Upon impactor collisions, temperature increments are determined at interface joints and domain volumes using Green's functions, mirrored by source images with respect to warped ellipsoid domain boundaries. Heat source efficiency is calibrated via laboratory data to compensate for thermal expansion and impactor inelasticity, and the thermal analysis is coupled to a dynamic mechanics model of the particulate fracture. This thermomechanical model shows good agreement with the fractal dimensions of the observed microstructure from ball milling experiments. The model is intended to provide a comprehensive physical understanding of the fundamental process mechanism. In addition, the model could serve as a real-time thermal observer for closed-loop process control, as well as for interfacial diffusion and reaction analysis during ball milling.

  13. 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

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

    PubMed

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

    2008-10-01

    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 vertebrates 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.

  15. 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.

  16. Non-Debye dielectric relaxation in biological structures arises from their fractal nature.

    PubMed

    Raicu, V; Sato, T; Raicu, G

    2001-08-01

    What differentiates biological tissues from one another, thereby allowing their accomplishment of a physiological function, is their organization at supracellular and cellular levels. We developed general dielectric models for Cantorian (or treelike) fractal networks of transmission lines that mimic supracellular organization in numerous biological tissues and tissue surfaces, and which are compatible with both in vitro and in vivo measuring techniques. By varying a set of adjustable physical and geometrical parameters pertaining to the structure, we could numerically reproduce a variety of dielectric dispersion curves-most of them of a composite type-that suitably described experimental data from relatively organized biological tissues. We therefore conclude that the well-documented non-Debye dielectric behavior of biological structures reflects their self-similar architecture.

  17. 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.

  18. The fractal structure and the dynamics of aggregation of synthetic melanin in low pH aqueous solutions

    NASA Astrophysics Data System (ADS)

    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 df =1.8 for the DLA clusters and df =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.

  19. Laplacian growth phenomena with the third boundary condition: Crossover from dense structure to diffusion-limited aggregation fractal

    NASA Astrophysics Data System (ADS)

    Nagatani, Takashi

    1989-12-01

    A Laplacian growth model with the third boundary condition, (1-P)∂Φ/∂n-PΦ=0, is considered in order to study the effect of the sticking probability of the diffusion-limited aggregation (DLA), where Φ is the harmonic function satisfying the Laplace equation and ∂Φ/∂n the derivative normal to the interface. The crossover from the dense structure to the DLA fractal is investigated by using a two-parameter position-space renormalization-group method. A global flow diagram in two-parameter space is obtained. It is found that there are two nontrivial fixed points, the Eden point and the DLA point. The DLA point corresponding to the DLA fractal is stable in all directions, while the Eden point is a saddle point. When the sticking probability P is not 1, the aggregate must eventually cross over to the DLA fractal. The crossover exponent φ and crossover radius r× are calculated.

  20. 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

  1. Structure meets function: actin filaments and myosin motors in the axon.

    PubMed

    Arnold, Don B; Gallo, Gianluca

    2014-04-01

    This review focuses on recent advances in the understanding of the organization and roles of actin filaments, and associated myosin motor proteins, in regulating the structure and function of the axon shaft. 'Patches' of actin filaments have emerged as a major type of actin filament organization in axons. In the distal axon, patches function as precursors to the formation of filopodia and branches. At the axon initial segment, patches locally capture membranous organelles and contribute to polarized trafficking. The trapping function of patches at the initial segment can be ascribed to interactions with myosin motors, and likely also applies to patches in the more distal axon. Finally, submembranous rings of actin filaments were recently described in axons, which form an actin-spectrin cytoskeleton, likely contributing to the maintenance of axon integrity. Continued investigation into the roles of axonal actin filaments and myosins will shed light on fundamental aspects of the development, adult function and the repair of axons in the nervous system. © 2013 International Society for Neurochemistry.

  2. 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.

  3. CORTICAL CYTOPLASMIC FILAMENTS OF CLEAVING EGGS: A STRUCTURAL ELEMENT CORRESPONDING TO THE CONTRACTILE RING

    PubMed Central

    Szollosi, Daniel

    1970-01-01

    A sheath consisting of filaments 50–70 A in diameter has been demonstrated in association with the expanded, leading margins of the cleavage furrow in unilaterally and symmetrically cleaving eggs of a jellyfish and a polychaete worm, respectively. The observations suggest that the filament system might provide a structural basis for the existence of the contractile gel that, according to a hypothesis by Marsland and Landau, accomplishes cleavage. The filamentous sheath is present only in the furrow region and is arranged in an arcuate manner in unilaterally cleaving eggs and circumferentially in symmetrical cleavage. The filaments appear to be of finite length, and a number of them must overlap to span the length of the furrow. Contraction may be accomplished if the filaments slide relative to each other. However, contraction per se was experimentally not demonstrated in the studied systems. The disappearance of microvilli and the merocrine type secretion of mucoid droplets at the interdigitating or "spinning" membrane region of unilateral cleavage suggest that the unfolding of a pleated membrane and the insertion of intracytoplasmic membranes might contribute, at least in part, to the necessary extra cell membrane. PMID:4390970

  4. 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.

  5. Structure, sarcomeric organization, and thin filament binding of cardiac myosin-binding protein-C.

    PubMed

    Craig, Roger; Lee, Kyoung Hwan; Mun, Ji Young; Torre, Iratxe; Luther, Pradeep K

    2014-03-01

    Myosin-binding protein-C (MyBP-C) is an accessory protein of the myosin filaments of vertebrate striated muscle. In the heart, it plays a key role in modulating contractility in response to β-adrenergic stimulation. Mutations in the cardiac isoform (cMyBP-C) are a leading cause of inherited hypertrophic cardiomyopathy. Understanding cMyBP-C function and its role in disease requires knowledge of the structure of the molecule, its organization in the sarcomere, and its interactions with other sarcomeric proteins. Here we review the main structural features of this modular, elongated molecule and the properties of some of its key domains. We describe observations suggesting that the bulk of the molecule extends perpendicular to the thick filament, enabling it to reach neighboring thin filaments in the sarcomere. We review structural and functional evidence for interaction of its N-terminal domains with actin and how this may modulate thin filament activation. We also discuss the effects that phosphorylation of cMyBP-C has on some of these structural features and how this might relate to cMyBP-C function in the beating heart.

  6. GTPase Activity, Structure, and Mechanical Properties of Filaments Assembled from Bacterial Cytoskeleton Protein MreB

    PubMed Central

    Esue, Osigwe; Wirtz, Denis; Tseng, Yiider

    2006-01-01

    MreB, a major component of the recently discovered bacterial cytoskeleton, displays a structure homologous to its eukaryotic counterpart actin. Here, we study the assembly and mechanical properties of Thermotoga maritima MreB in the presence of different nucleotides in vitro. We found that GTP, not ADP or GDP, can mediate MreB assembly into filamentous structures as effectively as ATP. Upon MreB assembly, both GTP and ATP release the gamma phosphate at similar rates. Therefore, MreB is an equally effective ATPase and GTPase. Electron microscopy and quantitative rheology suggest that the morphologies and micromechanical properties of filamentous ATP-MreB and GTP-MreB are similar. In contrast, mammalian actin assembly is favored in the presence of ATP over GTP. These results indicate that, despite high structural homology of their monomers, T. maritima MreB and actin filaments display different assembly, morphology, micromechanics, and nucleotide-binding specificity. Furthermore, the biophysical properties of T. maritima MreB filaments, including high rigidity and propensity to form bundles, suggest a mechanism by which MreB helical structure may be involved in imposing a cylindrical architecture on rod-shaped bacterial cells. PMID:16428401

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

    PubMed

    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.

  9. Physiological Heterogeneity: Fractals Link Determinism and Randomness in Structures and Functions

    PubMed Central

    Bassingthwaighte, James B.

    2010-01-01

    Spatial variation in concentrations or flows within an organ and temporal variation in reaction rates or flows appear to broaden as one refines the scale of observation. How can we characterize heterogeneity independently of scale? Fractals come to our rescue! A system is fractal if its features adhere to the same rules through a succession of different scales. Fractals efficiently describe many types of observations, geometric and kinetic, and help to integrate physiological knowledge. PMID:20871797

  10. 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

  11. 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.

  12. 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

  13. Structural and fractal characterization of tungstophosphoric acid modified titanium dioxide photocatalyst

    NASA Astrophysics Data System (ADS)

    Petrović, S.; Rožić, Lj; Vuković, Z.; Grbić, B.; Radić, N.; Stojadinović, S.; Vasilić, R.

    2017-04-01

    This article presents the comparison of structural and fractal properties of nanocrystalline titanium dioxide (TiO2) and TiO2 modified with tungstophosphoric acid (TiO2/HPW) and their impact on the photocatalytic degradation of hazardous water pollutants. TiO2 and TiO2/HPW samples were synthesized by a combined sol-gel and hydrothermal processing. The XRD analysis of pure TiO2 samples revealed that phase composition was mainly dependent on the calcination temperature, changing from amorphous TiO2 to crystalline anatase and rutile by increasing the temperature. On the other hand, the XRD of TiO2/HPW samples calcined at temperatures above 600 °C showed crystalline peaks associated to formation of WO3 and WO2.92 crystalline domains. The N2 adsorption-desorption isotherm and pore size distribution of TiO2/HPW samples detected the existence of mesoporous characteristic with very narrow bimodal pores in the mesoporous region. The structural heterogeneity of samples was analyzed by means of pore size distribution functions, while the variation in fractal dimension were determined from the nitrogen adsorption isotherms, using the modified Frenkel-Halsey-Hill method. The results demonstrate that the approach is capable of characterizing complex textures such as those present in the TiO2 and TiO2/HPW photocatalysts. Besides, the effect of calcinations condition on photocatalytic properties of the samples was also investigated. The highest efficiency with respect to methyl orange photodecomposition was observed for TiO2/HPW photocatalysts calcined at 700 °C.

  14. Fractal structures of single-walled carbon nanotubes in biologically relevant conditions: role of chirality vs. media conditions.

    PubMed

    Khan, Iftheker A; Aich, Nirupam; Afrooz, A R M Nabiul; Flora, Joseph R V; Schierz, P Ariette; Ferguson, P Lee; Sabo-Attwood, Tara; Saleh, Navid B

    2013-11-01

    Aggregate structure of covalently functionalized chiral specific semiconducting single-walled carbon nanotubes (SWNTs) was systematically studied employing static light scattering (SLS). Fractal dimensions (Df) of two specific chirality SWNTs-SG65 and SG76 with (6, 5) and (7, 6) chiral enrichments-were measured under four biological exposure media conditions, namely: Dulbecco's Modified Eagle Medium (DMEM), Minimum Essential Medium (MEM), Roswell Park Memorial Institute (RPMI) 1640 medium, and 0.9% saline solution. The SWNTs exhibited chiral dependence on Df with SG65 showing more fractal or loosely bound aggregate structures, i.e., lower Df values (range of 2.24±0.03 to 2.64±0.05), compared to the SG76 sample (range of 2.58±0.13 to 2.90±0.08). All the Df values reported are highly reproducible, measured from multiple SLS runs and estimated with 'random block-effects' statistical analysis that yielded all p values to be <0.001. The key mechanism for such difference in Df between the SWNT samples was identified as the difference in van der Waals (VDW) interaction energies of these samples, where higher VDW of SG76 resulted in tighter packing density. Effect of medium type showed lower sensitivity; however, presence of di-valent cations (Ca(2+)) in DMEM and MEM media resulted in relatively loose or more fractal aggregates. Moreover, presence of fetal bovine serum (FBS) and bovine serum albumin (BSA), used to mimic the in vitro cell culture condition, reduced the Df values, i.e., created more fractal structures. Steric hindrance to aggregation was identified as the key mechanism for creating the fractal structures. Also, increase in FBS concentration from 1% to 10% resulted in increasingly lower Df values. Published by Elsevier Ltd.

  15. Multilamellar Structures and Filament Bundles Are Found on the Cell Surface during Bunyavirus Egress

    PubMed Central

    Sanz-Sánchez, Laura; Risco, Cristina

    2013-01-01

    Inside cells, viruses build specialized compartments for replication and morphogenesis. We observed that virus release associates with specific structures found on the surface of mammalian cells. Cultured adherent cells were infected with a bunyavirus and processed for oriented sectioning and transmission electron microscopy. Imaging of cell basal regions showed sophisticated multilamellar structures (MLS) and extracellular filament bundles with attached viruses. Correlative light and electron microscopy confirmed that both MLS and filaments proliferated during the maximum egress of new viruses. MLS dimensions and structure were reminiscent of those reported for the nanostructures on gecko fingertips, which are responsible for the extraordinary attachment capacity of these lizards. As infected cells with MLS were more resistant to detachment than control cells, we propose an adhesive function for these structures, which would compensate for the loss of adherence during release of new virus progeny. PMID:23799021

  16. 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.

  17. Sizes, graphitic structures and fractal geometry of light-duty diesel engine particulates.

    SciTech Connect

    Lee, K. O.; Zhu, J.; Ciatti, S.; Choi, M. Y.; Energy Systems; Drexel Univ.

    2003-01-01

    The particulate matter of a light-duty diesel engine was characterized in its morphology, sizes, internal microstructures, and fractal geometry. A thermophoretic sampling system was employed to collect particulates directly from the exhaust manifold of a 1.7-liter turbocharged common-rail direct-injection diesel engine. The particulate samples collected at various engine-operating conditions were then analyzed by using a high-resolution transmission electron microscope (TEM) and an image processing/data acquisition system. Results showed that mean primary particle diameters (dp), and radii of gyration (Rg), ranged from 19.4 nm to 32.5 nm and 77.4 nm to 134.1 nm, respectively, through the entire engine-operating conditions of 675 rpm (idling) to 4000 rpm and 0% to 100% loads. It was also revealed that the other important parameters sensitive to the particulate formation, such as exhaust-gas recirculation (EGR) rate, equivalence ratio, and temperature, affected particle sizes significantly. Bigger primary particles were measured at higher EGR rates, higher equivalence ratios (fuel-rich), and lower exhaust temperatures. Fractal dimensions (D{sup f}) were measured at a range of 1.5 - 1.7, which are smaller than those measured for heavy-duty direct-injection diesel engine particulates in our previous study. This finding implies that the light-duty diesel engine used in this study produces more stretched chain-like shape particles, while the heavy-duty diesel engine emits more spherical particles. The microstructures of diesel particulates were observed at high TEM magnifications and further analyzed by a Raman spectroscope. Raman spectra revealed an atomic structure of the particulates produced at high engine loads, which is similar to that of typical graphite.

  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. STRUCTURE AND DYNAMICS OF QUIESCENT FILAMENT CHANNELS OBSERVED BY HINODE/XRT AND STEREO/EUVI

    SciTech Connect

    Su Yingna; Van Ballegooijen, Adriaan; Golub, Leon

    2010-09-20

    We present a study of the structure and dynamics of quiescent filament channels observed by Hinode/XRT and STEREO/EUVI at the solar minimum 23/24 from 2006 November to 2008 December. For 12 channels identified on the solar disk (Group I channels), we find that the morphology of the structure on the two sides of the channel is asymmetric in both X-rays and EUV: the eastern side has curved features while the western side has straight features. We interpret the results in terms of a magnetic flux rope model. The asymmetry in the morphology is due to the variation in axial flux of the flux rope along the channel, which causes the field lines from one polarity to turn into the flux rope (curved feature), while the field lines from the other polarity are connected to very distant sources (straight). For most of the 68 channels identified by cavities at the east and west limbs (Group II channels), the asymmetry cannot be clearly identified, which is likely due to the fact that the axial flux may be relatively constant along such channels. Corresponding cavities are identified only for 5 of the 12 Group I channels, while Group II channels are identified for all of the 68 cavity pairs. The studied filament channels are often observed as dark channels in X-rays and EUV. Sheared loops within Group I channels are often seen in X-rays, but are rarely seen in Group II channels as shown in the X-ray Telescope daily synoptic observations. A survey of the dynamics of studied filament channels shows that filament eruptions occur at an average rate of 1.4 filament eruptions per channel per solar rotation.

  20. 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

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

    PubMed

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

    2014-10-28

    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.

  2. High-resolution structure of the presynaptic RAD51 filament on single-stranded DNA by electron cryo-microscopy

    PubMed Central

    Short, Judith M.; Liu, Yang; Chen, Shaoxia; Soni, Neelesh; Madhusudhan, Mallur S.; Shivji, Mahmud K.K.; Venkitaraman, Ashok R.

    2016-01-01

    Homologous DNA recombination (HR) by the RAD51 recombinase enables error-free DNA break repair. To execute HR, RAD51 first forms a presynaptic filament on single-stranded (ss) DNA, which catalyses pairing with homologous double-stranded (ds) DNA. Here, we report a structure for the presynaptic human RAD51 filament at 3.5–5.0Å resolution using electron cryo-microscopy. RAD51 encases ssDNA in a helical filament of 103Å pitch, comprising 6.4 protomers per turn, with a rise of 16.1Å and a twist of 56.2°. Inter-protomer distance correlates with rotation of an α-helical region in the core catalytic domain that is juxtaposed to ssDNA, suggesting how the RAD51–DNA interaction modulates protomer spacing and filament pitch. We map Fanconi anaemia-like disease-associated RAD51 mutations, clarifying potential phenotypes. We predict binding sites on the presynaptic filament for two modules present in each BRC repeat of the BRCA2 tumour suppressor, a critical HR mediator. Structural modelling suggests that changes in filament pitch mask or expose one binding site with filament-inhibitory potential, rationalizing the paradoxical ability of the BRC repeats to either stabilize or inhibit filament formation at different steps during HR. Collectively, our findings provide fresh insight into the structural mechanism of HR and its dysregulation in human disease. PMID:27596592

  3. Effect of rotating helical magnetic field on the turbulence fractal structure and transport in the tokamak edge

    NASA Astrophysics Data System (ADS)

    Budaev, V. P.; Kikuchi, Y.; Toyoda, M.; Uesugi, Y.; Takamura, S.

    2003-03-01

    Plasma edge fluctuations measured with Langmuir probe in relation to the turbulence structure and associated enhanced transport have been studied in the tokamak HYBTOK-II with a variation of the rotating helical magnetic field (RHF) frequency in the range of 5-30 kHz. Edge fluctuations have non-Gaussianity statistics caused by intermittent bursts with time scale of 40-100 μs. The variation in the RHF frequency has a selective effect on the edge turbulent fractal structure and the turbulent flux, demonstrating a selective control of the transport process. A delayed synchronization control of resonant drift wave modes by the RHF is considered as a candidate mechanism to explain the RHF frequency dependence of the edge turbulent fractal structure.

  4. Dynamic structure factor of vibrating fractals: proteins as a case study.

    PubMed

    Reuveni, Shlomi; Klafter, Joseph; Granek, Rony

    2012-01-01

    We study the dynamic structure factor S(k,t) of proteins at large wave numbers k, kR(g)≫1, where R(g) is the gyration radius. At this regime measurements are sensitive to internal dynamics, and we focus on vibrational dynamics of folded proteins. Exploiting the analogy between proteins and fractals, we perform a general analytic calculation of the displacement two-point correlation functions, <[u(−>)(i)(t)-u(−>)(j)(0)](2)>. We confront the derived expressions with numerical evaluations that are based on protein data bank (PDB) structures and the Gaussian network model (GNM) for a few proteins and for the Sierpinski gasket as a controlled check. We use these calculations to evaluate S(k,t) with arrested rotational and translational degrees of freedom, and show that the decay of S(k,t) is dominated by the spatially averaged mean-square displacement of an amino acid. The latter has been previously shown to evolve subdiffusively in time, <[u(−>)(i)(t)-u(−>)(i)(0)](2)> ~t(ν), where ν is the anomalous diffusion exponent that depends on the spectral dimension d(s) and fractal dimension d(f). As a result, for wave numbers obeying k(2))(2)>≳1, S(k,t) effectively decays as a stretched exponential S(k,t)≃S(k)e(-(Γ(k)t)(β)) with β≃ν, where the relaxation rate is Γ(k)~(k(B)T/mω(o)(2))(1/β)k(2/β), T is the temperature, and mω(o)(2) the GNM effective spring constant describing the interaction between neighboring amino acids. The static structure factor is dominated by the fractal character of the native fold, S(k)~k(-d(f)), with negligible to marginal influence of vibrations. The analytical expressions are first confronted with numerically based calculations on the Sierpinski gasket, and very good agreement is found between simulations and theory. We then perform PDB-GNM-based numerical calculations for a few proteins, and an effective stretched exponential decay of the dynamic structure factor is found, albeit their relatively small size

  5. Establishing an Ambulatory Medicine Quality and Safety Oversight Structure: Leveraging the Fractal Model.

    PubMed

    Kravet, Steven J; Bailey, Jennifer; Demski, Renee; Pronovost, Peter

    2016-07-01

    Academic health systems face challenges in the governance and oversight of quality and safety efforts across their organizations. Ambulatory practices, which are growing in number, size, and complexity, face particular challenges in these areas. In February 2014, leaders at Johns Hopkins Medicine (JHM) implemented a governance, oversight, and accountability structure for quality and safety efforts across JHM ambulatory practices. This model was based on the fractal approach, which balances independence and interdependence and provides horizontal and vertical support. It set expectations of accountability at all levels from the Board of Trustees to frontline staff and featured a cascading structure that reached all units and ambulatory practices. This model leveraged an Ambulatory Quality Council led by a physician and nurse dyad to provide the infrastructure to share best practices, continuously improve, and define accountable local leaders. This model was incorporated into the quality and safety infrastructure across JHM. Improved outcomes in the domains of patient safety/risk reduction, externally reported quality measures, patient care/experience, and value have been demonstrated. An additional benefit was an improvement in Medicaid value-based purchasing metrics, which are linked to several million dollars of revenue. As this model matures, it will serve as a mechanism to align quality standards and programs across regional, national, and international partners and to provide a clear quality structure as new practices join the health system. Future efforts will link this model to JHM's academic mission, enhancing education to address Accreditation Council for Graduate Medical Education core competencies.

  6. 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.

  7. 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

  8. Discriminatory ability of fractal and grey level co-occurrence matrix methods in structural analysis of hippocampus layers.

    PubMed

    Pantic, Igor; Dacic, Sanja; Brkic, Predrag; Lavrnja, Irena; Jovanovic, Tomislav; Pantic, Senka; Pekovic, Sanja

    2015-04-07

    Fractal and grey level co-occurrence matrix (GLCM) analysis represent two mathematical computer-assisted algorithms that are today thought to be able to accurately detect and quantify changes in tissue architecture during various physiological and pathological processes. However, despite their numerous applications in histology and pathology, their sensitivity, specificity and validity regarding evaluation of brain tissue remain unclear. In this article we present the results indicating that certain parameters of fractal and GLCM analysis have high discriminatory ability in distinguishing two morphologically similar regions of rat hippocampus: stratum lacunosum-moleculare and stratum radiatum. Fractal and GLCM algorithms were performed on a total of 240 thionine-stained hippocampus micrographs of 12 male Wistar albino rats. 120 digital micrographs represented stratum lacunosum-moleculare, and another 120 stratum radiatum. For each image, 7 parameters were calculated: fractal dimension, lacunarity, GLCM angular second moment, GLCM contrast, inverse difference moment, GLCM correlation, and GLCM variance. GLCM variance (VAR) resulted in the largest area under the Receiver operating characteristic (ROC) curve of 0.96, demonstrating an outstanding discriminatory power in analysis of stratum lacunosum-moleculare (average VAR equaled 478.1 ± 179.8) and stratum radiatum (average VAR of 145.9 ± 59.2, p < 0.0001). For the criterion VAR ≤ 227.5, sensitivity and specificity were 90% and 86.7%, respectively. GLCM correlation as a parameter also produced large area under the ROC curve of 0.95. Our results are in accordance with the findings of our previous study regarding brain white mass fractal and textural analysis. GLCM algorithm as an image analysis method has potentially high applicability in structural analysis of brain tissue cytoarcitecture.

  9. A study of the fractal structure of the precipitate and the mechanism of its formation from the gallbladder bile of a patient

    NASA Astrophysics Data System (ADS)

    Liu, S.; Kong, X.; Xie, A.; Shen, Y.; Zhu, J.; Li, C.; Zhang, Q.

    2007-12-01

    The precipitation of three kinds of structures from gallbladder bile of a patient, fractal structure, regular crystal structure, and small disperse granules, was observed in the same sample using Field Emission Gun-Scanning Electron Microscopy (FEG-SEM). The results indicated that there was a transition from a linear equilibrium system to a nonlinear and nonequilibrium system, which was discussed using the theory of entropy. The chemical compositions of these three different kinds of precipitates were determined by energy dispersive X-ray spectroscopy (EDS). This experimental result revealed that Na and Cl played important roles in the formation of the fractal and crystal structures. Besides, the Aggregation-Diffusion-Fractal (ADF) model was used to explain the growth mechanism of the fractal.

  10. In vivo formation steps of the hard alpha-keratin intermediate filament along a hair follicle: evidence for structural polymorphism.

    PubMed

    Rafik, Mériem Er; Briki, Fatma; Burghammer, Manfred; Doucet, Jean

    2006-04-01

    Several aspects of the intermediate filaments' molecular architecture remain mysterious despite decades of study. The growth process and the final architecture may depend on the physical, chemical, and biochemical environment. Aiming at clarifying this issue, we have revisited the structure of the human hair follicle by means of X-ray microdiffraction. We conclude that the histology-based growth zones along the follicle are correlated to the fine architecture of the filaments deduced from X-ray microdiffraction. Our analysis reveals the existence of two major polymorph intermediate filament architectures. Just above the bulb, the filaments are characterized by a diameter of 100 Angstroms and a low-density core. The following zone upwards is characterized by the lateral aggregation of the filaments into a compact network of filaments, by a contraction of their diameter (to 75 Angstroms) and by the setting up of a long-range longitudinal ordering. In the upper zone, the small structural change associated with the tissue hardening likely concerns the terminal domains. The architecture of the intermediate filament in the upper zones could be specific to hard alpha-keratin whilst the other architecture found in the lower zone could be representative for intermediate filaments in a different environment.

  11. Diffusion on regular random fractals

    NASA Astrophysics Data System (ADS)

    Aarão Reis, Fábio D. A.

    1996-12-01

    We study random walks on structures intermediate to statistical and deterministic fractals called regular random fractals, constructed introducing randomness in the distribution of lacunas of Sierpinski carpets. Random walks are simulated on finite stages of these fractals and the scaling properties of the mean square displacement 0305-4470/29/24/007/img1 of N-step walks are analysed. The anomalous diffusion exponents 0305-4470/29/24/007/img2 obtained are very near the estimates for the carpets with the same dimension. This result motivates a discussion on the influence of some types of lattice irregularity (random structure, dead ends, lacunas) on 0305-4470/29/24/007/img2, based on results on several fractals. We also propose to use these and other regular random fractals as models for real self-similar structures and to generalize results for statistical systems on fractals.

  12. The language of fractals

    SciTech Connect

    Juergens, H.; Peitgen, H.O.; Saupe, D. )

    1990-08-01

    The pathological structures conjured up by 19th-century mathematicians have, in recent years, taken the form of fractals, mathematical figures that have fractional dimension rather than the integral dimensions of familiar geometric figures (such as one-dimensional lines or two-dimensional planes). Fractals are much more than a mathematical curiosity. They offer an extremely compact method for describing objects and formations. Many structures have an underlying geometric regularity, known as scale invariance or self-similarity. If one examines these objects at different size scales, one repeatedly encounters the same fundamental elements. The repetitive pattern defines the fractional, or fractal, dimension of the structure. Fractal geometry seems to describe natural shapes and forms more gracefully and succinctly than does Euclidean geometry. Scale invariance has a noteworthy parallel in contemporary chaos theory, which reveals that many phenomena, even though they follow strict deterministic rules, are in principle unpredictable. Chaotic events, such as turbulence in the atmosphere or the beating of a human heart, show similar patterns of variation on different time scales, much as scale-invariant objects show similar structural patterns on different spatial scales. The correspondence between fractals and chaos is no accident. Rather it is a symptom of a deep-rooted relation: fractal geometry is the geometry of chaos.

  13. 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.

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

  15. Fractal structure and characteristic scale in the distributions of earthquake epicentres, active faults and rivers in Japan

    NASA Astrophysics Data System (ADS)

    Lei, Xinglin; Kusunose, Kinichiro

    1999-12-01

    Using a box-counting method, we examined the fractal structures of the spatial distributions of three geological systems in Japan, namely those of earthquake epicentres, active faults, and rivers. Our results show that, in the scale range from 1 to 100 km, all geological systems have a common characteristic scale of ~13 km, which divides the spatial distribution into two bands: a smaller scale r<13 km and larger scale r>13 km (where r is the box size). In both bands, the three systems obey a power law distribution, and therefore it is proposed that all geological systems have a band-limited fractal structure. Since the characteristic scale of ~13 km is in agreement with the depth of the brittle-ductile transition zone of the crust, we suggest that it is a common feature of the heterogeneity of the crust.

  16. Effect of rotating helical magnetic field on the turbulence fractal structure and transport in the tokamak edge plasma

    NASA Astrophysics Data System (ADS)

    Budaev, V.; Kikuchi, Y.; Uesugi, Y.; Takamura, S.

    2004-06-01

    Fractal structure of the edge turbulence and enhanced turbulent transport have been studied in the tokamak HYBTOK-II with a variation of the rotating helical magnetic field (RHF) frequency in the range 5-30 kHz. Edge fluctuations have non-Gaussian statistics caused by intermittent bursts with a time scale of 40-100 µs. The variation in the RHF frequency has a selective effect on the fractal structure of edge turbulence and the turbulent flux, demonstrating a selective control of the transport process. A delayed synchronization control of resonant drift wave modes by the RHF is considered as a candidate mechanism to explain the dependence of the effect on the RHF frequency.

  17. High-birefringence photonic crystal fiber structures based on the binary morse-thue fractal sequence

    NASA Astrophysics Data System (ADS)

    Al-Muraeb, Ahmed; Abdel-Aty-Zohdy, Hoda

    2016-09-01

    A novel index-guiding Silica glass-core hexagonal High-Birefringence Photonic Crystal Fiber (HB-PCF) is proposed, with five rings of standard cladding air circular holes arranged in four formations inspired by the Binary Morse-Thue fractal Sequence (BMTS). The form birefringence, confinement loss, chromatic dispersion, effective mode area, and effective normalized frequency are evaluated for the four PCFs operating within (1.8 - 2 μm) eye-safe wavelength range. Modeling and analysis of the four PCF formations are performed deploying full-vector analysis in Finite Element Method (FEM) using COMSOL Multiphysics. Respecting fabrication and in light of commercial availability in designing the proposed PCF structures, a high birefringence of up to (6.549 × 10-3 at 2 μm) is achieved with dispersionfree single-mode operation. Confinement loss as low as (3.2 × 10-5 - 6.5 × 10-4 dB/m for 1.8 - 2 μm range) is achieved as well. Comparison against previously reported PCF structures reveals the desirably higher birefringence of our BMTS HB-PCF. The proposed PCFs are of vital use in various optical systems (e.g.: multi-wavelength fiber ring laser systems, and tunable lasers), catering for applications such as: optical sensing, LIDAR systems, material processing, optical signal processing, and optical communication.

  18. 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.

  19. Density filament and helical field line structures in three dimensional Weibel-mediated collisionless shocks

    NASA Astrophysics Data System (ADS)

    Moritaka, Toseo; Sakawa, Youichi; Kuramitsu, Yasuhiro; Morita, Taichi; Yamaura, Yuta; Ishikawa, Taishi; Takabe, Hideaki

    2016-03-01

    Collisionless shocks mediated by Weibel instability are attracting attention for their relevance to experimental demonstrations of astrophysical shocks in high-intensity laser facilities. The three dimensional structure of Weibel-mediated shocks is investigated through a fully kinetic particle-in-cell simulation. The structures obtained are characterized by the following features: (i) helical magnetic field lines elongated in the direction upstream of the shock region, (ii) high and low density filaments inside the helical field lines. These structures originate from the interaction between counter-streaming plasma flow and magnetic vortexes caused by Weibel instability, and potentially affect the shock formation mechanism.

  20. Studying neutral hydrogen structures during the epoch of reionization using fractal dimensions

    NASA Astrophysics Data System (ADS)

    Bandyopadhyay, Bidisha; Choudhury, T. Roy; Seshadri, T. R.

    2017-04-01

    Fractal dimensions can be used to characterize the clustering and lacunarities in density distributions. We use generalized fractal dimensions to study the neutral hydrogen distribution (H I) during the epoch of reionization. Using a semi-numeric model of ionized bubbles to generate the H I field, we calculate the fractal dimensions for length-scales ∼10 h-1cMpc. We find that the H I field displays significant multifractal behaviour and is not consistent with homogeneity at these scales when the mass-averaged neutral fraction bar{x}_{H I}^M ≳ 0.5. This multifractal nature is driven entirely by the shapes and distribution of the ionized regions. The sensitivity of the fractal dimension to the neutral fraction implies that it can be used for constraining reionization history. We find that the fractal dimension is relatively less sensitive to the value of the minimum mass of ionizing haloes when it is in the range ∼109-1010h-1M⊙. Interestingly, the fractal dimension is very different when the reionization proceeds inside-out compared to when it is outside-in. Thus, the multifractal nature of H I density field at high redshifts can be used to study the nature of reionization.

  1. A new type of vacuum sensors with sensitive elements based on multicomponent oxide nanomaterials with fractal structures

    NASA Astrophysics Data System (ADS)

    Karmanov, A. A.; Averin, I. A.; Pronin, I. A.; Yakushova, N. D.; Igoshina, S. E.; Moshnikov, V. A.; Vishnevskaya, G. V.

    2017-07-01

    A new type of vacuum sensors with sensitive elements based on two- and three-component oxide nanomaterials with fractal structures is proposed. It is shown that a sensory response for two-component oxide systems based on SiO2-SnO2 is determined by their quantitative composition - mass fraction of tin dioxide. An increase in sensitivity to changes in ambient pressure for three-component oxide nanomaterials has been demonstrated.

  2. Nucleoprotein filament formation is the structural basis for bacterial protein H-NS gene silencing

    NASA Astrophysics Data System (ADS)

    Lim, Ci Ji; Lee, Sin Yi; Kenney, Linda J.; Yan, Jie

    2012-07-01

    H-NS is an abundant nucleoid-associated protein in bacteria that globally silences genes, including horizontally-acquired genes related to pathogenesis. Although it has been shown that H-NS has multiple modes of DNA-binding, which mode is employed in gene silencing is still unclear. Here, we report that in H-NS mutants that are unable to silence genes, are unable to form a rigid H-NS nucleoprotein filament. These results indicate that the H-NS nucleoprotein filament is crucial for its gene silencing function, and serves as the fundamental structural basis for gene silencing by H-NS and likely other H-NS-like bacterial proteins.

  3. 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.

  4. Three-dimensional structure of actin filaments and of an actin gel made with actin-binding protein

    PubMed Central

    1983-01-01

    Purified muscle actin and mixtures of actin and actin-binding protein were examined in the transmission electron microscope after fixation, critical point drying, and rotary shadowing. The three-dimensional structure of the protein assemblies was analyzed by a computer-assisted graphic analysis applicable to generalized filament networks. This analysis yielded information concerning the frequency of filament intersections, the filament length between these intersections, the angle at which filaments branch at these intersections, and the concentration of filaments within a defined volume. Purified actin at a concentration of 1 mg/ml assembled into a uniform mass of long filaments which overlap at random angles between 0 degrees and 90 degrees. Actin in the presence of macrophage actin-binding protein assembled into short, straight filaments, organized in a perpendicular branching network. The distance between branch points was inversely related to the molar ratio of actin-binding protein to actin. This distance was what would be predicted if actin filaments grew at right angles off of nucleation sites on the two ends of actin-binding protein dimers, and then annealed. The results suggest that actin in combination with actin-binding protein self-assembles to form a three- dimensional network resembling the peripheral cytoskeleton of motile cells. PMID:6682423

  5. Three-dimensional structure of actin filaments and of an actin gel made with actin-binding protein.

    PubMed

    Niederman, R; Amrein, P C; Hartwig, J

    1983-05-01

    Purified muscle actin and mixtures of actin and actin-binding protein were examined in the transmission electron microscope after fixation, critical point drying, and rotary shadowing. The three-dimensional structure of the protein assemblies was analyzed by a computer-assisted graphic analysis applicable to generalized filament networks. This analysis yielded information concerning the frequency of filament intersections, the filament length between these intersections, the angle at which filaments branch at these intersections, and the concentration of filaments within a defined volume. Purified actin at a concentration of 1 mg/ml assembled into a uniform mass of long filaments which overlap at random angles between 0 degrees and 90 degrees. Actin in the presence of macrophage actin-binding protein assembled into short, straight filaments, organized in a perpendicular branching network. The distance between branch points was inversely related to the molar ratio of actin-binding protein to actin. This distance was what would be predicted if actin filaments grew at right angles off of nucleation sites on the two ends of actin-binding protein dimers, and then annealed. The results suggest that actin in combination with actin-binding protein self-assembles to form a three-dimensional network resembling the peripheral cytoskeleton of motile cells.

  6. 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

  7. On the Mass Fractal Character of Si-Based Structural Networks in Amorphous Polymer Derived Ceramics.

    PubMed

    Sen, Sabyasachi; Widgeon, Scarlett

    2015-03-17

    The intermediate-range packing of SiNxC4-x (0 ≤ x ≤ 4) tetrahedra in polysilycarbodiimide and polysilazane-derived amorphous SiCN ceramics is investigated using (29)Si spin-lattice relaxation nuclear magnetic resonance (SLR NMR) spectroscopy. The SiCN network in the polysilylcarbodiimide-derived ceramic consists predominantly of SiN₄ tetrahedra that are characterized by a 3-dimensional spatial distribution signifying compact packing of such units to form amorphous Si₃N₄ clusters. On the other hand, the SiCN network of the polysilazane-derived ceramic is characterized by mixed bonded SiNxC4-x tetrahedra that are inefficiently packed with a mass fractal dimension of Df ~2.5 that is significantly lower than the embedding Euclidean dimension (D = 3). This result unequivocally confirms the hypothesis that the presence of dissimilar atoms, namely, 4-coordinated C and 3-coordinated N, in the nearest neighbor environment of Si along with some exclusion in connectivity between SiCxN4-x tetrahedra with widely different N:C ratios and the absence of bonding between C and N result in steric hindrance to an efficient packing of these structural units. It is noted that similar inefficiencies in packing are observed in polymer-derived amorphous SiOC ceramics as well as in proteins and binary hard sphere systems.

  8. On the Mass Fractal Character of Si-Based Structural Networks in Amorphous Polymer Derived Ceramics

    PubMed Central

    Sen, Sabyasachi; Widgeon, Scarlett

    2015-01-01

    The intermediate-range packing of SiNxC4−x (0 ≤ x ≤ 4) tetrahedra in polysilycarbodiimide and polysilazane-derived amorphous SiCN ceramics is investigated using 29Si spin-lattice relaxation nuclear magnetic resonance (SLR NMR) spectroscopy. The SiCN network in the polysilylcarbodiimide-derived ceramic consists predominantly of SiN4 tetrahedra that are characterized by a 3-dimensional spatial distribution signifying compact packing of such units to form amorphous Si3N4 clusters. On the other hand, the SiCN network of the polysilazane-derived ceramic is characterized by mixed bonded SiNxC4−x tetrahedra that are inefficiently packed with a mass fractal dimension of Df ~2.5 that is significantly lower than the embedding Euclidean dimension (D = 3). This result unequivocally confirms the hypothesis that the presence of dissimilar atoms, namely, 4-coordinated C and 3-coordinated N, in the nearest neighbor environment of Si along with some exclusion in connectivity between SiCxN4−x tetrahedra with widely different N:C ratios and the absence of bonding between C and N result in steric hindrance to an efficient packing of these structural units. It is noted that similar inefficiencies in packing are observed in polymer-derived amorphous SiOC ceramics as well as in proteins and binary hard sphere systems.

  9. Turbulent wakes of fractal objects.

    PubMed

    Staicu, Adrian; Mazzi, Biagio; Vassilicos, J C; van de Water, Willem

    2003-06-01

    Turbulence of a windtunnel flow is stirred using objects that have a fractal structure. The strong turbulent wakes resulting from three such objects which have different fractal dimensions are probed using multiprobe hot-wire anemometry in various configurations. Statistical turbulent quantities are studied within inertial and dissipative range scales in an attempt to relate changes in their self-similar behavior to the scaling of the fractal objects.

  10. Fractals in dentistry.

    PubMed

    Sánchez, Iván; Uzcátegui, Gladys

    2011-04-01

    To systematically review applications of fractal geometry in different aspects of dental practice. In this review, we present a short introduction to fractals and specifically address the following topics: treatment and healing monitoring, dental materials, dental tissue, caries, osteoporosis, periodontitis, cancer, Sjögren's syndrome, diagnosis of several other conditions and a discussion on the reliability of FD determinations from dental radiographs. Google Scholar, Ovid MEDLINE, ScienceDirect, etc. (up to August 2010). The review considered original studies, reviews and conference proceedings, published in English or Spanish. Abstracts and posters were not taken into account. Fractal geometry has found plenty of applications in several branches of dental practice. It provides a way to quantify the complexity of structures. Whereas one desires to study a radiograph, an histological section or the signal from a transducer, there are several methods available to determine the degree of complexity using fractal analysis. Several pathological conditions can alter the complexity of anatomical structures, and this change can be detectable with the help of fractal parameters. Although during the last two decades there have been plenty of works on the field, reported cases having enough reproducibility, with different groups showing similar results are not very common. Further replications are needed before we can establish statistically significant correlations amongst fractal parameters and pathological conditions. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. Fractal analysis and its impact factors on pore structure of artificial cores based on the images obtained using magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Wang, Heming; Liu, Yu; Song, Yongchen; Zhao, Yuechao; Zhao, Jiafei; Wang, Dayong

    2012-11-01

    Pore structure is one of important factors affecting the properties of porous media, but it is difficult to describe the complexity of pore structure exactly. Fractal theory is an effective and available method for quantifying the complex and irregular pore structure. In this paper, the fractal dimension calculated by box-counting method based on fractal theory was applied to characterize the pore structure of artificial cores. The microstructure or pore distribution in the porous material was obtained using the nuclear magnetic resonance imaging (MRI). Three classical fractals and one sand packed bed model were selected as the experimental material to investigate the influence of box sizes, threshold value, and the image resolution when performing fractal analysis. To avoid the influence of box sizes, a sequence of divisors of the image was proposed and compared with other two algorithms (geometric sequence and arithmetic sequence) with its performance of partitioning the image completely and bringing the least fitted error. Threshold value selected manually and automatically showed that it plays an important role during the image binary processing and the minimum-error method can be used to obtain an appropriate or reasonable one. Images obtained under different pixel matrices in MRI were used to analyze the influence of image resolution. Higher image resolution can detect more quantity of pore structure and increase its irregularity. With benefits of those influence factors, fractal analysis on four kinds of artificial cores showed the fractal dimension can be used to distinguish the different kinds of artificial cores and the relationship between fractal dimension and porosity or permeability can be expressed by the model of D = a - bln(x + c).

  12. Measuring Fractality

    PubMed Central

    Stadnitski, Tatjana

    2012-01-01

    When investigating fractal phenomena, the following questions are fundamental for the applied researcher: (1) What are essential statistical properties of 1/f noise? (2) Which estimators are available for measuring fractality? (3) Which measurement instruments are appropriate and how are they applied? The purpose of this article is to give clear and comprehensible answers to these questions. First, theoretical characteristics of a fractal pattern (self-similarity, long memory, power law) and the related fractal parameters (the Hurst coefficient, the scaling exponent α, the fractional differencing parameter d of the autoregressive fractionally integrated moving average methodology, the power exponent β of the spectral analysis) are discussed. Then, estimators of fractal parameters from different software packages commonly used by applied researchers (R, SAS, SPSS) are introduced and evaluated. Advantages, disadvantages, and constrains of the popular estimators (d^ML, power spectral density, detrended fluctuation analysis, signal summation conversion) are illustrated by elaborate examples. Finally, crucial steps of fractal analysis (plotting time series data, autocorrelation, and spectral functions; performing stationarity tests; choosing an adequate estimator; estimating fractal parameters; distinguishing fractal processes from short-memory patterns) are demonstrated with empirical time series. PMID:22586408

  13. 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.…

  14. Exploring Fractals.

    ERIC Educational Resources Information Center

    Dewdney, A. K.

    1991-01-01

    Explores the subject of fractal geometry focusing on the occurrence of fractal-like shapes in the natural world. Topics include iterated functions, chaos theory, the Lorenz attractor, logistic maps, the Mandelbrot set, and mini-Mandelbrot sets. Provides appropriate computer algorithms, as well as further sources of information. (JJK)

  15. Fractal Math.

    ERIC Educational Resources Information Center

    Gray, Shirley B.

    1992-01-01

    This article traces the historical development of fractal geometry from early in the twentieth century and offers an explanation of the mathematics behind the recursion formulas and their representations within computer graphics. Also included are the fundamentals behind programing for fractal graphics in the C Language with appropriate…

  16. Exploring Fractals.

    ERIC Educational Resources Information Center

    Dewdney, A. K.

    1991-01-01

    Explores the subject of fractal geometry focusing on the occurrence of fractal-like shapes in the natural world. Topics include iterated functions, chaos theory, the Lorenz attractor, logistic maps, the Mandelbrot set, and mini-Mandelbrot sets. Provides appropriate computer algorithms, as well as further sources of information. (JJK)

  17. Measuring fractality.

    PubMed

    Stadnitski, Tatjana

    2012-01-01

    WHEN INVESTIGATING FRACTAL PHENOMENA, THE FOLLOWING QUESTIONS ARE FUNDAMENTAL FOR THE APPLIED RESEARCHER: (1) What are essential statistical properties of 1/f noise? (2) Which estimators are available for measuring fractality? (3) Which measurement instruments are appropriate and how are they applied? The purpose of this article is to give clear and comprehensible answers to these questions. First, theoretical characteristics of a fractal pattern (self-similarity, long memory, power law) and the related fractal parameters (the Hurst coefficient, the scaling exponent α, the fractional differencing parameter d of the autoregressive fractionally integrated moving average methodology, the power exponent β of the spectral analysis) are discussed. Then, estimators of fractal parameters from different software packages commonly used by applied researchers (R, SAS, SPSS) are introduced and evaluated. Advantages, disadvantages, and constrains of the popular estimators ([Formula: see text] power spectral density, detrended fluctuation analysis, signal summation conversion) are illustrated by elaborate examples. Finally, crucial steps of fractal analysis (plotting time series data, autocorrelation, and spectral functions; performing stationarity tests; choosing an adequate estimator; estimating fractal parameters; distinguishing fractal processes from short-memory patterns) are demonstrated with empirical time series.

  18. 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.…

  19. Determination of the Fractal Dimensionality of Large-Scale Structure With Type Ia Supernovae by the Method of Pairwise Distances

    NASA Astrophysics Data System (ADS)

    Raikov, A. A.; Orlov, V. V.; Gerasim, R. V.

    2014-06-01

    A pairwise distance technique developed by the authors is used to identify signs of fractal structure in sets of extragalactic supernovae (822 type Ia supernovae in the regions 300° ≤ α ≤ 360° and 0° ≤ α ≤ 60° , - 5° ≤ δ ≤ 5°). Since the region of space occupied by the objects in the sample is highly oblate, we use Mandelbrot's codimensionality theorem. Three cosmological models are examined: a model with a euclidean metric, a "tired light" model, and the standard ΛCDM model. Estimates of a fractal dimensionality of D ≅ 2.69 are obtained for the first two models and D ≅ 2.64 for the ΛCDM model.

  20. Fabrication of low cost composite tooling for filament winding large structures

    NASA Astrophysics Data System (ADS)

    Miller, Timothy S.; Fortin, Christopher J.

    A TQM/concurrent engineering approach has been used to create a low cost filament-winding mandrel for large launch-vehicle structure fabrication. The process involves the fabrication of a low cost/low temperature master model, followed by the building of the mandrel and its backup structure within the master. Mandrels fabricated by these means are able to maintain full vacuum integrity and dimensional stability throughout high-temperature cure cycles; the reduced thermal mass of the mandrel results in part-cure cycles that are shorter than those associated with conventional mandrel materials.

  1. 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.

  2. Crystal structure of the coat protein of the flexible filamentous papaya mosaic virus.

    PubMed

    Yang, Shaoqing; Wang, Tao; Bohon, Jen; Gagné, Marie-Ève Laliberté; Bolduc, Marilène; Leclerc, Denis; Li, Huilin

    2012-09-14

    Papaya mosaic virus (PapMV) is a filamentous plant virus that belongs to the Alphaflexiviridae family. Flexible filamentous viruses have defied more than two decades of effort in fiber diffraction, and no high-resolution structure is available for any member of the Alphaflexiviridae family. Here, we report our structural characterization of PapMV by X-ray crystallography and cryo-electron microscopy three-dimensional reconstruction. We found that PapMV is 135Å in diameter with a helical symmetry of ~10 subunits per turn. Crystal structure of the C-terminal truncated PapMV coat protein (CP) reveals a novel all-helix fold with seven α-helices. Thus, the PapMVCP structure is different from the four-helix-bundle fold of tobacco mosaic virus in which helix bundling dominates the subunit interface in tobacco mosaic virus and conveys rigidity to the rod virus. PapMV CP was crystallized as an asymmetrical dimer in which one protein lassoes the other by the N-terminal peptide. Mutation of residues critical to the inter-subunit lasso interaction abolishes CP polymerization. The crystal structure suggests that PapMV may polymerize via the consecutive N-terminal loop lassoing mechanism. The structure of PapMV will be useful for rational design and engineering of the PapMV nanoparticles into innovative vaccines.

  3. Filamentous Structure of Hard β-Keratins in the Epidermal Appendages of Birds and Reptiles.

    PubMed

    Fraser, R D Bruce; Parry, David A D

    The structures of avian and reptilian epidermal appendages, such as feathers, claws and scales, have been modelled using X-ray diffraction and electron microscopy data, combined with sequence analyses. In most cases, a family of closely related molecules makes up the bulk of the appendage, and each of these molecules contains a central β-rich 34-residue segment, which has been identified as the principal component of the framework of the 3.4 nm diameter filaments. The N- and C-terminal segments form the matrix component of the filament/matrix complex. The 34-residue β-rich central domains occur in pairs, related by either a parallel dyad or a perpendicular dyad axis, and form a β-sandwich stabilized by apolar interactions. They are also twisted in a right-handed manner. In feather, the filaments are packed into small sheets and it is possible to determine their likely orientation within the sheets from the low-angle X-ray diffraction data. The physical properties of the various epidermal appendages can be related to the amino acid sequence and composition of defined molecular segments characteristic of the chains concerned.

  4. Structural basis of the relaxed state of a Ca2+-regulated myosin filament and its evolutionary implications.

    PubMed

    Woodhead, John L; Zhao, Fa-Qing; Craig, Roger

    2013-05-21

    Myosin filaments of muscle are regulated either by phosphorylation of their regulatory light chains or Ca(2+) binding to the essential light chains, contributing to on-off switching or modulation of contraction. Phosphorylation-regulated filaments in the relaxed state are characterized by an asymmetric interaction between the two myosin heads, inhibiting their actin binding or ATPase activity. Here, we have tested whether a similar interaction switches off activity in myosin filaments regulated by Ca(2+) binding. Cryo-electron microscopy and single-particle image reconstruction of Ca(2+)-regulated (scallop) filaments reveals a helical array of myosin head-pair motifs above the filament surface. Docking of atomic models of scallop myosin head domains into the motifs reveals that the heads interact in a similar way to those in phosphorylation-regulated filaments. The results imply that the two major evolutionary branches of myosin regulation--involving phosphorylation or Ca(2+) binding--share a common structural mechanism for switching off thick-filament activity in relaxed muscle. We suggest that the Ca(2+)-binding mechanism evolved from the more ancient phosphorylation-based system to enable rapid response of myosin-regulated muscles to activation. Although the motifs are similar in both systems, the scallop structure is more tilted and higher above the filament backbone, leading to different intermolecular interactions. The reconstruction reveals how the myosin tail emerges from the motif, connecting the heads to the filament backbone, and shows that the backbone is built from supramolecular assemblies of myosin tails. The reconstruction provides a native structural context for understanding past biochemical and biophysical studies of this model Ca(2+)-regulated myosin.

  5. 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.

  6. 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.

  7. Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly

    PubMed Central

    Taylor, Keenan C.; Buvoli, Massimo; Korkmaz, Elif Nihal; Buvoli, Ada; Zheng, Yuqing; Heinze, Nathan T.; Cui, Qiang; Leinwand, Leslie A.; Rayment, Ivan

    2015-01-01

    The rod of sarcomeric myosins directs thick filament assembly and is characterized by the insertion of four skip residues that introduce discontinuities in the coiled-coil heptad repeats. We report here that the regions surrounding the first three skip residues share high structural similarity despite their low sequence homology. Near each of these skip residues, the coiled-coil transitions to a nonclose-packed structure inducing local relaxation of the superhelical pitch. Moreover, molecular dynamics suggest that these distorted regions can assume different conformationally stable states. In contrast, the last skip residue region constitutes a true molecular hinge, providing C-terminal rod flexibility. Assembly of myosin with mutated skip residues in cardiomyocytes shows that the functional importance of each skip residue is associated with rod position and reveals the unique role of the molecular hinge in promoting myosin antiparallel packing. By defining the biophysical properties of the rod, the structures and molecular dynamic calculations presented here provide insight into thick filament formation, and highlight the structural differences occurring between the coiled-coils of myosin and the stereotypical tropomyosin. In addition to extending our knowledge into the conformational and biological properties of coiled-coil discontinuities, the molecular characterization of the four myosin skip residues also provides a guide to modeling the effects of rod mutations causing cardiac and skeletal myopathies. PMID:26150528

  8. Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly

    DOE PAGES

    Taylor, Keenan C.; Buvoli, Massimo; Korkmaz, Elif Nihal; ...

    2015-07-06

    The rod of sarcomeric myosins directs thick filament assembly and is characterized by the insertion of four skip residues that introduce discontinuities in the coiled-coil heptad repeats. We report in this paper that the regions surrounding the first three skip residues share high structural similarity despite their low sequence homology. Near each of these skip residues, the coiled-coil transitions to a nonclose-packed structure inducing local relaxation of the superhelical pitch. Moreover, molecular dynamics suggest that these distorted regions can assume different conformationally stable states. In contrast, the last skip residue region constitutes a true molecular hinge, providing C-terminal rod flexibility.more » Assembly of myosin with mutated skip residues in cardiomyocytes shows that the functional importance of each skip residue is associated with rod position and reveals the unique role of the molecular hinge in promoting myosin antiparallel packing. By defining the biophysical properties of the rod, the structures and molecular dynamic calculations presented here provide insight into thick filament formation, and highlight the structural differences occurring between the coiled-coils of myosin and the stereotypical tropomyosin. Finally, in addition to extending our knowledge into the conformational and biological properties of coiled-coil discontinuities, the molecular characterization of the four myosin skip residues also provides a guide to modeling the effects of rod mutations causing cardiac and skeletal myopathies.« less

  9. Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly

    SciTech Connect

    Taylor, Keenan C.; Buvoli, Massimo; Korkmaz, Elif Nihal; Buvoli, Ada; Zheng, Yuqing; Heinze, Nathan T.; Cui, Qiang; Leinwand, Leslie A.; Rayment, Ivan

    2015-07-06

    The rod of sarcomeric myosins directs thick filament assembly and is characterized by the insertion of four skip residues that introduce discontinuities in the coiled-coil heptad repeats. We report in this paper that the regions surrounding the first three skip residues share high structural similarity despite their low sequence homology. Near each of these skip residues, the coiled-coil transitions to a nonclose-packed structure inducing local relaxation of the superhelical pitch. Moreover, molecular dynamics suggest that these distorted regions can assume different conformationally stable states. In contrast, the last skip residue region constitutes a true molecular hinge, providing C-terminal rod flexibility. Assembly of myosin with mutated skip residues in cardiomyocytes shows that the functional importance of each skip residue is associated with rod position and reveals the unique role of the molecular hinge in promoting myosin antiparallel packing. By defining the biophysical properties of the rod, the structures and molecular dynamic calculations presented here provide insight into thick filament formation, and highlight the structural differences occurring between the coiled-coils of myosin and the stereotypical tropomyosin. Finally, in addition to extending our knowledge into the conformational and biological properties of coiled-coil discontinuities, the molecular characterization of the four myosin skip residues also provides a guide to modeling the effects of rod mutations causing cardiac and skeletal myopathies.

  10. Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly.

    PubMed

    Taylor, Keenan C; Buvoli, Massimo; Korkmaz, Elif Nihal; Buvoli, Ada; Zheng, Yuqing; Heinze, Nathan T; Cui, Qiang; Leinwand, Leslie A; Rayment, Ivan

    2015-07-21

    The rod of sarcomeric myosins directs thick filament assembly and is characterized by the insertion of four skip residues that introduce discontinuities in the coiled-coil heptad repeats. We report here that the regions surrounding the first three skip residues share high structural similarity despite their low sequence homology. Near each of these skip residues, the coiled-coil transitions to a nonclose-packed structure inducing local relaxation of the superhelical pitch. Moreover, molecular dynamics suggest that these distorted regions can assume different conformationally stable states. In contrast, the last skip residue region constitutes a true molecular hinge, providing C-terminal rod flexibility. Assembly of myosin with mutated skip residues in cardiomyocytes shows that the functional importance of each skip residue is associated with rod position and reveals the unique role of the molecular hinge in promoting myosin antiparallel packing. By defining the biophysical properties of the rod, the structures and molecular dynamic calculations presented here provide insight into thick filament formation, and highlight the structural differences occurring between the coiled-coils of myosin and the stereotypical tropomyosin. In addition to extending our knowledge into the conformational and biological properties of coiled-coil discontinuities, the molecular characterization of the four myosin skip residues also provides a guide to modeling the effects of rod mutations causing cardiac and skeletal myopathies.

  11. CCFold: rapid and accurate prediction of coiled-coil structures and application to modeling intermediate filaments.

    PubMed

    Guzenko, Dmytro; Strelkov, Sergei V

    2017-09-04

    Accurate molecular structure of the protein dimer representing the elementary building block of intermediate filaments (IFs) is essential towards the understanding of the filament assembly, rationalizing their mechanical properties and explaining the effect of disease-related IF mutations. The dimer contains a ~300-residue long α-helical coiled coil which cannot be assessed by either direct experimental structure determination or modelling using standard approaches. At the same time, coiled coils are well-represented in structural databases. Here we present CCFold, a generally applicable threading-based algorithm which produces coiled-coil models from protein sequence only. The algorithm is based on a statistical analysis of experimentally determined structures and can handle any hydrophobic repeat patterns in addition to the most common heptads. We demonstrate that CCFold outperforms general-purpose computational folding in terms of accuracy, while being faster by orders of magnitude. By combining the CCFold algorithm and Rosetta folding we generate representative dimer models for all IF protein classes. The source code is freely available at https://github.com/biocryst/IF ; a web server to run the program is at http://pharm.kuleuven.be/Biocrystallography/cc. sergei.strelkov@kuleuven.be. Supplementary data are available at Bioinformatics online.

  12. 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.

  13. Filament wound composite thermal isolator structures for cryogenic dewars and instruments

    SciTech Connect

    Morris, E.E.

    1982-01-01

    Studies showing high tensile strength, low thermal conductivity, and adequate fatigue strength capabiliies in conjunction with low resin outgassing properties of S-90 fiber glass with SCI REZ 080 and 081 epoxy resins has resulted in use of filament wound tension straps, struts, and conical shells as thermal isolators in several high-performance cryogenic applications. These thermal isolator structures and their use in the following cryogenic systems are discussed in this paper: hydrogen and oxygen dewars for space shuttle, helium tank for the infra-red astronomy satellite, spacecraft refrigerators, and infrared telescope. Mechanical and thermo-physical properties of the composite laminates are presented.

  14. Fractal processes in soil water retention

    SciTech Connect

    Tyler, S.W.; Wheatcraft, S.W. )

    1990-05-01

    The authors propose a physical conceptual model for soil texture and pore structure that is based on the concept of fractal geometry. The motivation for a fractal model of soil texture is that some particle size distributions in granular soils have already been shown to display self-similar scaling that is typical of fractal objects. Hence it is reasonable to expect that pore size distributions may also display fractal scaling properties. The paradigm that they used for the soil pore size distribution is the Sierpinski carpet, which is a fractal that contains self similar holes (or pores) over a wide range of scales. The authors evaluate the water retention properties of regular and random Sierpinski carpets and relate these properties directly to the Brooks and Corey (or Campbell) empirical water retention model. They relate the water retention curves directly to the fractal dimension of the Sierpinski carpet and show that the fractal dimension strongly controls the water retention properties of the Sierpinski carpet soil. Higher fractal dimensions are shown to mimic clay-type soils, with very slow dewatering characteristics and relatively low fractal dimensions are shown to mimic a sandy soil with relatively rapid dewatering characteristics. Their fractal model of soil water retention removes the empirical fitting parameters from the soil water retention models and provides paramters which are intrinsic to the nature of the fractal porous structure. The relative permeability functions of Burdine and Mualem are also shown to be fractal directly from fractal water retention results.

  15. Collaborative protein filaments.

    PubMed

    Ghosal, Debnath; Löwe, Jan

    2015-09-14

    It is now well established that prokaryotic cells assemble diverse proteins into dynamic cytoskeletal filaments that perform essential cellular functions. Although most of the filaments assemble on their own to form higher order structures, growing evidence suggests that there are a number of prokaryotic proteins that polymerise only in the presence of a matrix such as DNA, lipid membrane or even another filament. Matrix-assisted filament systems are frequently nucleotide dependent and cytomotive but rarely considered as part of the bacterial cytoskeleton. Here, we categorise this family of filament-forming systems as collaborative filaments and introduce a simple nomenclature. Collaborative filaments are frequent in both eukaryotes and prokaryotes and are involved in vital cellular processes including chromosome segregation, DNA repair and maintenance, gene silencing and cytokinesis to mention a few. In this review, we highlight common principles underlying collaborative filaments and correlate these with known functions.

  16. 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

  17. Changes in Bacterial and Eukaryotic Community Structure after Mass Lysis of Filamentous Cyanobacteria Associated with Viruses†

    PubMed Central

    van Hannen, Erik J.; Zwart, Gabriel; van Agterveld, Miranda P.; Gons, Herman J.; Ebert, Jeannine; Laanbroek, Hendrikus J.

    1999-01-01

    During an experiment in two laboratory-scale enclosures filled with lake water (130 liters each) we noticed the almost-complete lysis of the cyanobacterial population. Based on electron microscopic observations of viral particles inside cyanobacterial filaments and counts of virus-like particles, we concluded that a viral lysis of the filamentous cyanobacteria had taken place. Denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA fragments qualitatively monitored the removal of the cyanobacterial species from the community and the appearance of newly emerging bacterial species. The majority of these bacteria were related to the Cytophagales and actinomycetes, bacterial divisions known to contain species capable of degrading complex organic molecules. A few days after the cyanobacteria started to lyse, a rotifer species became dominant in the DGGE profile of the eukaryotic community. Since rotifers play an important role in the carbon transfer between the microbial loop and higher trophic levels, these observations confirm the role of viruses in channeling carbon through food webs. Multidimensional scaling analysis of the DGGE profiles showed large changes in the structures of both the bacterial and eukaryotic communities at the time of lysis. These changes were remarkably similar in the two enclosures, indicating that such community structure changes are not random but occur according to a fixed pattern. Our findings strongly support the idea that viruses can structure microbial communities. PMID:9925618

  18. Structural changes in myosin motors and filaments during relaxation of skeletal muscle

    PubMed Central

    Brunello, E; Fusi, L; Reconditi, M; Linari, M; Bianco, P; Panine, P; Narayanan, T; Piazzesi, G; Lombardi, V; Irving, M

    2009-01-01

    Structural changes in myosin motors and filaments during relaxation from short tetanic contractions of intact single fibres of frog tibialis anterior muscles at sarcomere length 2.14 μm, 4°C were investigated by X-ray diffraction. Force declined at a steady rate for several hundred milliseconds after the last stimulus, while sarcomere lengths remained almost constant. During this isometric phase of relaxation the intensities of the equatorial and meridional M3 X-ray reflections associated with the radial and axial distributions of myosin motors also recovered at a steady rate towards their resting values, consistent with progressive net detachment of myosin motors from actin filaments. Stiffness measurements confirmed that the fraction of motors attached to actin declined at a constant rate, but also revealed a progressive increase in force per motor. The interference fine structure of the M3 reflection suggested that actin-attached myosin motors are displaced towards the start of their working stroke during isometric relaxation. There was negligible recovery of the intensities of the meridional and layer-line reflections associated with the quasi-helical distribution of myosin motors in resting muscle during isometric relaxation, and the 1.5% increase in the axial periodicity of the myosin filament associated with muscle activation was not reversed. When force had decreased to roughly half its tetanus plateau value, the isometric phase of relaxation abruptly ended, and the ensuing chaotic relaxation had an exponential half-time of ca 60 ms. Recovery of the equatorial X-ray intensities was largely complete during chaotic relaxation, but the other X-ray signals recovered more slowly than force. PMID:19651765

  19. [Fractal art in separative sciences].

    PubMed

    Guillaume, Y C

    2002-01-01

    Fractal geometry has provided a mathematical formalism for describing complex and dynamical structures. It has been applied successfully in a variety of areas such as astronomy, economics and biology. Because of its success in such a variety of areas it is natural to develop fractal application in separative sciences.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  1. Structural data suggest that the active and inactive forms of the RecA filament are not simply interconvertible.

    PubMed

    Yu, X; Egelman, E H

    1992-09-05

    We have used electron microscopy to examine the two major conformational states of the helical filament formed by the RecA protein of Escherichia coli. The compressed filament, formed in the absence of a nucleotide cofactor either as a self-polymer or on a single-stranded DNA molecule, is characterized in solution by about 6.1 subunits per turn of a 76 A pitch helix, and appears to be inactive with respect to all RecA activity. The active state of the filament, formed with ATP or an ATP analog on either a single or double-stranded DNA substrate, has about 6.2 subunits per turn of a 94 A pitch helix. Measurements of the contour length of RecA-covered single-stranded DNA circles in ice, formed in the absence of nucleotide cofactor, indicate that each RecA subunit binds five bases, in contrast to the three bases or base-pairs per subunit in the active state. The different stoichiometries of DNA binding suggests that the two polymeric forms are not interconvertible, as has been suggested on biochemical grounds. A three-dimensional reconstruction of the inactive state shows the same general features as the 83 A pitch filament present in the RecA crystal. This structural similarity and the fact that the crystal does not contain ATP or DNA suggests that the crystal structure is more similar to the compressed filament than the active, extended filament.

  2. 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)

  3. 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)

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

    DOE PAGES

    Chan, Chun; Fan, Jun; Messer, Andrew E.; ...

    2016-04-22

    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 monomersmore » are likely to form distinctive homopolymers, with mutant filaments being very stiff, and not supporting proper myosin binding. Lastly, 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.« less

  5. 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

  6. 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.

  7. 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.

  8. 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).

  9. 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.

  10. Purification and structural characterization of a filamentous, mucin-like proteophosphoglycan secreted by Leishmania parasites.

    PubMed

    Ilg, T; Stierhof, Y D; Craik, D; Simpson, R; Handman, E; Bacic, A

    1996-08-30

    Parasitic protozoa of the genus Leishmania secrete a filamentous macromolecule that forms networks and appears to be associated with cell aggregation. We report here the purification of this parasite antigen from Leishmania major culture supernatant and its compositional (75.6% carbohydrate, 20% phosphate, 4.4% amino acids, w/w), structural, and ultrastructural characterization as a highly unusual proteophosphoglycan (PPG). Mild acid hydrolysis, which cleaves preferentially hexose 1-phosphate bonds, releases the PPG glycans. Their structures are Galbeta1-4Man, Manalpha1-2Man, Galbeta1-3Galbeta1-4Man, PO4-6(Galbeta1-3)0-2Galbeta1-4Man, and PO4-6(Arabeta1-2Galbeta1-3)Galbeta1-4Man. These glycans are also components of the parasite glycolipid lipophosphoglycan, but their relative abundance and structural organization in PPG are different. Some of them represent novel forms of protein glycosylation. 31P NMR on native PPG demonstrates that phosphate is exclusively in phosphodiester bonds and that the basic structure R-Manalpha1-PO4-6-Gal-R connects the glycans. A phosphodiester linkage to phosphoserine (most likely R-Manalpha1-PO4-Ser) anchors the PPG oligosaccharides to the polypeptide. PPG has a unique amino acid composition; glycosylated phosphoserine (>43 mol %), serine, alanine, and proline account for more than 87 mol % and appear to be clustered in large proteinase-resistant domains. Electron microscopy of purified PPG reveals cable-like, flexible, long (to 6 microm), and unbranched filaments. The overall structure of PPG shows many similarities to mammalian mucins. Potential functions of this novel mucin-like molecule for the parasites are discussed.

  11. Structural investigation of endoglucanase 2 from the filamentous fungus Penicillium verruculosum

    NASA Astrophysics Data System (ADS)

    Vakhrusheva, A. V.; Nemashkalov, V. A.; Kravchenko, O. V.; Tishchenko, S. V.; Gabdulkhakov, A. G.; Kljashtorny, V. G.; Korotkova, O. G.; Gusakov, A. V.; Sinitsyn, A. P.

    2017-03-01

    Enzyme additives capable of degrading non-starch polysaccharides of cereal cell walls, which are major ingredients used in animal feed, can improve the efficiency of livestock production. Non-starch polysaccharides have antinutritional properties that interfere with efficient digestion and assimilation of nutrients by animals. Therefore, the improvement of the properties and characteristics of enzyme additive is an important issue. The three-dimensional structure of one of the key industrial enzymes involved in the degradation of non-starch polysaccharides — endoglucanase 2 from the filamentous fungus Penicillium verruculosum — was determined (PDB ID: 5I6S). The catalytic site of this enzyme was established. Based on the enzyme structure, it was suggested that the pH optimum of the enzyme activity can be shifted from acidic to neutral or alkaline pH values.

  12. Crenactin from Pyrobaculum calidifontis is closely related to actin in structure and forms steep helical filaments

    PubMed Central

    Izoré, Thierry; Duman, Ramona; Kureisaite-Ciziene, Danguole; Löwe, Jan

    2014-01-01

    Polymerising proteins of the actin family are nearly ubiquitous. Crenactins, restricted to Crenarchaea, are more closely related to actin than bacterial MreB. Crenactins occur in gene clusters hinting at an unknown, but conserved function. We solved the crystal structure of crenactin at 3.2 Å resolution. The protein crystallises as a continuous right-handed helix with 8 subunits per complete turn, spanning 419 Å. The structure of crenactin shows several loops that are longer than in actin, but overall, crenactin is closely related to eukaryotic actin, with an RMSD of 1.6 Å. Crenactin filaments imaged by electron microscopy showed polymers with very similar helical parameters. PMID:24486010

  13. Giant axonal neuropathy alters the structure of keratin intermediate filaments in human hair.

    PubMed

    Soomro, Asfia; Alsop, Richard J; Negishi, Atsuko; Kreplak, Laurent; Fudge, Douglas; Kuczmarski, Edward R; Goldman, Robert D; Rheinstädter, Maikel C

    2017-04-01

    Giant axonal neuropathy (GAN) follows an autosomal recessive genetic inheritance and impedes the peripheral and central nervous system due to axonal swellings that are packed with neurofilaments. The patients display a number of phenotypes, including hypotonia, muscle weakness, decreased reflexes, ataxia, seizures, intellectual disability, pale skin and often curled hair. We used X-ray diffraction and tensile testing to determine potential changes to the structure of keratin intermediate filaments (IFs) in the hair of patients with GAN. A statistically significant decrease in the 47 and the 27 Å diffraction signals were observed. Tensile tests determined that the hair was slightly stiffer, stronger and more extensible in GAN patients. These results suggest that the structure of keratin IFs in hair is altered in GAN, and the findings are compatible with an increased positional disorder of the keratin tetramers within the hair fibres. © 2017 The Author(s).

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

    PubMed

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

    2015-12-15

    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.

  15. 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

  16. Plasticity in PYD assembly revealed by cryo-EM structure of the PYD filament of AIM2

    PubMed Central

    Lu, Alvin; Li, Yang; Yin, Qian; Ruan, Jianbin; Yu, Xiong; Egelman, Edward; Wu, Hao

    2015-01-01

    Absent in melanoma 2 (AIM2) is an essential cytosolic double-stranded DNA receptor that assembles with the adaptor, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and caspase-1 to form the AIM2 inflammasome, which leads to proteolytic maturation of cytokines and pyroptotic cell death. AIM2 contains an N-terminal Pyrin domain (PYD) that interacts with ASC through PYD/PYD interactions and nucleates ASCPYD filament formation. To elucidate the molecular basis of AIM2-induced ASCPYD polymerization, we generated AIM2PYD filaments fused to green fluorescent protein (GFP) and determined its cryo-electron microscopic (cryo-EM) structure. The map showed distinct definition of helices, allowing fitting of the crystal structure. Surprisingly, the GFP-AIM2PYD filament is a 1-start helix with helical parameters distinct from those of the 3-start ASCPYD filament. However, despite the apparent symmetry difference, helical net and detailed interface analyses reveal minimal changes in subunit packing. GFP-AIM2PYD nucleated ASCPYD filament formation in comparable efficiency as untagged AIM2PYD, suggesting assembly plasticity in both AIM2PYD and ASCPYD. The DNA-binding domain of AIM2 is able to form AIM2/DNA filaments, within which the AIM2PYD is brought into proximity to template ASCPYD filament assembly. Because ASC is able to interact with many PYD-containing receptors for the formation of inflammasomes, the observed structural plasticity may be critically important for this versatility in the PYD/PYD interactions. PMID:26583071

  17. Refining the structure of the Halobacterium salinarum flagellar filament using the iterative helical real space reconstruction method: insights into polymorphism.

    PubMed

    Trachtenberg, Shlomo; Galkin, Vitold E; Egelman, Edward H

    2005-02-25

    The eubacterial flagellar filament is an external, self-assembling, helical polymer approximately 220 A in diameter constructed from a highly conserved monomer, flagellin, which polymerizes externally at the distal end. The archaeal filament is only approximately 100 A in diameter, assembles at the proximal end and is constructed from different, glycosylated flagellins. Although the phenomenology of swimming is similar to that of eubacteria, the symmetry of the archebacterial filament is entirely different. Here, we extend our previous study on the flagellar coiled filament structure of strain R1M1 of Halobacterium salinarum. We use strain M175 of H.salinarum, which forms poly-flagellar bundles at high yield which, under conditions of relatively low ionic-strength (0.8 M versus 5 M) and low pH ( approximately 2.5 versus approximately 6.8), form straight filaments. We demonstrated previously that a single-particle approach to helical reconstruction has many advantages over conventional Fourier-Bessel methods when dealing with variable helical symmetry and heterogeneity. We show here that when this method is applied to the ordered helical structure of the archebacterial uncoiled flagellar filament, significant extensions in resolution can be obtained readily when compared to applying traditional helical techniques. The filament population can be separated into classes of different morphologies, which may represent polymorphic states. Using cryo-negatively stained images, a resolution of approximately 10-15 A has been achieved. Single alpha-helices can be fit into the reconstruction, supporting the proposed similarity of the structure to that of type IV bacterial pili.

  18. Plasticity in PYD assembly revealed by cryo-EM structure of the PYD filament of AIM2.

    PubMed

    Lu, Alvin; Li, Yang; Yin, Qian; Ruan, Jianbin; Yu, Xiong; Egelman, Edward; Wu, Hao

    Absent in melanoma 2 (AIM2) is an essential cytosolic double-stranded DNA receptor that assembles with the adaptor, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and caspase-1 to form the AIM2 inflammasome, which leads to proteolytic maturation of cytokines and pyroptotic cell death. AIM2 contains an N-terminal Pyrin domain (PYD) that interacts with ASC through PYD/PYD interactions and nucleates ASC(PYD) filament formation. To elucidate the molecular basis of AIM2-induced ASC(PYD) polymerization, we generated AIM2(PYD) filaments fused to green fluorescent protein (GFP) and determined its cryo-electron microscopic (cryo-EM) structure. The map showed distinct definition of helices, allowing fitting of the crystal structure. Surprisingly, the GFP-AIM2(PYD) filament is a 1-start helix with helical parameters distinct from those of the 3-start ASC(PYD) filament. However, despite the apparent symmetry difference, helical net and detailed interface analyses reveal minimal changes in subunit packing. GFP-AIM2(PYD) nucleated ASC(PYD) filament formation in comparable efficiency as untagged AIM2(PYD), suggesting assembly plasticity in both AIM2(PYD) and ASC(PYD). The DNA-binding domain of AIM2 is able to form AIM2/DNA filaments, within which the AIM2(PYD) is brought into proximity to template ASC(PYD) filament assembly. Because ASC is able to interact with many PYD-containing receptors for the formation of inflammasomes, the observed structural plasticity may be critically important for this versatility in the PYD/PYD interactions.

  19. 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.

  20. Fractal Nature of the Electronic Structure of a Penrose Tiling Lattice in a Magnetic Field

    NASA Astrophysics Data System (ADS)

    Hatakeyama, Tetsuo; Kamimura, Hiroshi

    1989-01-01

    The one-electron energy spectrum of a Penrose tiling lattice in a magnetic field is studied with a tight-binding Hamiltonian. We show the following remarkable results characteristic of a Penrose lattice. (1) The density of states in a magnetic field has a central peak with zero width at zero energy. It is shown that the zero-energy states correspond to the ring states in which wavefunction has nonvanishing amplitudes only at the sites circling the origin. (2) The magnetic field dependence of the energy spectrum shows a butterfly shape caused by Landau quantization. (3) The magnetic field dependence of the energy spectrum also shows a fractal nature. In particular it is characterized by two periods whose ratio is equal to the golden mean (1+\\sqrt{5})/2, and two periods comprising a Fibonacci sequence. We have clarified the origin of this fractal behavior of the energy spectrum analytically.

  1. 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. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  2. 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.

  3. Terahertz spectroscopy of plasmonic fractals.

    PubMed

    Agrawal, A; Matsui, T; Zhu, W; Nahata, A; Vardeny, Z V

    2009-03-20

    We use terahertz time-domain spectroscopy to study the transmission properties of metallic films perforated with aperture arrays having deterministic or stochastic fractal morphologies ("plasmonic fractals"), and compare them with random aperture arrays. All of the measured plasmonic fractals show transmission resonances and antiresonances at frequencies that correspond to prominent features in their structure factors in k space. However, in sharp contrast to periodic aperture arrays, the resonant transmission enhancement decreases with increasing array size. This property is explained using a density-density correlation function, and is utilized for determining the underlying fractal dimensionality, D(<2). Furthermore, a sum rule for the transmission resonances and antiresonances in plasmonic fractals relative to the transmission of the corresponding random aperture arrays is obtained, and is shown to be universal.

  4. 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.

  5. Astrophysical fractals - An overview and prospects

    NASA Technical Reports Server (NTRS)

    Perdang, J.

    1990-01-01

    Different astrophysical circumstances under which fractal structures have been identified so far, or are likely to be identified in the future, are reviewed. The observed fractals can be classified into 2 main groups: (1) fractal configurations in space-time, materializing as fractals defined over the time axis at a given position in space, or over the physical configuration space at a fixed instant in time; and (2) fractals in parameter spaces. The theoretical interpretation of the origin of the spatial fractal geometry of the most conspicuous 'irregular' astronomical bodies is still wanting in the context of standard continuum models. In contrast, the less conventional discrete models (cellular automata) naturally produce such spatially fractal structures.

  6. Astrophysical fractals - An overview and prospects

    NASA Technical Reports Server (NTRS)

    Perdang, J.

    1990-01-01

    Different astrophysical circumstances under which fractal structures have been identified so far, or are likely to be identified in the future, are reviewed. The observed fractals can be classified into 2 main groups: (1) fractal configurations in space-time, materializing as fractals defined over the time axis at a given position in space, or over the physical configuration space at a fixed instant in time; and (2) fractals in parameter spaces. The theoretical interpretation of the origin of the spatial fractal geometry of the most conspicuous 'irregular' astronomical bodies is still wanting in the context of standard continuum models. In contrast, the less conventional discrete models (cellular automata) naturally produce such spatially fractal structures.

  7. Emergence of fractal scaling in complex networks.

    PubMed

    Wei, Zong-Wen; Wang, Bing-Hong

    2016-09-01

    Some real-world networks are shown to be fractal or self-similar. It is widespread that such a phenomenon originates from the repulsion between hubs or disassortativity. Here we show that this common belief fails to capture the causality. Our key insight to address it is to pinpoint links critical to fractality. Those links with small edge betweenness centrality (BC) constitute a special architecture called fractal reference system, which gives birth to the fractal structure of those reported networks. In contrast, a small amount of links with high BC enable small-world effects, hiding the intrinsic fractality. With enough of such links removed, fractal scaling spontaneously arises from nonfractal networks. Our results provide a multiple-scale view on the structure and dynamics and place fractality as a generic organizing principle of complex networks on a firmer ground.

  8. Emergence of fractal scaling in complex networks

    NASA Astrophysics Data System (ADS)

    Wei, Zong-Wen; Wang, Bing-Hong

    2016-09-01

    Some real-world networks are shown to be fractal or self-similar. It is widespread that such a phenomenon originates from the repulsion between hubs or disassortativity. Here we show that this common belief fails to capture the causality. Our key insight to address it is to pinpoint links critical to fractality. Those links with small edge betweenness centrality (BC) constitute a special architecture called fractal reference system, which gives birth to the fractal structure of those reported networks. In contrast, a small amount of links with high BC enable small-world effects, hiding the intrinsic fractality. With enough of such links removed, fractal scaling spontaneously arises from nonfractal networks. Our results provide a multiple-scale view on the structure and dynamics and place fractality as a generic organizing principle of complex networks on a firmer ground.

  9. 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.

  10. Lessons from a tarantula: new insights into muscle thick filament and myosin interacting-heads motif structure and function.

    PubMed

    Alamo, Lorenzo; Koubassova, Natalia; Pinto, Antonio; Gillilan, Richard; Tsaturyan, Andrey; Padrón, Raúl

    2017-09-04

    The tarantula skeletal muscle X-ray diffraction pattern suggested that the myosin heads were helically arranged on the thick filaments. Electron microscopy (EM) of negatively stained relaxed tarantula thick filaments revealed four helices of heads allowing a helical 3D reconstruction. Due to its low resolution (5.0 nm), the unambiguous interpretation of densities of both heads was not possible. A resolution increase up to 2.5 nm, achieved by cryo-EM of frozen-hydrated relaxed thick filaments and an iterative helical real space reconstruction, allowed the resolving of both heads. The two heads, "free" and "blocked", formed an asymmetric structure named the "interacting-heads motif" (IHM) which explained relaxation by self-inhibition of both heads ATPases. This finding made tarantula an exemplar system for thick filament structure and function studies. Heads were shown to be released and disordered by Ca(2+)-activation through myosin regulatory light chain phosphorylation, leading to EM, small angle X-ray diffraction and scattering, and spectroscopic and biochemical studies of the IHM structure and function. The results from these studies have consequent implications for understanding and explaining myosin super-relaxed state and thick filament activation and regulation. A cooperative phosphorylation mechanism for activation in tarantula skeletal muscle, involving swaying constitutively Ser35 mono-phosphorylated free heads, explains super-relaxation, force potentiation and post-tetanic potentiation through Ser45 mono-phosphorylated blocked heads. Based on this mechanism, we propose a swaying-swinging, tilting crossbridge-sliding filament for tarantula muscle contraction.

  11. The structural basis of the filament-matrix texture in the avian/reptilian group of hard β-keratins.

    PubMed

    Fraser, R D Bruce; Parry, David A D

    2011-02-01

    Avian hard keratin has a filament-matrix texture in which the filaments contain a helical array of twisted β-sheets and the matrix has unusually high concentrations of cysteine, glycine, and tyrosine. X-ray diffraction studies have established that similar filaments exist in the hard keratins of crocodiles, turtles, tuataras, lizards and snakes. Here, the relationship between amino acid sequence and the filament-matrix texture is explored in a wide variety of avian and reptilian hard keratins. Universally, the molecules contain three distinct domains: a central domain rich in β-favoring residues associated with the filament framework, and N- and C-terminal domains associated with the matrix and with crosslinking via disulfide bonds. A variety of structural probes were employed to identify the β-framework of the filaments and a common pattern 34 residues in length was found in all cases. In addition, detailed analyses of the sequences in the two "matrix" domains revealed profound differences between the Archosaurs (birds, crocodiles and turtles), where the N-terminal domains were very similar, and the Squamates (snakes and lizards) where the N-terminal domains varied widely in length and composition, in some cases exhibiting a subdomain structure, and segments of highly homologous sequence. The C-terminal domains in both branches varied widely in composition but almost all exhibit a subdomain structure characterized by a terminal sequence rich in cysteine and arginine residues. A revised model for the molecular organization in avian and reptilian hard keratins is presented and similarities and differences in the matrix domains are noted. Copyright © 2010 Elsevier Inc. All rights reserved.

  12. 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.

  13. 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

  14. 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…

  15. 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…

  16. Structural and fractal properties of particles emitted from spark ignition engines.

    PubMed

    Chakrabarty, Rajan K; Moosmüller, Hans; Arnott, W Patrick; Garro, Mark A; Walker, John

    2006-11-01

    Size, morphology, and microstructure of particles emitted from one light-duty passenger vehicle (Buick Century; model year 1990; PM (particulate matter) mass emission rate 3.1 mg/km) and two light-duty trucks (Chevrolet C2; model year 1973; PM mass emission rate 282 mg/km, and Chevrolet El Camino; model year 1976; PM mass emission rate 31 mg/km), running California's unified driving cycles (UDC) on a chassis dynamometer, were studied using scanning electron microscopy (SEM). SEM images yielded particle properties including three-dimensional density fractal dimensions, monomer and agglomerate number size distributions, and three different shape descriptors, namely aspect ratio, root form factor, and roundness. The density fractal dimension of the particles was between 1.7 and 1.78, while the number size distribution of the particles placed the majority of the particles in the accumulation mode (0.1-0.3 microm). The shape descriptors were found to decrease with increasing particle size. Partial melting of particles, a rare and previously unreported phenomenon, was observed upon exposure of particles emitted during phase 2 of the UDC to the low accelerating voltage electron beam of the SEM. The rate of melting was quantified for individual particles, establishing a near linear relationship between the melting rate and the organic carbon 1 to elemental carbon ratio.

  17. Structure and dynamics of the Pf1 filamentous bacteriophage coat protein in micelles

    SciTech Connect

    Schiksnis, R.A.; Bogusky, M.J.; Tsang, P.; Opella, S.J.

    1987-03-10

    The major coat protein of filamentous bacteriophage adopts its membrane-bound conformation in detergent micelles. High-resolution /sup 1/H and /sup 15/N NMR experiments are used to characterize the structure and dynamics of residues 30-40 in the hydrophobic midsection of Pf1 coat protein in sodium dodecyl sulfate micelles. Uniform and specific-site /sup 15/N labels enable the immobile backbone sites to be identified by their /sup 1/H//sup 15/N heteronuclear nuclear Overhauser effect and allow the assignment of /sup 1/H and /sup 15/N resonances. About one-third of the amide N-H protons in the protein undergo very slow exchange with solvent deuterons, which is indicative of sites in highly structured environments. The combination of results from /sup 1/H//sup 15/N heteronuclear correlation, /sup 1/H homonuclear correlation, and /sup 1/H homonuclear Overhauser effect experiments assigns the resonances to specific residues and demonstrates that residues 30-40 of the coat protein have a helical secondary structure.

  18. Using Data Mining and Computational Approaches to Study Intermediate Filament Structure and Function.

    PubMed

    Parry, David A D

    2016-01-01

    Experimental and theoretical research aimed at determining the structure and function of the family of intermediate filament proteins has made significant advances over the past 20 years. Much of this has either contributed to or relied on the amino acid sequence databases that are now available online, and the data mining approaches that have been developed to analyze these sequences. As the quality of sequence data is generally high, it follows that it is the design of the computational and graphical methodologies that are of especial importance to researchers who aspire to gain a greater understanding of those sequence features that specify both function and structural hierarchy. However, these techniques are necessarily subject to limitations and it is important that these be recognized. In addition, no single method is likely to be successful in solving a particular problem, and a coordinated approach using a suite of methods is generally required. A final step in the process involves the interpretation of the results obtained and the construction of a working model or hypothesis that suggests further experimentation. While such methods allow meaningful progress to be made it is still important that the data are interpreted correctly and conservatively. New data mining methods are continually being developed, and it can be expected that even greater understanding of the relationship between structure and function will be gleaned from sequence data in the coming years. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. An acidic protein aligns magnetosomes along a filamentous structure in magnetotactic bacteria

    NASA Astrophysics Data System (ADS)

    Scheffel, André; Gruska, Manuela; Faivre, Damien; Linaroudis, Alexandros; Plitzko, Jürgen M.; Schüler, Dirk

    2006-03-01

    Magnetotactic bacteria are widespread aquatic microorganisms that use unique intracellular organelles to navigate along the Earth's magnetic field. These organelles, called magnetosomes, consist of membrane-enclosed magnetite crystals that are thought to help to direct bacterial swimming towards growth-favouring microoxic zones at the bottom of natural waters. Questions in the study of magnetosome formation include understanding the factors governing the size and redox-controlled synthesis of the nano-sized magnetosomes and their assembly into a regular chain in order to achieve the maximum possible magnetic moment, against the physical tendency of magnetosome agglomeration. A deeper understanding of these mechanisms is expected from studying the genes present in the identified chromosomal `magnetosome island', for which the connection with magnetosome synthesis has become evident. Here we use gene deletion in Magnetospirillum gryphiswaldense to show that magnetosome alignment is coupled to the presence of the mamJ gene product. MamJ is an acidic protein associated with a novel filamentous structure, as revealed by fluorescence microscopy and cryo-electron tomography. We suggest a mechanism in which MamJ interacts with the magnetosome surface as well as with a cytoskeleton-like structure. According to our hypothesis, magnetosome architecture represents one of the highest structural levels achieved in prokaryotic cells.

  20. Structural properties of highly conductive ultra-nanocrystalline diamond films grown by hot-filament CVD

    NASA Astrophysics Data System (ADS)

    Mertens, M.; Lin, I.-N.; Manoharan, D.; Moeinian, A.; Brühne, K.; Fecht, H. J.

    2017-01-01

    In this work we show the correlation of the electrical conductivity of ultra-nanocrystalline (UNCD) diamond films grown by hot filament chemical vapor deposition (HFCVD) with their structural properties. The substrate temperature, the methane to hydrogen ratio and the pressure are the main factor influencing the growth of conductive UNCD films, which extends from electrical resistive diamond films (<10-4 S/cm) to highly conductive diamond films with a specific conductivity of 300 S/cm. High-resolution-transmission-electron-microscopy (HRTEM) and electron-energy-loss-spectroscopy (EELS) have been done on the highly conductive diamond films, to show the origin of the high electrical conductivity. The HRTEM results show random oriented diamond grains and a large amount of nano-graphite between the diamond crystals. EELS investigations are confirming these results. Raman measurements are correlated with the specific conductivity, which shows structural changes of sp2 carbons bonds as function of conductivity. Hall experiments complete the results, which lead to a model of an electron mobility based conductivity, which is influenced by the structural properties of the grain boundary regions in the ultra-nanocrystalline diamond films.

  1. 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.

  2. The structure of the coronal soft X-ray source associated with the dark filament disappearance of 1991 September 28 using the Yohkoh Soft X-ray Telescope

    NASA Technical Reports Server (NTRS)

    Mcallister, Alan; Uchida, Yutaka; Tsuneta, Saku; Strong, Keith T.; Acton, Loren W.; Hiei, Eijiro; Bruner, Marilyn E.; Watanabe, Takashi; Shibata, Kazunari

    1992-01-01

    The structure of the coronal soft X-ray source associated with the dark filament disappearance on September 28, 1991, observed with the Soft X-ray Telescope, is examined as a possible example of the 'eruption-reconnection' model of filament disappearance. The results suggest, however, that this model may not fit. There is a strong possibility that much of the dark filament mass remains in the heated unwinding axial field.

  3. Fractal features of seismic noise

    NASA Astrophysics Data System (ADS)

    Caserta, A.; Consolini, G.; Michelis, P. De

    2003-04-01

    We present experimental observations and data analysis concerning the fractal features of seismic noise in the frequency range from 1 Hz to 40 Hz. In detail, we investigate the 3D average squared soil displacement and the distribution function of its fluctuations for different near-surface geological structures. We found that the seismic noise is consistent with a persistent fractal brownian motion characterized by a Hurst exponent grather than 1/2. Moreover, a clear dependence of the fractal nature of the seismic noise on the near-surface local geology has been found.

  4. Thermal collapse of snowflake fractals

    NASA Astrophysics Data System (ADS)

    Gallo, T.; Jurjiu, A.; Biscarini, F.; Volta, A.; Zerbetto, F.

    2012-08-01

    Snowflakes are thermodynamically unstable structures that would ultimately become ice balls. To investigate their dynamics, we mapped atomistic molecular dynamics simulations of small ice crystals - built as filled von Koch fractals - onto a discrete-time random walk model. Then the walkers explored the thermal evolution of high fractal generations. The in silico experiments showed that the evolution is not entirely random. The flakes step down one fractal generation before forfeiting their architecture. The effect may be used to trace the thermal history of snow.

  5. The fractal geometry of life.

    PubMed

    Losa, Gabriele A

    2009-01-01

    The extension of the concepts of Fractal Geometry (Mandelbrot [1983]) toward the life sciences has led to significant progress in understanding complex functional properties and architectural / morphological / structural features characterising cells and tissues during ontogenesis and both normal and pathological development processes. It has even been argued that fractal geometry could provide a coherent description of the design principles underlying living organisms (Weibel [1991]). Fractals fulfil a certain number of theoretical and methodological criteria including a high level of organization, shape irregularity, functional and morphological self-similarity, scale invariance, iterative pathways and a peculiar non-integer fractal dimension [FD]. Whereas mathematical objects are deterministic invariant or self-similar over an unlimited range of scales, biological components are statistically self-similar only within a fractal domain defined by upper and lower limits, called scaling window, in which the relationship between the scale of observation and the measured size or length of the object can be established (Losa and Nonnenmacher [1996]). Selected examples will contribute to depict complex biological shapes and structures as fractal entities, and also to show why the application of the fractal principle is valuable for measuring dimensional, geometrical and functional parameters of cells, tissues and organs occurring within the vegetal and animal realms. If the criteria for a strict description of natural fractals are met, then it follows that a Fractal Geometry of Life may be envisaged and all natural objects and biological systems exhibiting self-similar patterns and scaling properties may be considered as belonging to the new subdiscipline of "fractalomics".

  6. Effect of filament twist on the structure and properties of Ag-sheathed Bi2223 tape

    NASA Astrophysics Data System (ADS)

    Nakamura, Y.; Kurihara, C.; Machida, T.; Inada, R.; Oota, A.

    2009-10-01

    Ag-sheathed Bi2223 tapes show good performances and are ready for many prototype applications. However, drastic reduction of AC loss is strongly required for practical AC power applications. To reduce the AC loss under AC external magnetic field, the introduction of filament twisting with high resistive barrier is effective, but the filament twisting tends to decrease the Jc value. This decrease in Jc is a problem to balance low AC loss with high Ic value. In this study, the effect of filament twisting on the microstructure and Jc property was investigated to overcome the Jc reduction. The Bi2223 tapes sheathed with Ag-Cu alloy were fabricated with a standard PIT method. Although the formation of Bi2223 phase was not affected by filament twisting from the XRD analysis and SEM observation, the Jc values of the twisted tapes decreased about 30% compared to that of non-twisted tape. In the case of the same twist pitch, the sample rolled under large pass reduction ratio showed relatively high Jc value. This high Jc would be caused by the high aspect ratio of the filament of those tapes, in which the grain alignment along the filament interface would be well. On the other hand, a reason for the Jc reduction of twist tapes is proposed to be the misorientation at grain boundaries of Bi2223 grains in the transference region near the edges of the tape, where the filaments move up and down in the thickness direction.

  7. Global Simulations of Differentially Rotating Magnetized Disks: Formation of Low-beta Filaments and Structured Coronae.

    PubMed

    Machida; Hayashi; Matsumoto

    2000-03-20

    We present the results of three-dimensional global magnetohydrodynamic simulations of the Parker-shearing instability in a differentially rotating torus initially threaded by toroidal magnetic fields. An equilibrium model of a magnetized torus is adopted as an initial condition. When beta0=Pgas&solm0;Pmag approximately 1 at the initial state, magnetic flux buoyantly escapes from the disk and creates looplike structures similar to those in the solar corona. Inside the torus, the growth of nonaxisymmetric magnetorotational (or Balbus & Hawley) instability generates magnetic turbulence. Magnetic field lines are tangled on a small scale, but on a large scale they show low azimuthal wavenumber spiral structure. After several rotation periods, the system oscillates around a state with beta approximately 5. We found that magnetic pressure-dominated (beta<1) filaments are created in the torus. The volume filling factor of the region in which beta

  8. Crystal structures of two tetrameric β-carbonic anhydrases from the filamentous ascomycete Sordaria macrospora.

    PubMed

    Lehneck, Ronny; Neumann, Piotr; Vullo, Daniela; Elleuche, Skander; Supuran, Claudiu T; Ficner, Ralf; Pöggeler, Stefanie

    2014-04-01

    Carbonic anhydrases (CAs) are metalloenzymes catalyzing the reversible hydration of carbon dioxide to bicarbonate (hydrogen carbonate) and protons. CAs have been identified in archaea, bacteria and eukaryotes and can be classified into five groups (α, β, γ, δ, ζ) that are unrelated in sequence and structure. The fungal β-class has only recently attracted attention. In the present study, we investigated the structure and function of the plant-like β-CA proteins CAS1 and CAS2 from the filamentous ascomycete Sordaria macrospora. We demonstrated that both proteins can substitute for the Saccharomyces cerevisiae β-CA Nce103 and exhibit an in vitro CO2 hydration activity (kcat /Km of CAS1: 1.30 × 10(6) m(-1) ·s(-1) ; CAS2: 1.21 × 10(6 ) m(-1) ·s(-1) ). To further investigate the structural properties of CAS1 and CAS2, we determined their crystal structures to a resolution of 2.7 Å and 1.8 Å, respectively. The oligomeric state of both proteins is tetrameric. With the exception of the active site composition, no further major differences have been found. In both enzymes, the Zn(2) (+) -ion is tetrahedrally coordinated; in CAS1 by Cys45, His101 and Cys104 and a water molecule and in CAS2 by the side chains of four residues (Cys56, His112, Cys115 and Asp58). Both CAs are only weakly inhibited by anions, making them good candidates for industrial applications. CAS1 and CAS2 bind by x-ray crystallography (View interaction) Structural data have been deposited in the Protein Data Bank database under accession numbers 4O1J for CAS1 and 4O1K for CAS2. © 2014 FEBS.

  9. Structure and assembly of P-pili: A protruding hinge region used for assembly of a bacterial adhesion filament

    PubMed Central

    Mu, Xiang-Qi; Bullitt, Esther

    2006-01-01

    High-resolution structures of macromolecular complexes offer unparalleled insight into the workings of biological systems and hence the interplay of these systems in health and disease. We have adopted a multifaceted approach to understanding the pathogenically important structure of P-pili, the class I adhesion pili from pyelonephritic Escherichia coli. Our approach combines electron cryomicroscopy, site-directed mutagenesis, homology modeling, and energy calculations, resulting in a high-resolution model of PapA, the major structural element of these pili. Fitting of the modeled PapA subunit into the electron cryomicroscopy data provides a detailed view of these pilins within the supramolecular architecture of the pilus filament. A structural hinge in the N-terminal region of the subunit is located at the site of a newly resolved electron density that protrudes from the P-pilus surface. The structural flexibility provided by this hinge is necessary for assembly of P-pili, illustrating one solution to construction of large macromolecular complexes from small repeating units. These data support our hypothesis that domain-swapped pilin subunits transit the outer cell membrane vertically and rotate about the hinge for final positioning into the pilus filament. Our data confirm and supply a structural basis for much previous genetic, biochemical, and structural data. This model of the P-pilus filament provides an insight into the mechanism of assembly of a macromolecular complex essential for initiation of kidney infection by these bacteria. PMID:16782819

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

    PubMed Central

    1991-01-01

    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

  11. Featuring dark coronal structures: physical signatures of filaments and coronal holes for automated recognition

    NASA Astrophysics Data System (ADS)

    Palacios, Judith; Cid, Consuelo; Saiz, Elena; Cerrato, Yolanda; Guerrero, Antonio

    2014-01-01

    Filaments may be mistaken for coronal holes when observed in extreme ultraviolet (EUV) images; however, a closer and more careful look reveals that their photometric properties are different. The combination of EUV images with photospheric magnetograms shows some characteristic differences between filaments and coronal holes. We have performed analyses with 7 different SDO/AIA wavelengths (94, 131, 171, 211, 193, 304, 335 Å) and SDO/HMI magnetograms obtained in September 2011 and March 2012 to study coronal holes and filaments from the photometric, magnetic, and also geometric point of view, since projection effects play an important role on the aforementioned traits.

  12. 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...

  13. Solid-state NMR studies of the dynamics and structure of mouse keratin intermediate filaments

    SciTech Connect

    Mack, J.W.; Torchia, D.A.; Steinert, P.M.

    1988-07-26

    The molecular dynamics and structural organization of mouse epidermal keratin intermediate filaments (IF) have been studied via solid-state nuclear magnetic resonance (NMR) experiments performed on IF labeled both in vivo and in vitro with isotopically enriched amino acids. As a probe of the organization of the peripheral glycine-rich end domains of the IF, carbon-13 NMR experiments have been performed on subfilamentous forms (prekeratin) and on IF reassembled in vitro that had been labeled with either (1-/sup 13/C)glycine or (2-/sup 13/C)glycine, as more than 90% of the glycines of the keratins are located in the end domains. Measurements of carbon relaxation times, nuclear Overhauser enhancements, and signal intensities show that the motions of the peptide backbone in the end domains are effectively isotropic. These results indicate that the end domains of IF are remarkably flexible and have little or no structural order. To probe the structural organization of the coiled-coil rod domains of the IF, separate samples of native keratin IF, raised in primary tissue culture, were labeled with L-(1-/sup 13/C)leucine, L-(/sup 2/H/sub 10/)leucine, or L-(2,3,3-/sup 2/H/sub 3/)leucine, as greater than 90% of the leucyl residues of the keratin IF types studied are located in the coiled coils which form the central core of IF. Deuterium NMR experiments performed on IF labeled with deuteriated leucines indeed reveal a marked degree of peptide backbone rigidity within the coiled coils, confirming the initial conclusions of the carbon-13 data. These data, demonstrating relative peptide backbone rigidity yet side-chain flexibility, are interpreted to mean that the coiled coils of these keratin IF are not tightly packed together but rather form a somewhat looser structure which permits a significant degree of side-chain mobility.

  14. Fractal analysis of deformation-induced dislocation patterns

    SciTech Connect

    Zaiser, M. ); Bay, K. . Inst. fuer Theoretische und Angewandte Physik); Haehner, P. . Joint Research Centre TU Braunschweig . Inst. fuer Metallphysik und Nukleare Festkoerperphysik)

    1999-06-22

    The paper reports extensive analyses of the fractal geometry of cellular dislocation structures observed in Cu deformed in multiple-slip orientation. Several methods presented for the determination of fractal dimensions are shown to give consistent results. Criteria are formulated which allow the distinguishing of fractal from non-fractal patterns, and implications of fractal dislocation patterning for quantitative metallography are discussed in detail. For an interpretation of the findings a theoretical model is outlined according to which dislocation cell formation is associated to a noise-induced structural transition far from equilibrium. This allows relating the observed fractal dimensions to the stochastic properties of deformation by collective dislocation glide.

  15. 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.

  16. Primary edge localized mode filament structure in the National Spherical Torus Experimenta)

    NASA Astrophysics Data System (ADS)

    Maqueda, R. J.; Maingi, R.; NSTX Team

    2009-05-01

    Edge localized modes (ELMs) are routinely seen in the National Spherical Torus Experiment (NSTX) [M. Ono, Nucl. Fusion 40, 557 (2000)]. These unstable modes give rise to plasma filaments that burst radially outward during the nonlinear phase of the instability, moving across flux surfaces into the scrape-off layer. Fast-frame visible imaging is used in NSTX to study the evolution and characteristics of the post-ELM filaments. These edge filaments, which are well aligned with the local magnetic field, are seen to evolve from a perturbation of the edge that within 40-50 μs develops into the relatively high density/temperature primary filaments. The distribution of primary filaments in toroidal angle is seen to agree with a random model with moderate average toroidal mode numbers. At the same time, gas puff imaging shows that the perturbation of the edge leading to the burst of the ELM into the scrape-off layer is characterized by a broadband increase in fluctuations at much smaller poloidal wavelengths (λpol˜2-12 cm). These two measurements suggest that early development of turbulence may play a role in the development of primary ELM filamentation.

  17. Structure of the filamentous phage pIV multimer by cryo-electron microscopy.

    PubMed

    Opalka, Natacha; Beckmann, Roland; Boisset, Nicolas; Simon, Martha N; Russel, Marjorie; Darst, Seth A

    2003-01-17

    The homo-multimeric pIV protein constitutes a channel required for the assembly and export of filamentous phage across the outer membrane of Escherichia coli. We present a 22 A-resolution three-dimensional reconstruction of detergent-solubilized pIV by cryo-electron microscopy associated with image analysis. The structure reveals a barrel-like complex, 13.5 nm in diameter and 24 nm in length, with D14 point-group symmetry, consisting of a dimer of unit multimers. Side views of each unit multimer exhibit three cylindrical domains named the N-ring, the M-ring and the C-ring. Gold labeling of pIV engineered to contain a single cysteine residue near the N or C terminus unambiguously identified the N-terminal region as the N-ring, and the C-terminal region was inferred to make up the C-ring. A large pore, ranging in inner diameter from 6.0 nm to 8.8 nm, runs through the middle of the multimer, but a central domain, the pore gate, blocks it. Moreover, the pore diameter at the N-ring is smaller than the phage particle. We therefore propose that the pIV multimer undergoes a large conformational change during phage transport, with reorganization of the central domain to open the pore, and widening at the N-ring in order to accommodate the 6.5 nm diameter phage particle.

  18. THE RAPID FORMATION OF A FILAMENT CAUSED BY MAGNETIC RECONNECTION BETWEEN TWO SETS OF DARK THREADLIKE STRUCTURES

    SciTech Connect

    Yang, Bo; Jiang, Yunchun; Yang, Jiayan; Yu, Shunping; Xu, Zhe E-mail: yjy@ynao.ac.cn

    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.

  19. 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.

  20. The ALP-Enigma protein ALP-1 functions in actin filament organization to promote muscle structural integrity in Caenorhabditis elegans.

    PubMed

    Han, Hsiao-Fen; Beckerle, Mary C

    2009-05-01

    Mutations that affect the Z-disk-associated ALP-Enigma proteins have been linked to human muscular and cardiac diseases. Despite their clear physiological significance for human health, the mechanism of action of ALP-Enigma proteins is largely unknown. In Caenorhabditis elegans, the ALP-Enigma protein family is encoded by a single gene, alp-1; thus C. elegans provides an excellent model to study ALP-Enigma function. Here we present a molecular and genetic analysis of ALP-Enigma function in C. elegans. We show that ALP-1 and alpha-actinin colocalize at dense bodies where actin filaments are anchored and that the proper localization of ALP-1 at dense bodies is dependent on alpha-actinin. Our analysis of alp-1 mutants demonstrates that ALP-1 functions to maintain actin filament organization and participates in muscle stabilization during contraction. Reducing alpha-actinin activity enhances the actin filament phenotype of the alp-1 mutants, suggesting that ALP-1 and alpha-actinin function in the same cellular process. Like alpha-actinin, alp-1 also interacts genetically with a connectin/titin family member, ketn-1, to provide mechanical stability for supporting body wall muscle contraction. Taken together, our data demonstrate that ALP-1 and alpha-actinin function together to stabilize actin filaments and promote muscle structural integrity.

  1. Fractal zone plates with variable lacunarity.

    PubMed

    Monsoriu, Juan; Saavedra, Genaro; Furlan, Walter

    2004-09-06

    Fractal zone plates (FZPs), i.e., zone plates with fractal structure, have been recently introduced in optics. These zone plates are distinguished by the fractal focusing structure they provide along the optical axis. In this paper we study the effects on this axial response of an important descriptor of fractals: the lacunarity. It is shown that this parameter drastically affects the profile of the irradiance response along the optical axis. In spite of this fact, the axial behavior always has the self-similarity characteristics of the FZP itself.

  2. 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.

  3. The pore structure and fractal characteristics of shales with low thermal maturity from the Yuqia Coalfield, northern Qaidam Basin, northwestern China

    NASA Astrophysics Data System (ADS)

    Hou, Haihai; Shao, Longyi; Li, Yonghong; Li, Zhen; Zhang, Wenlong; Wen, Huaijun

    2016-12-01

    The continental shales from the Middle Jurassic Shimengou Formation of the northern Qaidam Basin, northwestern China, have been investigated in recent years because of their shale gas potential. In this study, a total of twenty-two shale samples were collected from the YQ-1 borehole in the Yuqia Coalfield, northern Qaidam Basin. The total organic carbon (TOC) contents, pore structure parameters, and fractal characteristics of the samples were investigated using TOC analysis, low-temperature nitrogen adsorption experiments, and fractal analysis. The results show that the average pore size of the Shimengou shales varied from 8.149 nm to 20.635 nm with a mean value of 10.74 nm, which is considered mesopore-sized. The pores of the shales are mainly inkbottle- and slit-shaped. The sedimentary environment plays an essential role in controlling the TOC contents of the low maturity shales, with the TOC values of shales from deep to semi-deep lake facies (mean: 5.23%) being notably higher than those of the shore-shallow lake facies (mean: 0.65%). The fractal dimensions range from 2.4639 to 2.6857 with a mean of 2.6122, higher than those of marine shales, which indicates that the pore surface was rougher and the pore structure more complex in these continental shales. The fractal dimensions increase with increasing total pore volume and total specific surface area, and with decreasing average pore size. With increasing TOC contents in shales, the fractal dimensions increase first and then decrease, with the highest value occurring at 2% of TOC content, which is in accordance with the trends between the TOC and both total specific surface area and total pore volume. The pore structure complexity and pore surface roughness of these low-maturity shales would be controlled by the combined effects of both sedimentary environments and the TOC contents.

  4. 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.

  5. Filament turbulence

    NASA Astrophysics Data System (ADS)

    Davidsen, Joern

    2010-03-01

    How much information do you need to distinguish between different mechanisms for spatiotemporal chaos in three-dimensions? In this talk, I will show that the observation of the dynamics on the surface of a medium can be sufficient. Studying mechanisms for filament turbulence in the context of reaction-diffusion media, we found numerically that two major classes of instabilities leave a very different signature on what can be observed on the surface of a three-dimensional medium. These results are of direct relevance in the context of ventricular fibrillation - a turbulent electrical wave activity that destroys the coherent contraction of the ventricular muscle and its main pumping function leading to sudden cardiac death. While it has been proposed that the three-dimensional structure of the heart plays an important role in this type of filament turbulence, only the surface of the heart is currently accessible to experimental observation preventing the study of the full dynamics. Our results suggest that such observations might be sufficient.

  6. Order-fractal transitions in abstract paintings

    SciTech Connect

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

    2016-08-15

    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. -- Highlights: •We determined the degree of order in Jackson Pollock paintings using the Hausdorff–Besicovitch dimension. •We detected a fractal-order transition from Pollock’s paintings between 1947 and 1951. •We suggest that Jackson Pollock could have painted Teri’s Find.

  7. Power dissipation in fractal AC circuits

    NASA Astrophysics Data System (ADS)

    Chen, Joe P.; Rogers, Luke G.; Anderson, Loren; Andrews, Ulysses; Brzoska, Antoni; Coffey, Aubrey; Davis, Hannah; Fisher, Lee; Hansalik, Madeline; Loew, Stephen; Teplyaev, Alexander

    2017-08-01

    We extend Feynman’s analysis of an infinite ladder circuit to fractal circuits, providing examples in which fractal circuits constructed with purely imaginary impedances can have characteristic impedances with positive real part. Using (weak) self-similarity of our fractal structures, we provide algorithms for studying the equilibrium distribution of energy on these circuits. This extends the analysis of self-similar resistance networks introduced by Fukushima, Kigami, Kusuoka, and more recently studied by Strichartz et al.

  8. Fractal scattering of microwaves from soils.

    PubMed

    Oleschko, K; Korvin, G; Balankin, A S; Khachaturov, R V; Flores, L; Figueroa, B; Urrutia, J; Brambila, F

    2002-10-28

    Using a combination of laboratory experiments and computer simulation we show that microwaves reflected from and transmitted through soil have a fractal dimension correlated to that of the soil's hierarchic permittivity network. The mathematical model relating the ground-penetrating radar record to the mass fractal dimension of soil structure is also developed. The fractal signature of the scattered microwaves correlates well with some physical and mechanical properties of soils.

  9. Lagrangian and Hamiltonian Mechanics on Fractals Subset of Real-Line

    NASA Astrophysics Data System (ADS)

    Golmankhaneh, Alireza Khalili; Golmankhaneh, Ali Khalili; Baleanu, Dumitru

    2013-11-01

    A discontinuous media can be described by fractal dimensions. Fractal objects has special geometric properties, which are discrete and discontinuous structure. A fractal-time diffusion equation is a model for subdiffusive. In this work, we have generalized the Hamiltonian and Lagrangian dynamics on fractal using the fractional local derivative, so one can use as a new mathematical model for the motion in the fractal media. More, Poisson bracket on fractal subset of real line is suggested.

  10. Self-Oligomerizing Structure of the Flagellar Cap Protein FliD and Its Implication in Filament Assembly.

    PubMed

    Song, Wan Seok; Cho, So Yeon; Hong, Ho Jeong; Park, Sun Cheol; Yoon, Sung-Il

    2017-03-24

    FliD is a self-oligomerizing structural protein that caps the growing end of the bacterial flagellar filament. FliD also plays a key role in the flagellar system by continuously adding a new flagellin protein to the tip of the filament. To structurally characterize FliD oligomerization and to provide a FliD-mediated flagellin polymerization mechanism, we have determined the crystal structures of FliD proteins from Escherichia coli and Salmonella enterica serovar Typhimurium (ecFliD and stFliD, respectively). ecFliD consists of three domains (D1, D2, and D3) and forms a hexamer plate of the D2 and D3 domains that resembles a six-pointed star with legs consisting of the D1 domain. In contrast, the D2 and D3 domains of stFliD assemble into a pentamer as a five-pointed star plate. Despite their distinct oligomeric states, ecFliD and stFliD engage a common molecular surface for oligomerization. FliD also features interdomain and intersubunit flexibility, suggesting that FliD reorganizes its domains and adjacent subunits depending on the FliD binding partner. The similarity of the FliD shape to flagellin and the structural dynamics of FliD led us to propose a FliD-catalyzed filament elongation mechanism. In this model, FliD occupies a position in place of a nascent flagellin until the flagellin reaches the growing end of the filament, and then, FliD moves aside to repeat the positional replacement.

  11. 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.

  12. Thermal conductivity, viscosity, and electrical conductivity of iron oxide with a cloud fractal structure

    NASA Astrophysics Data System (ADS)

    Jamilpanah, Pouya; Pahlavanzadeh, Hassan; Kheradmand, Amanj

    2017-04-01

    In the present study, nanoscale iron oxide was synthesized using a hydrothermal method; XRD analysis revealed that all the produced crystals are iron oxide. FESEM microscopic imaging showed that particles are on the scale of nano and their morphology is cloud fractal. To study the laboratory properties of thermal conductivity, viscosity, and electrical conductivity of the nanoparticles, they were dispersed in ethylene glycol-based fluid and the nanofluid was in a two-step synthesis during this process. The experiments were carried out with a weight fraction between 0 and 2 % at temperatures between 25 and 45 °C. According to the results of the experiments, increasing the density of nanoparticles in the fluid increases thermal conductivity, as it was predicted in all theoretical models. On the other hand, nano viscosity increases as the weight fraction increases while it decreases as temperature goes up. Electrical conductivity also increases with raising the temperature and weight fraction. Theoretical models were studied to predict Thermal conductivity, viscosity, and electrical conductivity of the nanofluid.

  13. 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.

  14. 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.

  15. Cryo-electron microscopy structure of human peroxiredoxin-3 filament reveals the assembly of a putative chaperone.

    PubMed

    Radjainia, Mazdak; Venugopal, Hariprasad; Desfosses, Ambroise; Phillips, Amy J; Yewdall, N Amy; Hampton, Mark B; Gerrard, Juliet A; Mitra, Alok K

    2015-05-05

    Peroxiredoxins (Prxs) are a ubiquitous class of thiol-dependent peroxidases that play an important role in the protection and response of cells to oxidative stress. The catalytic unit of typical 2-Cys Prxs are homodimers, which can self-associate to form complex assemblies that are hypothesized to have signaling and chaperone activity. Mitochondrial Prx3 forms dodecameric toroids, which can further stack to form filaments, the so-called high-molecular-weight (HMW) form that has putative holdase activity. We used single-particle analysis and helical processing of electron cryomicroscopy images of human Prx3 filaments induced by low pH to generate a ∼7-Å resolution 3D structure of the HMW form, the first such structure for a 2-Cys Prx. The pseudo-atomic model reveals interactions that promote the stacking of the toroids and shows that unlike previously reported data, the structure can accommodate a partially folded C terminus. The HMW filament lumen displays hydrophobic patches, which we hypothesize bestow holdase activity.

  16. Designing Phoxonic Metamaterials with Fractal Geometry

    NASA Astrophysics Data System (ADS)

    Ni, Sisi; Koh, Cheong Yang; Kooi, Steve; Thomas, Edwin

    2012-02-01

    Recently, the concepts of fractal geometry have been introduced into electromagnetic and plasmonic metamaterials. With their self-similarity, structures based on fractal geometry should exhibit multi-band character with high Q factors due to the scaling law. However, there exist few studies of phononic metamaterials based on fractal geometry. We use COMSOL to investigate the wave propagation in two dimensional systems possessing fractal geometries. The simulations of these systems, guided by our recently developed general design framework, help to understand the role of design in determining the phononic properties of the structures. Proposed structures are being fabricated via standard lithographic or 3D printing techniques. The wave behavior of the structures can be characterized using Brillouin Light Scattering, Scanning Acoustic Microscope and Near-field Scanning Optical Microscopy. Due to their sparse spatial distribution, fractal phononic structures show potential fir ``smart skin'', where multifunctional components can be fabricated on the same platform.

  17. 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.

  18. THE THREE-DIMENSIONAL STRUCTURE OF AN ACTIVE REGION FILAMENT AS EXTRAPOLATED FROM PHOTOSPHERIC AND CHROMOSPHERIC OBSERVATIONS

    SciTech Connect

    Yelles Chaouche, L.; Kuckein, C.; Martinez Pillet, V.; Moreno-Insertis, F.

    2012-03-20

    The three-dimensional structure of an active region filament is studied using nonlinear force-free field extrapolations based on simultaneous observations at a photospheric and a chromospheric height. To that end, we used the Si I 10827 A line and the He I 10830 A triplet obtained with the Tenerife Infrared Polarimeter at the Vacuum Tower Telescope (Tenerife). The two extrapolations have been carried out independently from each other and their respective spatial domains overlap in a considerable height range. This opens up new possibilities for diagnostics in addition to the usual ones obtained through a single extrapolation from, typically, a photospheric layer. Among those possibilities, this method allows the determination of an average formation height of the He I 10830 A signal of Almost-Equal-To 2 Mm above the surface of the Sun. It allows, as well, a cross-check of the obtained three-dimensional magnetic structures to verify a possible deviation from the force-free condition, especially at the photosphere. The extrapolations yield a filament formed by a twisted flux rope whose axis is located at about 1.4 Mm above the solar surface. The twisted field lines make slightly more than one turn along the filament within our field of view, which results in 0.055 turns Mm{sup -1}. The convex part of the field lines (as seen from the solar surface) constitutes dips where the plasma can naturally be supported. The obtained three-dimensional magnetic structure of the filament depends on the choice of the observed horizontal magnetic field as determined from the 180 Degree-Sign solution of the azimuth. We derive a method to check for the correctness of the selected 180 Degree-Sign ambiguity solution.

  19. Fractal analysis of complex microstructure in castings

    SciTech Connect

    Lu, S.Z.; Lipp, D.C.; Hellawell, A.

    1995-12-31

    Complex microstructures in castings are usually characterized descriptively which often raises ambiguity and makes it difficult to relate the microstructure to the growth kinetics or mechanical properties in processing modeling. Combining the principle of fractal geometry and computer image processing techniques, it is feasible to characterize the complex microstructures numerically by the parameters of fractal dimension, D, and shape factor, a, without ambiguity. Procedures of fractal measurement and analysis are described, and a test case of its application to cast irons is provided. The results show that the irregular cast structures may all be characterized numerically by fractal analysis.

  20. Comparison of two fractal interpolation methods

    NASA Astrophysics Data System (ADS)

    Fu, Yang; Zheng, Zeyu; Xiao, Rui; Shi, Haibo

    2017-03-01

    As a tool for studying complex shapes and structures in nature, fractal theory plays a critical role in revealing the organizational structure of the complex phenomenon. Numerous fractal interpolation methods have been proposed over the past few decades, but they differ substantially in the form features and statistical properties. In this study, we simulated one- and two-dimensional fractal surfaces by using the midpoint displacement method and the Weierstrass-Mandelbrot fractal function method, and observed great differences between the two methods in the statistical characteristics and autocorrelation features. From the aspect of form features, the simulations of the midpoint displacement method showed a relatively flat surface which appears to have peaks with different height as the fractal dimension increases. While the simulations of the Weierstrass-Mandelbrot fractal function method showed a rough surface which appears to have dense and highly similar peaks as the fractal dimension increases. From the aspect of statistical properties, the peak heights from the Weierstrass-Mandelbrot simulations are greater than those of the middle point displacement method with the same fractal dimension, and the variances are approximately two times larger. When the fractal dimension equals to 1.2, 1.4, 1.6, and 1.8, the skewness is positive with the midpoint displacement method and the peaks are all convex, but for the Weierstrass-Mandelbrot fractal function method the skewness is both positive and negative with values fluctuating in the vicinity of zero. The kurtosis is less than one with the midpoint displacement method, and generally less than that of the Weierstrass-Mandelbrot fractal function method. The autocorrelation analysis indicated that the simulation of the midpoint displacement method is not periodic with prominent randomness, which is suitable for simulating aperiodic surface. While the simulation of the Weierstrass-Mandelbrot fractal function method has

  1. Modeling Fractal Structure of City-Size Distributions Using Correlation Functions

    PubMed Central

    Chen, Yanguang

    2011-01-01

    Zipf's law is one the most conspicuous empirical facts for cities, however, there is no convincing explanation for the scaling relation between rank and size and its scaling exponent. Using the idea from general fractals and scaling, I propose a dual competition hypothesis of city development to explain the value intervals and the special value, 1, of the power exponent. Zipf's law and Pareto's law can be mathematically transformed into one another, but represent different processes of urban evolution, respectively. Based on the Pareto distribution, a frequency correlation function can be constructed. By scaling analysis and multifractals spectrum, the parameter interval of Pareto exponent is derived as (0.5, 1]; Based on the Zipf distribution, a size correlation function can be built, and it is opposite to the first one. By the second correlation function and multifractals notion, the Pareto exponent interval is derived as [1, 2). Thus the process of urban evolution falls into two effects: one is the Pareto effect indicating city number increase (external complexity), and the other the Zipf effect indicating city size growth (internal complexity). Because of struggle of the two effects, the scaling exponent varies from 0.5 to 2; but if the two effects reach equilibrium with each other, the scaling exponent approaches 1. A series of mathematical experiments on hierarchical correlation are employed to verify the models and a conclusion can be drawn that if cities in a given region follow Zipf's law, the frequency and size correlations will follow the scaling law. This theory can be generalized to interpret the inverse power-law distributions in various fields of physical and social sciences. PMID:21949753

  2. Modeling fractal structure of city-size distributions using correlation functions.

    PubMed

    Chen, Yanguang

    2011-01-01

    Zipf's law is one the most conspicuous empirical facts for cities, however, there is no convincing explanation for the scaling relation between rank and size and its scaling exponent. Using the idea from general fractals and scaling, I propose a dual competition hypothesis of city development to explain the value intervals and the special value, 1, of the power exponent. Zipf's law and Pareto's law can be mathematically transformed into one another, but represent different processes of urban evolution, respectively. Based on the Pareto distribution, a frequency correlation function can be constructed. By scaling analysis and multifractals spectrum, the parameter interval of Pareto exponent is derived as (0.5, 1]; Based on the Zipf distribution, a size correlation function can be built, and it is opposite to the first one. By the second correlation function and multifractals notion, the Pareto exponent interval is derived as [1, 2). Thus the process of urban evolution falls into two effects: one is the Pareto effect indicating city number increase (external complexity), and the other the Zipf effect indicating city size growth (internal complexity). Because of struggle of the two effects, the scaling exponent varies from 0.5 to 2; but if the two effects reach equilibrium with each other, the scaling exponent approaches 1. A series of mathematical experiments on hierarchical correlation are employed to verify the models and a conclusion can be drawn that if cities in a given region follow Zipf's law, the frequency and size correlations will follow the scaling law. This theory can be generalized to interpret the inverse power-law distributions in various fields of physical and social sciences.

  3. Purification of native myosin filaments from muscle.

    PubMed Central

    Hidalgo, C; Padrón, R; Horowitz, R; Zhao, F Q; Craig, R

    2001-01-01

    Analysis of the structure and function of native thick (myosin-containing) filaments of muscle has been hampered in the past by the difficulty of obtaining a pure preparation. We have developed a simple method for purifying native myosin filaments from muscle filament suspensions. The method involves severing thin (actin-containing) filaments into short segments using a Ca(2+)-insensitive fragment of gelsolin, followed by differential centrifugation to purify the thick filaments. By gel electrophoresis, the purified thick filaments show myosin heavy and light chains together with nonmyosin thick filament components. Contamination with actin is below 3.5%. Electron microscopy demonstrates intact thick filaments, with helical cross-bridge order preserved, and essentially complete removal of thin filaments. The method has been developed for striated muscles but can also be used in a modified form to remove contaminating thin filaments from native smooth muscle myofibrils. Such preparations should be useful for thick filament structural and biochemical studies. PMID:11606293

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

    SciTech Connect

    Burin, Michael J.

    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.

  5. Forces measured with micro-fabricated cantilevers during actomyosin interactions produced by filaments containing different myosin isoforms and loop 1 structures.

    PubMed

    Kalganov, Albert; Shalabi, Nabil; Zitouni, Nedjma; Kachmar, Linda Hussein; Lauzon, Anne-Marie; Rassier, Dilson E

    2013-03-01

    There is evidence that the actin-activated ATP kinetics and the mechanical work produced by muscle myosin molecules are regulated by two surface loops, located near the ATP binding pocket (loop 1), and in a region that interfaces with actin (loop 2). These loops regulate force and velocity of contraction, and have been investigated mostly in single molecules. There is a lack of information of the work produced by myosin molecules ordered in filaments and working cooperatively, which is the actual muscle environment. We use micro-fabricated cantilevers to measure forces produced by myosin filaments isolated from mollusk muscles, skeletal muscles, and smooth muscles containing variations in the structure of loop 1 (tonic and phasic myosins). We complemented the experiments with in-vitro assays to measure the velocity of actin motility. Smooth muscle myosin filaments produced more force than skeletal and mollusk myosin filaments when normalized per filament overlap. Skeletal muscle myosin propelled actin filaments in a higher sliding velocity than smooth muscle myosin. The values for force and velocity were consistent with previous studies using myosin molecules, and suggest a close correlation with the myosin isoform and structure of surface loop 1. The technique using micro-fabricated cantilevers to measure force of filaments allows for the investigation of the relation between myosin structure and contractility, allowing experiments to be conducted with an array of different myosin isoforms. Using the technique we observed that the work produced by myosin molecules is regulated by amino-acid sequences aligned in specific loops.

  6. Is the applicability of fractal statistics to sedimentary structures the result of scale-invariant stochastic processes or deterministic chaos

    SciTech Connect

    Turcotte, D.L. )

    1991-03-01

    Fractal statistics are the only statistics that are scale invariant. Examples in tectonics include distributions of faults, displacements on faults, distributions and permeabilities of fractures, and distributions of folds. Many aspects of sedimentology are also fractal including distributions of sedimentary sequences, variations in permeability, and shapes of boundaries. Since the underlying processes are likely to be scale invariant, it is reasonable to conclude that the number-size statistics of oil fields will be fractal. Log-normal statistics are often applied; they are not scale invariant. Two explanations for fractal statistics can be given. They may be the result of scale-invariant stochastic processes. Random walk (Brownian noise) is one example. Topography generally resembles Brownian noise, a power-law spectrum with fractal dimension D = 1.5. Alternatively fractal statistics can be the result of deterministic chaos. Turbulent flows are examples of deterministic chaos, the governing equations are deterministic but the resulting flows are statistical. Tectonic displacements can be shown to be the result of deterministic chaos; it is likely that erosion is another example.

  7. Photosynthesis irradiance parameters and community structure associated with coastal filaments and adjacent waters in the northern Arabian Sea

    NASA Astrophysics Data System (ADS)

    Toon, Rory K.; Lohrenz, Steven E.; Rathbun, Catherine E.; Michelle Wood, A.; Arnone, Robert A.; Jones, Burton H.; Kindle, John C.; Weidemann, Alan D.

    Comparisons were made among size-fractionated photosynthesis-irradiance ( P- E) parameters, chlorophyll a size distributions, and accessory pigment composition of natural phytoplankton assemblages in filaments, coastal upwelling waters, and an oligotrophic region of the northern Arabian Sea during the Fall Intermonsoon in 1995. Differences between P- E parameters, PBmax and αB, were observed between filaments and adjacent waters and were associated with differences in phytoplankton community structure. In a southern filament and coastal upwelled waters, the majority of the estimated biomass (chlorophyll a) was present in the larger (2-20 and 20-200 μm) size fractions; dominant accessory pigments were 19'-butanoyloxyfucoxanthin and peridinin. In higher salinity waters, high percentages of chlorophyll a and lutein/zeaxanthin were observed in the smallest size-fraction (<2 μm). Whole water values of PBmax ranged from 1.77 to 2.31 (g C g chl a-1 h -1) when the majority of the biomass was in the largest fractions. Higher values (more than 4.48 g C g chl a-1 h -1) were determined in whole water samples for communities comprised primarily of small cells. A size dependence was also observed in the value of αB, 0.017 or greater (g C g chl a-1 h -1)/(μmol quanta m -2 s -1) for whole water samples at stations dominated by small cells and 0.013 when derived from stations dominated by large cells. The observed pattern of larger phytoplankton associated with upwelling and filament waters was consistent with previous investigations and was, for the most part, comparable to findings in the California Current system. Our results show that differences in taxonomic composition and photosynthetic characteristics were indeed present between filament waters and other distinct regions; these results suggest that taxonomic variations may be associated with size-related variations in P- E parameters. Our findings provide a unique data set describing filament biology in the northern

  8. Atomic structure of the vimentin central α-helical domain and its implications for intermediate filament assembly.

    PubMed

    Chernyatina, Anastasia A; Nicolet, Stefan; Aebi, Ueli; Herrmann, Harald; Strelkov, Sergei V

    2012-08-21

    Together with actin filaments and microtubules, intermediate filaments (IFs) are the basic cytoskeletal components of metazoan cells. Over 80 human diseases have been linked to mutations in various IF proteins to date. However, the filament structure is far from being resolved at the atomic level, which hampers rational understanding of IF pathologies. The elementary building block of all IF proteins is a dimer consisting of an α-helical coiled-coil (CC) "rod" domain flanked by the flexible head and tail domains. Here we present three crystal structures of overlapping human vimentin fragments that comprise the first half of its rod domain. Given the previously solved fragments, a nearly complete atomic structure of the vimentin rod has become available. It consists of three α-helical segments (coils 1A, 1B, and 2) interconnected by linkers (L1 and L12). Most of the CC structure has a left-handed twist with heptad repeats, but both coil 1B and coil 2 also exhibit untwisted, parallel stretches with hendecad repeats. In the crystal structure, linker L1 was found to be α-helical without being involved in the CC formation. The available data allow us to construct an atomic model of the antiparallel tetramer representing the second level of vimentin assembly. Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.

  9. Specific Glucoside Transporters Influence Septal Structure and Function in the Filamentous, Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120.

    PubMed

    Nieves-Morión, Mercedes; Lechno-Yossef, Sigal; López-Igual, Rocío; Frías, José E; Mariscal, Vicente; Nürnberg, Dennis J; Mullineaux, Conrad W; Wolk, C Peter; Flores, Enrique

    2017-04-01

    When deprived of combined nitrogen, some filamentous cyanobacteria contain two cell types: vegetative cells that fix CO2 through oxygenic photosynthesis and heterocysts that are specialized in N2 fixation. In the diazotrophic filament, the vegetative cells provide the heterocysts with reduced carbon (mainly in the form of sucrose) and heterocysts provide the vegetative cells with combined nitrogen. Septal junctions traverse peptidoglycan through structures known as nanopores and appear to mediate intercellular molecular transfer that can be traced with fluorescent markers, including the sucrose analog esculin (a coumarin glucoside) that is incorporated into the cells. Uptake of esculin by the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 was inhibited by the α-glucosides sucrose and maltose. Analysis of Anabaena mutants identified components of three glucoside transporters that move esculin into the cells: GlsC (Alr4781) and GlsP (All0261) are an ATP-binding subunit and a permease subunit of two different ABC transporters, respectively, and HepP (All1711) is a major facilitator superfamily (MFS) protein that was shown previously to be involved in formation of the heterocyst envelope. Transfer of fluorescent markers (especially calcein) between vegetative cells of Anabaena was impaired by mutation of glucoside transporter genes. GlsP and HepP interact in bacterial two-hybrid assays with the septal junction-related protein SepJ, and GlsC was found to be necessary for the formation of a normal number of septal peptidoglycan nanopores and for normal subcellular localization of SepJ. Therefore, beyond their possible role in nutrient uptake in Anabaena, glucoside transporters influence the structure and function of septal junctions.IMPORTANCE Heterocyst-forming cyanobacteria have the ability to perform oxygenic photosynthesis and to assimilate atmospheric CO2 and N2 These organisms grow as filaments that fix these gases specifically in vegetative

  10. Specific Glucoside Transporters Influence Septal Structure and Function in the Filamentous, Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120

    PubMed Central

    Nieves-Morión, Mercedes; Lechno-Yossef, Sigal; López-Igual, Rocío; Frías, José E.; Mariscal, Vicente; Nürnberg, Dennis J.; Mullineaux, Conrad W.; Wolk, C. Peter

    2017-01-01

    ABSTRACT When deprived of combined nitrogen, some filamentous cyanobacteria contain two cell types: vegetative cells that fix CO2 through oxygenic photosynthesis and heterocysts that are specialized in N2 fixation. In the diazotrophic filament, the vegetative cells provide the heterocysts with reduced carbon (mainly in the form of sucrose) and heterocysts provide the vegetative cells with combined nitrogen. Septal junctions traverse peptidoglycan through structures known as nanopores and appear to mediate intercellular molecular transfer that can be traced with fluorescent markers, including the sucrose analog esculin (a coumarin glucoside) that is incorporated into the cells. Uptake of esculin by the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 was inhibited by the α-glucosides sucrose and maltose. Analysis of Anabaena mutants identified components of three glucoside transporters that move esculin into the cells: GlsC (Alr4781) and GlsP (All0261) are an ATP-binding subunit and a permease subunit of two different ABC transporters, respectively, and HepP (All1711) is a major facilitator superfamily (MFS) protein that was shown previously to be involved in formation of the heterocyst envelope. Transfer of fluorescent markers (especially calcein) between vegetative cells of Anabaena was impaired by mutation of glucoside transporter genes. GlsP and HepP interact in bacterial two-hybrid assays with the septal junction-related protein SepJ, and GlsC was found to be necessary for the formation of a normal number of septal peptidoglycan nanopores and for normal subcellular localization of SepJ. Therefore, beyond their possible role in nutrient uptake in Anabaena, glucoside transporters influence the structure and function of septal junctions. IMPORTANCE Heterocyst-forming cyanobacteria have the ability to perform oxygenic photosynthesis and to assimilate atmospheric CO2 and N2. These organisms grow as filaments that fix these gases specifically in

  11. Use of a fusion protein between GFP and an actin-binding domain to visualize transient filamentous-actin structures.

    PubMed

    Pang, K M; Lee, E; Knecht, D A

    1998-03-26

    Many important processes in eukaryotic cells involve changes in the quantity, location and the organization of actin filaments [1] [2] [3]. We have been able to visualize these changes in live cells using a fusion protein (GFP-ABD) comprising the green fluorescent protein (GFP) of Aequorea victoria and the 25 kDa highly conserved actin-binding domain (ABD) from the amino terminus of the actin cross-linking protein ABP-120 [4]. In live cells of the soil amoeba Dictyostelium that were expressing GFP-ABD, the three-dimensional architecture of the actin cortex was clearly visualized. The pattern of GFP-ABD fluorescence in these cells coincided with that of rhodamine-phalloidin, indicating that GFP-ABD specifically binds filamentous (F) actin. On the ventral surface of non-polarized vegetative cells, a broad ring of F actin periodically assembled and contracted, whereas in polarized cells there were transient punctate F-actin structures; cells cycled between the polarized and non-polarized morphologies. During the formation of pseudopods, an increase in fluorescence intensity coincided with the initial outward deformation of the membrane. This is consistent with the models of pseudopod extension that predict an increase in the local density of actin filaments. In conclusion, GFP-ABD specifically binds F actin and allows the visualization of F-actin dynamics and cellular behavior simultaneously.

  12. Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Å resolution

    PubMed Central

    Hu, Zhongjun; Taylor, Dianne W.; Reedy, Michael K.; Edwards, Robert J.; Taylor, Kenneth A.

    2016-01-01

    We describe a cryo–electron microscopy three-dimensional image reconstruction of relaxed myosin II–containing thick filaments from the flight muscle of the giant water bug Lethocerus indicus. The relaxed thick filament structure is a key element of muscle physiology because it facilitates the reextension process following contraction. Conversely, the myosin heads must disrupt their relaxed arrangement to drive contraction. Previous models predicted that Lethocerus myosin was unique in having an intermolecular head-head interaction, as opposed to the intramolecular head-head interaction observed in all other species. In contrast to the predicted model, we find an intramolecular head-head interaction, which is similar to that of other thick filaments but oriented in a distinctly different way. The arrangement of myosin’s long α-helical coiled-coil rod domain has been hypothesized as either curved layers or helical subfilaments. Our reconstruction is the first report having sufficient resolution to track the rod α helices in their native environment at resolutions ~5.5 Å, and it shows that the layer arrangement is correct for Lethocerus. Threading separate paths through the forest of myosin coiled coils are four nonmyosin peptides. We suggest that the unusual position of the heads and the rod arrangement separated by nonmyosin peptides are adaptations for mechanical signal transduction whereby applied tension disrupts the myosin heads as a component of stretch activation. PMID:27704041

  13. The complexity and fractal structures of CSI300 before and after the introduction of CSI300IF

    NASA Astrophysics Data System (ADS)

    He, Xiaoli; Wang, Hongwu; Du, Ziping

    2014-11-01

    This paper employs multifractal detrended fluctuation analysis (MF-DFA) approach to analyze the complexity and fractal structures of China Securities Index 300 (CSI300), which covers the period from April 5, 2006 to May 9, 2014. Through comparing the statistic properties before and after the introduction of CSI300 index futures (CSI300IF), we find that: (1) the price return series exhibits multifractal properties for the two periods; (2) by comparing the efficient measure based on the general Hurst exponent, we find the market becomes more efficient after the introduction of CSI300IF; (3) the width of multifractal spectrum becomes narrower, which means the complexity of the market is decreased. Therefore, the introduction of CSI300IF is beneficial to reduce the risk and increase the efficiency of Chinese securities market. Furthermore, the main sources of multifractality of these time series are examined through the shuffle method, and the results show that before CSI300IF the multifractality is mainly due to the long-range correlation properties between small and large fluctuations, while after CSI300IF it is more due to fat-tailed probability distributions.

  14. Structure of the coat protein in fd filamentous bacteriophage particles determined by solid-state NMR spectroscopy

    PubMed Central

    Zeri, Ana Carolina; Mesleh, Michael F.; Nevzorov, Alexander A.; Opella, Stanley J.

    2003-01-01

    The atomic resolution structure of fd coat protein determined by solid-state NMR spectroscopy of magnetically aligned filamentous bacteriophage particles differs from that previously determined by x-ray fiber diffraction. Most notably, the 50-residue protein is not a single curved helix, but rather is a nearly ideal straight helix between residues 7 and 38, where there is a distinct kink, and then a straight helix with a different orientation between residues 39 and 49. Residues 1–5 have been shown to be mobile and unstructured, and proline 6 terminates the helix. The structure of the coat protein in virus particles, in combination with the structure of the membrane-bound form of the same protein in bilayers, also recently determined by solid-state NMR spectroscopy, provides insight into the viral assembly process. In addition to their roles in molecular biology and biotechnology, the filamentous bacteriophages continue to serve as model systems for the development of experimental methods for determining the structures of proteins in biological supramolecular assemblies. New NMR results include the complete sequential assignment of the two-dimensional polarization inversion spin-exchange at the magic angle spectrum of a uniformly 15N-labeled 50-residue protein in a 1.6 × 107 Da particle in solution, and the calculation of the three-dimensional structure of the protein from orientational restraints with an accuracy equivalent to an rms deviation of ≈1Å. PMID:12750469

  15. The Sun-Earth connect 2: Modelling patterns of a fractal Sun in time and space using the fine structure constant

    NASA Astrophysics Data System (ADS)

    Baker, Robert G. V.

    2017-02-01

    Self-similar matrices of the fine structure constant of solar electromagnetic force and its inverse, multiplied by the Carrington synodic rotation, have been previously shown to account for at least 98% of the top one hundred significant frequencies and periodicities observed in the ACRIM composite irradiance satellite measurement and the terrestrial 10.7cm Penticton Adjusted Daily Flux data sets. This self-similarity allows for the development of a time-space differential equation (DE) where the solutions define a solar model for transmissions through the core, radiative, tachocline, convective and coronal zones with some encouraging empirical and theoretical results. The DE assumes a fundamental complex oscillation in the solar core and that time at the tachocline is smeared with real and imaginary constructs. The resulting solutions simulate for tachocline transmission, the solar cycle where time-line trajectories either 'loop' as Hermite polynomials for an active Sun or 'tail' as complementary error functions for a passive Sun. Further, a mechanism that allows for the stable energy transmission through the tachocline is explored and the model predicts the initial exponential coronal heating from nanoflare supercharging. The twisting of the field at the tachocline is then described as a quaternion within which neutrinos can oscillate. The resulting fractal bubbles are simulated as a Julia Set which can then aggregate from nanoflares into solar flares and prominences. Empirical examples demonstrate that time and space fractals are important constructs in understanding the behaviour of the Sun, from the impact on climate and biological histories on Earth, to the fractal influence on the spatial distributions of the solar system. The research suggests that there is a fractal clock underpinning solar frequencies in packages defined by the fine structure constant, where magnetic flipping and irradiance fluctuations at phase changes, have periodically impacted on the

  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. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Structure and Mutational Analyses of Escherichia coli ZapD Reveal Charged Residues Involved in FtsZ Filament Bundling

    PubMed Central

    Roach, Elyse J.; Wroblewski, Charles; Seidel, Laura; Berezuk, Alison M.; Brewer, Dyanne; Kimber, Matthew S.

    2016-01-01

    ABSTRACT Bacterial cell division is an essential and highly coordinated process. It requires the polymerization of the tubulin homologue FtsZ to form a dynamic ring (Z-ring) at midcell. Z-ring formation relies on a group of FtsZ-associated proteins (Zap) for stability throughout the process of division. In Escherichia coli, there are currently five Zap proteins (ZapA through ZapE), of which four (ZapA, ZapB, ZapC, and ZapD) are small soluble proteins that act to bind and bundle FtsZ filaments. In particular, ZapD forms a functional dimer and interacts with the C-terminal tail of FtsZ, but little is known about its structure and mechanism of action. Here, we present the crystal structure of Escherichia coli ZapD and show it forms a symmetrical dimer with centrally located α-helices flanked by β-sheet domains. Based on the structure of ZapD and its chemical cross-linking to FtsZ, we targeted nine charged ZapD residues for modification by site-directed mutagenesis. Using in vitro FtsZ sedimentation assays, we show that residues R56, R221, and R225 are important for bundling FtsZ filaments, while transmission electron microscopy revealed that altering these residues results in different FtsZ bundle morphology compared to those of filaments bundled with wild-type ZapD. ZapD residue R116 also showed altered FtsZ bundle morphology but levels of FtsZ bundling similar to that of wild-type ZapD. Together, these results reveal that ZapD residues R116, R221, and R225 likely participate in forming a positively charged binding pocket that is critical for bundling FtsZ filaments. IMPORTANCE Z-ring assembly underpins the formation of the essential cell division complex known as the divisome and is required for recruitment of downstream cell division proteins. ZapD is one of several proteins in E. coli that associates with the Z-ring to promote FtsZ bundling and aids in the overall fitness of the division process. In the present study, we describe the dimeric structure of E. coli

  2. Investigation of the Near Wake Flow Structure of a Fractal Square Turbulence Grid using Particle Image Velocimetry

    NASA Astrophysics Data System (ADS)

    Uzol, Oguz; Hazaveh, Hooman Amiri

    2016-11-01

    The 3D flow structure within the near wake of a four-iteration fractal square turbulence grid is obtained by combining data from closely-spaced horizontal and vertical two-dimensional PIV measurement planes. For this purpose, the grid is placed inside the entrance of the test section of a suction type wind tunnel. The experiments are conducted at a freestream velocity of 8 m/s, corresponding to a Reynolds number of 9000 based on effective mesh size. The freestream turbulence intensity is about 0.5%. The measurement volume extends about 7 effective mesh sizes downstream of the grid. Within the measurement volume, 1000 vector maps are obtained on each one of the 220 horizontal and 220 vertical 2D PIV planes that are separated from each other by 500 microns, which is close to the in-plane vector spacing of 600 microns. This dataset allowed us to calculate all components of mean velocity, velocity gradient tensor, and vorticity as well as the Reynolds stress tensor except for (v'w') component. Using the analyzed three-dimensional mean flow field data, we are able to observe the three dimensional structure of the wakes of the largest bars that dominate the flow field and the corresponding turbulence generation characteristics. We focus on how the wake geometry, decay characteristics and stress-strain relations get impacted by the presence of smaller wakes surrounding the largest wake regions. We also investigate how 3D mean flow non-uniformities get generated downstream of the grid such as lateral contraction and bulging of mean wake shapes.

  3. Fractal dimension assessment of brain white matter structural complexity post stroke in relation to upper-extremity motor function

    PubMed Central

    Zhang, Luduan; Butler, Andrew J.; Sun, Chang-Kai; Sahgal, Vinod; Wittenberg, George F.; Yue, Guang H.

    2008-01-01

    Little is known about the association between brain white matter (WM) structure and motor function in humans. This study investigated complexity of brain WM interior shape as determined by magnetic resonance imaging (MRI) and its relationship with upper-extremity (UE) motor function in patients post stroke. We hypothesized that (1) the WM complexity would decrease following stroke, and (2) higher WM complexity in non-affected cortical areas would be related to greater UE motor function. Thirty-eight stroke patients (16 with left-hemisphere lesions) underwent MRI anatomical brain scans. Fractal dimension (FD), a quantitative shape metric, was applied onto skeletonized brain WM images to evaluate WM internal structural complexity. Wolf Motor Function Test (WMFT) and Fugl-Meyer Motor Assessment (FM) scores were measured to assess motor function of the affected limb. The WM complexity was lower in the stroke-affected hemisphere. The FD was associated with better motor function in two subgroups: with left-subcortical lesions, FD values of the lesion-free areas of the left hemisphere were associated with better FM scores; with right-cortical lesions, FD values of lesion-free regions were robustly associated with better WMFT scores. These findings suggest that greater residual WM complexity is associated with less impaired UE motor function, which is more robust in patients with right-hemisphere lesions. No correlations were found between lesion volume and WMFT or FM scores. This study addressed WM complexity in stroke patients and its relationship with UE motor function. Measurement of brain WM reorganization may be a sensitive correlate of UE function in people recovering from stroke. PMID:18590710

  4. Structures of actin-bound Wiskott-Aldrich syndrome protein homology 2 (WH2) domains of Spire and the implication for filament nucleation

    PubMed Central

    Ducka, Anna M.; Joel, Peteranne; Popowicz, Grzegorz M.; Trybus, Kathleen M.; Schleicher, Michael; Noegel, Angelika A.; Huber, Robert; Holak, Tad A.; Sitar, Tomasz

    2010-01-01

    Three classes of proteins are known to nucleate new filaments: the Arp2/3 complex, formins, and the third group of proteins that contain ca. 25 amino acid long actin-binding Wiskott-Aldrich syndrome protein homology 2 domains, called the WH2 repeats. Crystal structures of the complexes between the actin-binding WH2 repeats of the Spire protein and actin were determined for the Spire single WH2 domain D, the double (SpirCD), triple (SpirBCD), quadruple (SpirABCD) domains, and an artificial Spire WH2 construct comprising three identical D repeats (SpirDDD). SpirCD represents the minimal functional core of Spire that can nucleate actin filaments. Packing in the crystals of the actin complexes with SpirCD, SpirBCD, SpirABCD, and SpirDDD shows the presence of two types of assemblies, “side-to-side” and “straight-longitudinal,” which can serve as actin filament nuclei. The principal feature of these structures is their loose, open conformations, in which the sides of actins that normally constitute the inner interface core of a filament are flipped inside out. These Spire structures are distant from those seen in the filamentous nuclei of Arp2/3, formins, and in the F-actin filament. PMID:20538977

  5. 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.

  6. Resistance Scaling Factor of the Pillow and Fractalina Fractals

    NASA Astrophysics Data System (ADS)

    Ignatowich, Michael J.; Kelleher, Daniel J.; Maloney, Catherine E.; Miller, David J.; Serhiyenko, Khrystyna

    2015-04-01

    Much is known in the analysis of a finitely ramified self-similar fractal when the fractal has a harmonic structure: a Dirichlet form which respects the self-similarity of a fractal. What is still an open question is when such a structure exists in general. In this paper, we introduce two fractals, the fractalina and the pillow, and compute their resistance scaling factor. This is the factor which dictates how the Dirichlet form scales with the self-similarity of the fractal. By knowing this factor one can compute the harmonic structure on the fractal. The fractalina has scaling factor (3+√ {41})/16, and the pillow fractal has scaling factor 1/√ [3]{2}.

  7. Fractals for physicians.

    PubMed

    Thamrin, Cindy; Stern, Georgette; Frey, Urs

    2010-06-01

    There is increasing interest in the study of fractals in medicine. In this review, we provide an overview of fractals, of techniques available to describe fractals in physiological data, and we propose some reasons why a physician might benefit from an understanding of fractals and fractal analysis, with an emphasis on paediatric respiratory medicine where possible. Among these reasons are the ubiquity of fractal organisation in nature and in the body, and how changes in this organisation over the lifespan provide insight into development and senescence. Fractal properties have also been shown to be altered in disease and even to predict the risk of worsening of disease. Finally, implications of a fractal organisation include robustness to errors during development, ability to adapt to surroundings, and the restoration of such organisation as targets for intervention and treatment. Copyright 2010 Elsevier Ltd. All rights reserved.

  8. 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)

  9. 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)

  10. 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)

  11. 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)

  12. Filamentous Structures Induced by a Phytoreovirus Mediate Viral Release from Salivary Glands in Its Insect Vector.

    PubMed

    Mao, Qianzhuo; Liao, Zhenfeng; Li, Jiajia; Liu, Yuyan; Wu, Wei; Chen, Hongyan; Chen, Qian; Jia, Dongsheng; Wei, Taiyun

    2017-06-15

    Numerous viral pathogens are persistently transmitted by insect vectors and cause agricultural or health problems. These viruses circulate in the vector body, enter the salivary gland, and then are released into the apical plasmalemma-lined cavities, where saliva is stored. The cavity plasmalemma of vector salivary glands thus represents the last membrane barrier for viral transmission. Here, we report a novel mechanism used by a persistent virus to overcome this essential barrier. We observed that the infection by rice gall dwarf virus (RGDV), a species of the genus Phytoreovirus in the family Reoviridae, induced the formation of virus-associated filaments constructed by viral nonstructural protein Pns11 within the salivary glands of its leafhopper vector, Recilia dorsalis Such filaments attached to actin-based apical plasmalemma and induced an exocytosis-like process for viral release into vector salivary gland cavities, through a direct interaction of Pns11 of RGDV and actin of R. dorsalis Failure of virus-induced filaments assembly by RNA interference with synthesized double-stranded RNA targeting the Pns11 gene inhibited the dissemination of RGDV into salivary cavities, preventing viral transmission by R. dorsalis For the first time, we show that a virus can exploit virus-induced inclusion as a vehicle to pass through the apical plasmalemma into vector salivary gland cavities, thus overcoming the last membrane barrier for viral transmission by insect vectors.IMPORTANCE Understanding how persistent viruses overcome multiple tissue and membrane barriers within the insect vectors until final transmission is the key for viral disease control. The apical plasmalemma of the cavities where saliva is stored in the salivary glands is the last barrier for viral transmission by insect vectors; however, the mechanism is still poorly understood. Here we show that a virus has evolved to exploit virus-induced filaments to perform an exocytosis-like process that enables viral

  13. Fractal aggregates in Titan's atmosphere

    NASA Astrophysics Data System (ADS)

    Cabane, M.; Rannou, P.; Chassefiere, E.; Israel, G.

    1993-04-01

    The cluster structure of Titan's atmosphere was modeled by using an Eulerian microphysical model with the specific formulation of microphysical laws applying to fractal particles. The growth of aggregates in the settling phase was treated by introducing the fractal dimension as a parameter of the model. The model was used to obtain a vertical distribution of size and number density of the aggregates for different production altitudes. Results confirm previous estimates of the formation altitude of photochemical aerosols. The vertical profile of the effective radius of aggregates was calculated as a function of the visible optical depth.

  14. Designing fractal nanostructured biointerfaces for biomedical applications.

    PubMed

    Zhang, Pengchao; Wang, Shutao

    2014-06-06

    Fractal structures in nature offer a unique "fractal contact mode" that guarantees the efficient working of an organism with an optimized style. Fractal nanostructured biointerfaces have shown great potential for the ultrasensitive detection of disease-relevant biomarkers from small biomolecules on the nanoscale to cancer cells on the microscale. This review will present the advantages of fractal nanostructures, the basic concept of designing fractal nanostructured biointerfaces, and their biomedical applications for the ultrasensitive detection of various disease-relevant biomarkers, such microRNA, cancer antigen 125, and breast cancer cells, from unpurified cell lysates and the blood of patients. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. 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.

  16. Fractal interpretation of intermittency

    SciTech Connect

    Hwa, R.C.

    1991-12-01

    Implication of intermittency in high-energy collisions is first discussed. Then follows a description of the fractal interpretation of intermittency. A basic quantity with asymptotic fractal behavior is introduced. It is then shown how the factorial moments and the G moments can be expressed in terms of it. The relationship between the intermittency indices and the fractal indices is made explicit.

  17. 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.…

  18. 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.…

  19. Fresnel diffraction of fractal grating and self-imaging effect.

    PubMed

    Wang, Junhong; Zhang, Wei; Cui, Yuwei; Teng, Shuyun

    2014-04-01

    Based on the self-similarity property of fractal, two types of fractal gratings are produced according to the production and addition operations of multiple periodic gratings. Fresnel diffractions of fractal grating are analyzed theoretically, and the general mathematic expressions of the diffraction intensity distributions of fractal grating are deduced. The gray-scale patterns of the 2D diffraction distributions of fractal grating are provided through numerical calculations. The diffraction patterns take on the periodicity along the longitude and transverse directions. The 1D diffraction distribution at some certain distances shows the same structure as the fractal grating. This indicates that the self-image of fractal grating is really formed in the Fresnel diffraction region. The experimental measurement of the diffraction intensity distribution of fractal grating with different fractal dimensions and different fractal levels is performed, and the self-images of fractal grating are obtained successfully in experiments. The conclusions of this paper are helpful for the development of the application of fractal grating.

  20. Structural Analysis of Human Cofilin 2/Filamentous Actin Assemblies: Atomic-Resolution Insights from Magic Angle Spinning NMR Spectroscopy

    PubMed Central

    Yehl, Jenna; Kudryashova, Elena; Reisler, Emil; Kudryashov, Dmitri; Polenova, Tatyana

    2017-01-01

    Cellular actin dynamics is an essential element of numerous cellular processes, such as cell motility, cell division and endocytosis. Actin’s involvement in these processes is mediated by many actin-binding proteins, among which the cofilin family plays unique and essential role in accelerating actin treadmilling in filamentous actin (F-actin) in a nucleotide-state dependent manner. Cofilin preferentially interacts with older filaments by recognizing time-dependent changes in F-actin structure associated with the hydrolysis of ATP and release of inorganic phosphate (Pi) from the nucleotide cleft of actin. The structure of cofilin on F-actin and the details of the intermolecular interface remain poorly understood at atomic resolution. Here we report atomic-level characterization by magic angle spinning (MAS) NMR of the muscle isoform of human cofilin 2 (CFL2) bound to F-actin. We demonstrate that resonance assignments for the majority of atoms are readily accomplished and we derive the intermolecular interface between CFL2 and F-actin. The MAS NMR approach reported here establishes the foundation for atomic-resolution characterization of a broad range of actin-associated proteins bound to F-actin. PMID:28303963

  1. 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.

  2. 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.

  3. The organization of the wall filaments and characterization of the matrix structures of Toxoplasma gondii cyst form.

    PubMed

    Lemgruber, Leandro; Lupetti, Pietro; Martins-Duarte, Erica S; De Souza, Wanderley; Vommaro, Rossiane C

    2011-12-01

    The encystation process is a key step in Toxoplasma gondii life cycle, allowing the parasite to escape from the host immune system and the transmission among the hosts. A detailed characterization of the formation and structure of the cyst stage is essential for a better knowledge of toxoplasmosis. Here we isolated cysts from mice brains and analysed the cyst wall structure and cyst matrix organization using different electron microscopy techniques. Images obtained showed that the cyst wall presented a filamentous aspect, with circular openings on its surface. The filaments were organized in two layers: a compact one, facing the exterior of the whole cyst and a more loosen one, facing the matrix. Within the cyst wall, we observed tubules and a large number of vesicles. The cyst matrix presented vesicles of different sizes and tubules, which were organized in a network connecting the bradyzoites to each other and to the cyst wall. Large vesicles, with a granular material in their lumen of glycidic nature were observed. Similar vesicles were also found associated with the posterior pole of the bradyzoites and in proximity to the cyst wall. © 2011 Blackwell Publishing Ltd.

  4. Localization and fractal spectra of optical phonon modes in quasiperiodic structures

    NASA Astrophysics Data System (ADS)

    Anselmo, D. H. A. L.; Dantas, A. L.; Medeiros, S. K.; Albuquerque, E. L.; Freire, V. N.

    2005-04-01

    The dispersion relation and localization profile of confined optical phonon modes in quasiperiodic structures, made up of nitride semiconductor materials, are analyzed through a transfer-matrix approach. The quasiperiodic structures are characterized by the nature of their Fourier spectrum, which can be dense pure point (Fibonacci sequences) or singular continuous (Thue-Morse and Double-period sequences). These substitutional sequences are described in terms of a series of generations that obey peculiar recursion relations and/or inflation rules. We present a quantitative analysis of the localization and magnitude of the allowed band widths in the optical phonons spectra of these quasiperiodic structures, as well as how they scale as a function of the number of generations of the sequences.

  5. Fractal bimetallic plasmonic structures obtained by laser deposition of colloidal nanoparticles

    NASA Astrophysics Data System (ADS)

    Bukharov, D. N.; Arakelyan, S. M.; Kutrovskaya, S. V.; Kucherik, A. O.; Osipov, A. V.; Istratov, A. V.; Vartanyan, T. A.; Itina, T. E.; Kavokin, A. V.

    2017-09-01

    We produce bimetallic Au:Ag thin films by laser irradiation of the mixed solutions. After several laser scans, granular nanometric films are found to grow with a well-controlled composition, thickness and morphology. By changing laser scanning parameters, the film morphology can be varied from island structures to quasi-periodic arrays. The optical properties of the deposited structures are found to depend on the film composition, thickness and spacing between the particles. The transmittance spectra of the deposited films are shown to be governed by their morphology.

  6. The nano-fractal structured tungsten oxides films with high thermal stability prepared by the deposition of size-selected W clusters

    NASA Astrophysics Data System (ADS)

    Park, Eun Ji; Dollinger, Andreas; Huether, Lukas; Blankenhorn, Moritz; Koehler, Kerstine; Seo, Hyun Ook; Kim, Young Dok; Gantefoer, Gerd

    2017-06-01

    Size-selected W n - clusters ( n = 1650) were deposited on the highly ordered pyrolytic graphite surface at room temperature under high vacuum conditions by utilizing a magnetron sputtering source and a magnet sector field. Moreover, geometrical structure and surface chemical states of deposited clusters were analyzed by in situ scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy, respectively. The formation of 2-D islands (lateral size 150 nm) with multiple dendritic arms was observed by STM, and the structure of the individual W1650 clusters survived within the dendritic arms. To study the thermal stability of the nano-fractal structure under the atmospheric conditions, the sample was brought to the ambient air conditions and sequentially post-annealed at 200, 300, and 500 °C in the air. The nano-fractal structure was maintained after the 1st post-annealing process at 200 °C for 1 h in the air, and the subsequent 2nd post-annealing at 300 °C (for 1 h, in the air) also did not induce any noticeable change in the topological structure of the sample. The topological changes were observed only after the further post-annealing at a higher temperature (at 500 °C, 1 h) in the air. We show high potential use of these nano-structured films of tungsten oxides in ambient conditions.

  7. [Chaos and fractals and their applications in electrocardial signal research].

    PubMed

    Jiao, Qing; Guo, Yongxin; Zhang, Zhengguo

    2009-06-01

    Chaos and fractals are ubiquitous phenomena of nature. A system with fractal structure usually behaves chaos. As a complicated nonlinear dynamics system, heart has fractals structure and behaves as chaos. The deeper inherent mechanism of heart can be opened out when the chaos and fractals theory is utilized in the research of the electrical activity of heart. Generally a time series of a system was used for describing the status of the strange attractor of the system. The indices include Poincare plot, fractals dimension, Lyapunov exponent, entropy, scaling exponent, Hurst index and so on. In this article, the basic concepts and the methods of chaos and fractals were introduced firstly. Then the applications of chaos and fractals theories in the study of electrocardial signal were expounded with example of how they are used for ventricular fibrillation.

  8. 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.

  9. 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

  10. Spectral scalability and optical spectra of fractal multilayer structures: FDTD analysis

    NASA Astrophysics Data System (ADS)

    Simsek, Sevket; Palaz, Selami; Mamedov, Amirullah M.; Ozbay, Ekmel

    2017-01-01

    An investigation of the optical properties and band structures for the conventional and Fibonacci photonic crystals (PCs) based on SrTiO3 and Sb2Te3 is made in the present research. Here, we use one-dimensional SrTiO3- and Sb2Te3-based layers. We have theoretically calculated the photonic band structure and transmission spectra of SrTiO3- and Sb2Te3-based PC superlattices. The position of minima in the transmission spectrum correlates with the gaps obtained in the calculation. The intensity of the transmission depths is more intense in the case of higher refractive index contrast between the layers.

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

    PubMed

    Bernardes, Natalia E; Takeda, Agnes A S; 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.

  12. 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

  13. Structural analysis of RecA protein-DNA complexes by fluorescence-detected linear dichroism: absence of structural change of filament for pairing of complementary DNA strands.

    PubMed

    Morimatsu, Katsumi; Takahashi, Masayuki

    2006-11-15

    We have developed a simple measuring system for fluorescence-detected linear dichroism and applied it to the structural analysis of the RecA-DNA complex filaments, which are intermediates of the homologous recombination reaction. Taking advantage of the selectivity of fluorescence signals, we distinguished the linear dichroism signals of ethidium bromide and tryptophan residues in the RecA-DNA-ethidium bromide complex, whereas the conventional (absorption-detected) linear dichroism measurement provides only the sum of the signals because signals overlap each other and that of DNA. We further observed that the tryptophan residue at position 290 of RecA in the RecA-DNA-adenosine-5'-O-(3-thiotriphosphate) complex was oriented parallel to the long axis of the filament, in good agreement with the previous site-specific linear dichroism analysis, and that this orientation was not significantly modified by the pairing of the complementary DNA strand. These results suggest that the pairing reaction occurs without a large structural change of the RecA filament.

  14. Characterization of HI Filaments

    NASA Astrophysics Data System (ADS)

    Lubar, Emily; Verschuur, Gerrit L.

    2017-01-01

    We characterized the properties of dramatic interstellar HI filaments to learn more about the dynamics and structure of such features. Using Gauss fitting software, we searched the Effelsburg-Bonn HI Survey data for indications of a simple twisting (toroidal) motion across these filaments. Instead, we found that the structure was more complicated than expected. Apparent angular widths of several filaments were measured using the Galactic Arecibo L-band Feed Array HI (GALFA-HI), Bonn, and Leident/Argentine/Bonn (LAB) surveys. Based on filament widths and other parameters, we conclude that magnetism is the dominant force opposing internal motion and maintaining the structure of these filaments. The apparent width as a function of beam width closely follows a relationship reported in 1993 for HI features in general. They tend to subtend an angle two times the beam width, suggesting that the features remain unresolved.The Arecibo Observatory is operated by SRI International under a cooperative agreement with the National Science Foundation (AST-1100968), and in alliance with Ana G. Méndez-Universidad Metropolitana, and the Universities Space Research Association. The Arecibo Observatory REU is funded under grant AST-1559849 to Universidad Metropolitana.

  15. 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.

  16. 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.

  17. Filament Breakaway

    NASA Image and Video Library

    2017-04-18

    A dark, elongated filament rose up and broke to the lower left and out from the sun seen by NASA Solar Dynamics Observatory, Apr.9-10, 2017. Filaments are cooler clouds of plasma tethered above the sun surface by magnetic forces. They are notoriously unstable and tend not to last more than a few days before they collapse into the sun or break away into space. A video, taken in extreme ultraviolet light, covers about nine hours of activity. Videos are available at https://photojournal.jpl.nasa.gov/catalog/PIA21592

  18. 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.

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

    PubMed

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

    2016-01-19

    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.

  20. 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.

  1. 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

  2. Exploring fractal behaviour of blood oxygen saturation in preterm babies

    NASA Astrophysics Data System (ADS)

    Zahari, Marina; Hui, Tan Xin; Zainuri, Nuryazmin Ahmat; Darlow, Brian A.

    2017-04-01

    Recent evidence has been emerging that oxygenation instability in preterm babies could lead to an increased risk of retinal injury such as retinopathy of prematurity. There is a potential that disease severity could be better understood using nonlinear methods for time series data such as fractal theories [1]. Theories on fractal behaviours have been employed by researchers in various disciplines who were motivated to look into the behaviour or structure of irregular fluctuations in temporal data. In this study, an investigation was carried out to examine whether fractal behaviour could be detected in blood oxygen time series. Detection for the presence of fractals in oxygen data of preterm infants was performed using the methods of power spectrum, empirical probability distribution function and autocorrelation function. The results from these fractal identification methods indicate the possibility that these data exhibit fractal nature. Subsequently, a fractal framework for future research was suggested for oxygen time series.

  3. 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.

  4. 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

  5. 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.

  6. 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. Copyright © 2010 Elsevier Ltd. All rights reserved.

  7. Kiloparsec-Scale Simulations of Star Formation in Disk Galaxies III. Structure and Dynamics of Filaments and Clumps in Giant Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Butler, Michael J.; Tan, Jonathan C.; Van Loo, Sven

    2015-05-01

    We present hydrodynamic simulations of self-gravitating dense gas in a galactic disk, exploring scales ranging from 1 kpc down to ˜0.1 pc. Our primary goal is to understand how dense filaments form in giant molecular clouds (GMCs). These structures, often observed as infrared dark clouds (IRDCs) in the Galactic plane, are thought to be the precursors to massive stars and star clusters, so their formation may be the rate-limiting step controlling global star formation rates in galactic systems as described by the Kennicutt-Schmidt relation. Our study follows on from Van Loo et al., which carried out simulations to 0.5 pc resolution and examined global aspects of the formation of dense gas clumps and the resulting star formation rate. Here, using our higher resolution, we examine the detailed structural, kinematic, and dynamical properties of dense filaments and clumps, including mass surface density (Σ) probability distribution functions, filament mass per unit length and its dispersion, lateral Σ profiles, filament fragmentation, filament velocity gradients and infall, and degree of filament and clump virialization. Where possible, these properties are compared to observations of IRDCs. By many metrics, especially too large mass fractions of high {Σ }\\gt 1 g c{{m}-2} material, too high mass per unit length dispersion due to dense clump formation, too high velocity gradients, and too high velocity dispersion for a given mass per unit length, the simulated filaments differ from observed IRDCs. We thus conclude that IRDCs do not form from global fast collapse of GMCs. Rather, we expect that IRDC formation and collapse are slowed significantly by the influence of dynamically important magnetic fields, which may thus play a crucial role in regulating galactic star formation rates.

  8. The 7-stranded structure of relaxed scallop muscle myosin filaments: support for a common head configuration in myosin-regulated muscles.

    PubMed

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

    2009-05-01

    Isolated relaxed myosin filaments from the myosin-regulated scallop striated adductor muscle have been reconstructed using electron microscopy and single particle analysis of negatively stained filaments. Three-dimensional reconstruction using 7-fold rotational symmetry but without imposed helical symmetry confirmed that the myosin head array is a 7-stranded, right-handed long-pitch 24/1 helix (or left-handed short-pitch 10/1 helix) with the whole structure having an axial repeat of 1440A. Reconstruction using the full helical symmetry revealed details of the myosin head density distribution within the head crowns in the relaxed scallop myosin filament. The resulting density distribution can best be explained by an arrangement in which the two heads from the same myosin molecule interact together within each crown in a compact parallel fashion along the filament axis. The configuration is consistent with the published configuration of the two heads within vertebrate smooth muscle myosin molecules observed in two-dimensional crystals of smooth muscle myosin and in the structure of tarantula myosin filaments. All these three muscle types are myosin-regulated, providing further support for a general motif of intramolecular interacting-heads structure in the relaxed state of myosin-regulated muscles as was proposed earlier by Woodhead et al. [Woodhead, J.L., Zhao, F.-Q., Craig, R., Egelman, E.H., Alamo, L., Padron, R.. 2005. Atomic model of a myosin filament in the relaxed state. Nature 436, 1195-1199]. However, the orientation of the Wendt structure is different from that found by Woodhead in that the outer head projects outwards and the inner head lies closer to the filament backbone, as in earlier work done on the insect flight muscle myosin filaments [AL-Khayat, H.A., Hudson, L., Reedy, M.K., Irving, T.C., Squire, J.M., 2003. Myosin head configuration in relaxed insect flight muscle: X-ray modelled resting crossbridges in a pre-powerstroke state are poised for

  9. FUNDAMENTAL AREAS OF PHENOMENOLOGY (INCLUDING APPLICATIONS): Sprout Branching of Tumour Capillary Network Growth: Fractal Dimension and Multifractal Structure

    NASA Astrophysics Data System (ADS)

    Kou, Jian-Long; Lu, Hang-Jun; Wu, Feng-Min; Xu, You-Sheng

    2008-05-01

    A tumour vascular network, characterized as an irregularly stochastic growth, is different from the normal vascular network. We systematically analyse the dependence of the branching. It is found that anastomosis of tumour on time is according to a number of tumour images, and both the fractal dimensions and multifractal spectra of the tumours are obtained. In the cases studied, the fractal dimensions of the tumour vascular network increase with time and the multifractal spectrum not only rises entirely but also shifts right. In addition, the best drug delivery stage is discussed according to the difference of the singularity exponent δα(δα = αmax — αmin), which shows some change in the growth process of the tumour vascular network. A common underlying principle is obtained from our analysis along with previous results.

  10. Probing the Energetics of Dynactin Filament Assembly and the Binding of Cargo Adaptor Proteins Using Molecular Dynamics Simulation and Electrostatics-Based Structural Modeling.

    PubMed

    Zheng, Wenjun

    2017-01-10

    Dynactin, a large multiprotein complex, binds with the cytoplasmic dynein-1 motor and various adaptor proteins to allow recruitment and transportation of cellular cargoes toward the minus end of microtubules. The structure of the dynactin complex is built around an actin-like minifilament with a defined length, which has been visualized in a high-resolution structure of the dynactin filament determined by cryo-electron microscopy (cryo-EM). To understand the energetic basis of dynactin filament assembly, we used molecular dynamics simulation to probe the intersubunit interactions among the actin-like proteins, various capping proteins, and four extended regions of the dynactin shoulder. Our simulations revealed stronger intersubunit interactions at the barbed and pointed ends of the filament and involving the extended regions (compared with the interactions within the filament), which may energetically drive filament termination by the capping proteins and recruitment of the actin-like proteins by the extended regions, two key features of the dynactin filament assembly process. Next, we modeled the unknown binding configuration among dynactin, dynein tails, and a number of coiled-coil adaptor proteins (including several Bicaudal-D and related proteins and three HOOK proteins), and predicted a key set of charged residues involved in their electrostatic interactions. Our modeling is consistent with previous findings of conserved regions, functional sites, and disease mutations in the adaptor proteins and will provide a structural framework for future functional and mutational studies of these adaptor proteins. In sum, this study yielded rich structural and energetic information about dynactin and associated adaptor proteins that cannot be directly obtained from the cryo-EM structures with limited resolutions.

  11. The Dimension of Projections of Fractal Percolations

    NASA Astrophysics Data System (ADS)

    Rams, Michał; Simon, Károly

    2014-02-01

    Fractal percolation or Mandelbrot percolation is one of the most well studied families of random fractals. In this paper we study some of the geometric measure theoretical properties (dimension of projections and structure of slices) of these random sets. Although random, the geometry of those sets is quite regular. Our results imply that, denoting by a typical realization of the fractal percolation on the plane, If then for all lines ℓ the orthogonal projection E ℓ of E to ℓ has the same Hausdorff dimension as E,

  12. Statistics of the fractal structure and phase singularity of a plane light wave propagation in atmospheric turbulence.

    PubMed

    Rao, Ruizhong

    2008-01-10

    Numerical experiments are carried out for a plane wave propagating in the atmospheric turbulence for a weak to strong fluctuation condition, i.e., the Rytov index being in a large range of 2x10(-3) to 20. Mainly two categories of propagation events are explored for the same range of Rytov index. In one category the propagation distance and also the Fresnel length are kept fixed with the turbulence strength changing. In the other the turbulence strength is kept fixed with the distance changing. The statistical characteristics of the scintillation index, the maximum and minimum of the intensity, the fractal dimension of the intensity image, and the number density of the phase singularity are analyzed. The behaviors of the fractal dimension and the density of the phase singularity present obvious differences for the two categories of propagation. The fractal dimension depends both on the Rytov index and the Fresnel length. In both weak and strong fluctuation conditions the dimension generally increases with the Rytov index, but is at minimum at the onset region. The phase singularity density is coincident with the theoretical results under a weak fluctuation condition, and has a slowly increasing manner with the Rytov index in the strong fluctuation condition. The dependence on the Fresnel size is confident and there is no saturation for the phase singularity.

  13. Complex Flare Dynamics Initiated by a Filament-Filament Interaction

    NASA Astrophysics Data System (ADS)

    Zhu, Chunming; Liu, Rui; Alexander, David; Sun, Xudong; McAteer, James

    2015-04-01

    We report on a filament eruption that led to a relatively rare filament-filament interaction event. The filaments were located at different heights above the same segment of a circular polarity inversion line (PIL) around a condensed leading sunspot. The onset of the eruption of the lower of the two filaments was accompanied by a simultaneous descent of the upper filament resulting in a convergence and direct interaction of the two filaments. The interaction led to the subsequent merger of the filaments into a single magnetically complex structure that erupted to create a large solar flare and an array of complex dynamical activity. A hard X-ray coronal source and an associated enhancement of hot plasma are observed at the interface between the two interacting filaments. These phenomena are related to the production of a small C flare and the subsequent development of a much stronger M flare. Magnetic loop shrinkage and descending dark voids were observed at different locations as part of the large flare energy release giving us a unique insight into these dynamic flare phenomena.

  14. Adhesion and Disintegration Phenomena on Fractal Agar Gel Surfaces.

    PubMed

    Kudo, Ayano; Sato, Marika; Sawaguchi, Haruna; Hotta, Jun-Ichi; Mayama, Hiroyuki; Nonomura, Yoshimune

    2016-11-01

    In the present study, mechanical phenomena on fractal agar gel were analyzed to understand the interfacial properties of hydrophilic biosurfaces. The evaluation of adhesion strength between the fractal agar gel surfaces showed that the fractal structure inhibits the adhesion between the agar gel surfaces. In addition, when the disintegration behavior of an agar gel block was observed between fractal agar gel substrates, the rough structure prevented the sliding of an agar gel block. These findings are useful for understanding the biological significance of rough structure on the biological surfaces.

  15. Strain sensing behavior of textile structures made of stainless steel continuous filament yarns under uni-axial tensile loading

    NASA Astrophysics Data System (ADS)

    Yang, Bin; Tao, XiaoMing; Cai, Jiayang; Yu, TongXi

    2007-07-01

    The objective of this research was to determine the sensing behavior of various textile structures made of stainless steel continuous filament yarns for their potential measurement applications for large strain under high temperature. Four knitting structures are designed and tested. It is observed that the resistance change of the fabrics depends on the structure, the shift of the loop decreasing and the change of the contact resistance between yarns increasing are help to the repeat and sensitivity of the relative resistance change respectively. The relative resistance change also depends on the loading condition, such as strain rate, the maximum cycle strain and temperature. In our four knitting structures, single warp-knit has better repetition in strain sensing than the other three structures, this is because the loops in single warp-knit possess a stabilized behavior, and the plastic deformation is the smallest. The mechanisms of this strain sensing behavior have been investigated including the relationships between electrical resistance of yarn and yarn tensile strain, between yarn length transfer in the strain fabric and the fabric tensile strain, as well as contact resistance of the looped yarns. The major contributor has been deduced to be the change of contact resistance between looped yarns during the deformation.

  16. Fractal morphometry of cell complexity.

    PubMed

    Losa, Gabriele A

    2002-01-01

    Irregularity and self-similarity under scale changes are the main attributes of the morphological complexity of both normal and abnormal cells and tissues. In other words, the shape of a self-similar object does not change when the scale of measurement changes, because each part of it looks similar to the original object. However, the size and geometrical parameters of an irregular object do differ when it is examined at increasing resolution, which reveals more details. Significant progress has been made over the past three decades in understanding how irregular shapes and structures in the physical and biological sciences can be analysed. Dominant influences have been the discovery of a new practical geometry of Nature, now known as fractal geometry, and the continuous improvements in computation capabilities. Unlike conventional Euclidean geometry, which was developed to describe regular and ideal geometrical shapes which are practically unknown in nature, fractal geometry can be used to measure the fractal dimension, contour length, surface area and other dimension parameters of almost all irregular and complex biological tissues. We have used selected examples to illustrate the application of the fractal principle to measuring irregular and complex membrane ultrastructures of cells at specific functional and pathological stage.

  17. X-ray and cryo-EM structures of monomeric and filamentous actin-like protein MamK reveal changes associated with polymerization

    PubMed Central

    He, Shaoda; Savva, Christos G.

    2016-01-01

    Magnetotactic bacteria produce iron-rich magnetic nanoparticles that are enclosed by membrane invaginations to form magnetosomes so they are able to sense and act upon Earth’s magnetic field. In Magnetospirillum and other magnetotactic bacteria, to combine their magnetic moments, magnetosomes align along filaments formed by a bacterial actin homolog, MamK. Here, we present the crystal structure of a nonpolymerizing mutant of MamK from Magnetospirillum magneticum AMB-1 at 1.8-Å resolution, revealing its close similarity to actin and MreB. The crystals contain AMPPNP-bound monomeric MamK in two different conformations. To investigate conformational changes associated with polymerization, we used unmodified MamK protein and cryo-EM with helical 3D reconstruction in RELION to obtain a density map and a fully refined atomic model of MamK in filamentous form at 3.6-Å resolution. The filament is parallel (polar) double-helical, with a rise of 52.2 Å and a twist of 23.8°. As shown previously and unusually for actin-like filaments, the MamK subunits from each of the two strands are juxtaposed, creating an additional twofold axis along the filament. Compared with monomeric MamK, ADP-bound MamK in the filament undergoes a conformational change, rotating domains I and II against each other to further close the interdomain cleft between subdomains IB and IIB. The domain movement causes several loops to close around the nucleotide-binding pocket. Glu-143, a key residue for catalysis coordinating the magnesium ion, moves closer, presumably switching nucleotide hydrolysis upon polymerization—one of the hallmarks of cytomotive filaments of the actin type. PMID:27821762

  18. X-ray and cryo-EM structures of monomeric and filamentous actin-like protein MamK reveal changes associated with polymerization.

    PubMed

    Löwe, Jan; He, Shaoda; Scheres, Sjors H W; Savva, Christos G

    2016-11-22

    Magnetotactic bacteria produce iron-rich magnetic nanoparticles that are enclosed by membrane invaginations to form magnetosomes so they are able to sense and act upon Earth's magnetic field. In Magnetospirillum and other magnetotactic bacteria, to combine their magnetic moments, magnetosomes align along filaments formed by a bacterial actin homolog, MamK. Here, we present the crystal structure of a nonpolymerizing mutant of MamK from Magnetospirillum magneticum AMB-1 at 1.8-Å resolution, revealing its close similarity to actin and MreB. The crystals contain AMPPNP-bound monomeric MamK in two different conformations. To investigate conformational changes associated with polymerization, we used unmodified MamK protein and cryo-EM with helical 3D reconstruction in RELION to obtain a density map and a fully refined atomic model of MamK in filamentous form at 3.6-Å resolution. The filament is parallel (polar) double-helical, with a rise of 52.2 Å and a twist of 23.8°. As shown previously and unusually for actin-like filaments, the MamK subunits from each of the two strands are juxtaposed, creating an additional twofold axis along the filament. Compared with monomeric MamK, ADP-bound MamK in the filament undergoes a conformational change, rotating domains I and II against each other to further close the interdomain cleft between subdomains IB and IIB. The domain movement causes several loops to close around the nucleotide-binding pocket. Glu-143, a key residue for catalysis coordinating the magnesium ion, moves closer, presumably switching nucleotide hydrolysis upon polymerization-one of the hallmarks of cytomotive filaments of the actin type.

  19. 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)

  20. 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)

  1. 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.

  2. 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)

  3. 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)

  4. Filaments in Lupus I

    NASA Astrophysics Data System (ADS)

    Takahashi, Satoko; Rodon, J.; De Gregorio-Monsalvo, I.; Plunkett, A.

    2017-06-01

    The mechanisms behind the formation of sub-stellar mass sources are key to determine the populations at the low-mass end of the stellar distribution. Here, we present mapping observations toward the Lupus I cloud in C18O(2-1) and 13CO(2-1) obtained with APEX. We have identified a few velocity-coherent filaments. Each contains several substellar mass sources that are also identified in the 1.1mm continuum data (see also SOLA catalogue presentation). We will discuss the velocity structure, fragmentation properties of the identified filaments, and the nature of the detected sources.

  5. 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.

  6. Fractals in the Classroom

    NASA Astrophysics Data System (ADS)

    Knutson, Paul; Dahlberg, E. Dan

    2003-10-01

    In examples of fractals such as moon craters, rivers,2 cauliflower,3 and bread,4 the actual growth process of the fractal object is missed. In the simple experiment described here, one can observe and record the growth of calcium carbonate crystals — a ubiquitous material found in marble and seashells — in real time. The video frames can be digitized and analyzed to determine the fractal dimension.

  7. On the relationship between tumor structure and complexity of the spatial distribution of cancer cell nuclei: a fractal geometrical model of prostate carcinoma.

    PubMed

    Waliszewski, Przemyslaw; Wagenlehner, Florian; Gattenlöhner, Stefan; Weidner, Wolfgang

    2015-03-01

    A risk of the prostate cancer patient is defined by both the objective and subjective criteria, that is, PSA concentration, Gleason score, and pTNM-stage. The subjectivity of tumor grading influences the risk assessment owing to a large inter- and intra-observer variability. Pathologists propose a central prostate pathology review as a remedy for this problem; yet, the review cannot eliminate the subjectivity from the diagnostic algorithm. The spatial distribution of cancer cell nuclei changes during tumor progression. It implies changes in complexity measured by the capacity dimension D0, the information dimension D1, and the correlation dimension D2. The cornerstone of the approach is a model of prostate carcinomas composed of the circular fractals CF(4), CF(6 + 0), and CF(6 + 1). This model is both geometrical and analytical, that is, its structure is well-defined, the capacity fractal dimension D0 can be calculated for the infinite circular fractals, and the dimensions D0, D1, D2 can be computed for their finite counterparts representing distribution of cell nuclei. The model enabled both the calibration of the software and the validation of the measurements in 124 prostate carcinomas. The ROC analysis defined the cut-off D0 values for seven classes of complexity. The Gleason classification matched in part with the classification based on the D0 values. The mean ROC sensitivity was 81.3% and the mean ROC specificity 75.2%. Prostate carcinomas were re-stratified into seven classes of complexity according to their D0 values. This increased both the mean ROC sensitivity and the mean ROC specificity to 100%. All homogeneous Gleason patterns were subordinated to the class C1, C4, or C7. D0 = 1.5820 was the cut-off D0 value between the complexity class C2 and C3 representing low-risk cancers and intermediate-risk cancers, respectively. The global fractal dimensions eliminate the subjectivity in the diagnostic algorithm of prostate cancer. Those complexity

  8. Analyzing the photonic band gaps in two-dimensional plasma photonic crystals with fractal Sierpinski gasket structure based on the Monte Carlo method

    SciTech Connect

    Zhang, Hai-Feng; Liu, Shao-Bin

    2016-08-15

    In this paper, the properties of photonic band gaps (PBGs) in two types of two-dimensional plasma-dielectric photonic crystals (2D PPCs) under a transverse-magnetic (TM) wave are theoretically investigated by a modified plane wave expansion (PWE) method where Monte Carlo method is introduced. The proposed PWE method can be used to calculate the band structures of 2D PPCs which possess arbitrary-shaped filler and any lattice. The efficiency and convergence of the present method are discussed by a numerical example. The configuration of 2D PPCs is the square lattices with fractal Sierpinski gasket structure whose constituents are homogeneous and isotropic. The type-1 PPCs is filled with the dielectric cylinders in the plasma background, while its complementary structure is called type-2 PPCs, in which plasma cylinders behave as the fillers in the dielectric background. The calculated results reveal that the enough accuracy and good convergence can be obtained, if the number of random sampling points of Monte Carlo method is large enough. The band structures of two types of PPCs with different fractal orders of Sierpinski gasket structure also are theoretically computed for a comparison. It is demonstrate that the PBGs in higher frequency region are more easily produced in the type-1 PPCs rather than in the type-2 PPCs. Sierpinski gasket structure introduced in the 2D PPCs leads to a larger cutoff frequency, enhances and induces more PBGs in high frequency region. The effects of configurational parameters of two types of PPCs on the PBGs are also investigated in detail. The results show that the PBGs of the PPCs can be easily manipulated by tuning those parameters. The present type-1 PPCs are more suitable to design the tunable compacted devices.

  9. Analyzing the photonic band gaps in two-dimensional plasma photonic crystals with fractal Sierpinski gasket structure based on the Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Zhang, Hai-Feng; Liu, Shao-Bin

    2016-08-01

    In this paper, the properties of photonic band gaps (PBGs) in two types of two-dimensional plasma-dielectric photonic crystals (2D PPCs) under a transverse-magnetic (TM) wave are theoretically investigated by a modified plane wave expansion (PWE) method where Monte Carlo method is introduced. The proposed PWE method can be used to calculate the band structures of 2D PPCs which possess arbitrary-shaped filler and any lattice. The efficiency and convergence of the present method are discussed by a numerical example. The configuration of 2D PPCs is the square lattices with fractal Sierpinski gasket structure whose constituents are homogeneous and isotropic. The type-1 PPCs is filled with the dielectric cylinders in the plasma background, while its complementary structure is called type-2 PPCs, in which plasma cylinders behave as the fillers in the dielectric background. The calculated results reveal that the enough accuracy and good convergence can be obtained, if the number of random sampling points of Monte Carlo method is large enough. The band structures of two types of PPCs with different fractal orders of Sierpinski gasket structure also are theoretically computed for a comparison. It is demonstrate that the PBGs in higher frequency region are more easily produced in the type-1 PPCs rather than in the type-2 PPCs. Sierpinski gasket structure introduced in the 2D PPCs leads to a larger cutoff frequency, enhances and induces more PBGs in high frequency region. The effects of configurational parameters of two types of PPCs on the PBGs are also investigated in detail. The results show that the PBGs of the PPCs can be easily manipulated by tuning those parameters. The present type-1 PPCs are more suitable to design the tunable compacted devices.

  10. 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.

  11. 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.

  12. The role of disulfide bond formation in the structural transition observed in the intermediate filaments of developing hair.

    PubMed

    Bruce Fraser, R D; Parry, David A D

    2012-10-01

    Hair keratin is a composite structure in which intermediate filaments (IF) are embedded in a protein matrix. During the early stages of development in the hair follicle the redox potential is such that the cysteine residues in the IF are maintained in a reduced form. However, at a late stage of development the redox potential changes to produce an oxidizing environment and the IF undergo a structural transition involving both molecular slippage and radial compaction. In our earlier study the changes in the molecular parameters were estimated from knowledge of the sites of artificially induced crosslinks, and it was noted that the changes in these parameters realigned many of the cysteine residues to positions more favorable to disulfide bond formation. As the energy involved in the formation of disulfide bonds is much greater than that of hydrogen bonds or van der Waals interactions the structural transition is likely to be dominated by the requirement that the bonded cysteine residues occur at closely equivalent axial positions. This criterion was used in the present study to obtain more precise values for the molecular parameters in the oxidized fiber than has hitherto been possible. A comparison of the sequences of hair keratins and epidermal keratins suggests that the slippage observed in trichocyte IF during keratinization does not occur in epidermal IF. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. Generalized fragmentation functions for fractal jet observables

    NASA Astrophysics Data System (ADS)

    Elder, Benjamin T.; Procura, Massimiliano; Thaler, Jesse; Waalewijn, Wouter J.; Zhou, Kevin

    2017-06-01

    We introduce a broad class of fractal jet observables that recursively probe the collective properties of hadrons produced in jet fragmentation. To describe these collinear-unsafe observables, we generalize the formalism of fragmentation functions, which are important objects in QCD for calculating cross sections involving identified final-state hadrons. Fragmentation functions are fundamentally nonperturbative, but have a calculable renormalization group evolution. Unlike ordinary fragmentation functions, generalized fragmentation functions exhibit nonlinear evolution, since fractal observables involve correlated subsets of hadrons within a jet. Some special cases of generalized fragmentation functions are reviewed, including jet charge and track functions. We then consider fractal jet observables that are based on hierarchical clustering trees, where the nonlinear evolution equations also exhibit tree-like structure at leading order. We develop a numeric code for performing this evolution and study its phenomenological implications. As an application, we present examples of fractal jet observables that are useful in discriminating quark jets from gluon jets.

  14. Fractal geometry is heritable in trees.

    PubMed

    Bailey, Joseph K; Bangert, Randy K; Schweitzer, Jennifer A; Trotter, R Talbot; Shuster, Stephen M; Whitham, Thomas G

    2004-09-01

    Understanding the genetic basis to landscape vegetation structure is an important step that will allow us to examine ecological and evolutionary processes at multiple spatial scales. Here for the first time we show that the fractal architecture of a dominant plant on the landscape exhibits high broad-sense heritability and thus has a genetic basis. The fractal architecture of trees is known to influence ecological communities associated with them. In a unidirectional cottonwood-hybridizing complex (Populus angustifolia x P. fremontii) pure and hybrid cottonwoods differed significantly in their fractal architecture, with phenotypic variance among backcross hybrids exceeding that of F1 hybrids and of pure narrowleaf cottonwoods by two-fold. This result provides a crucial link between genes and fractal scaling theory, and places the study of landscape ecology within an evolutionary framework.

  15. Link between truncated fractals and coupled oscillators in biological systems.

    PubMed

    Paar, V; Pavin, N; Rosandić, M

    2001-09-07

    This article aims at providing a new theoretical insight into the fundamental question of the origin of truncated fractals in biological systems. It is well known that fractal geometry is one of the characteristics of living organisms. However, contrary to mathematical fractals which are self-similar at all scales, the biological fractals are truncated, i.e. their self-similarity extends at most over a few orders of magnitude of separation. We show that nonlinear coupled oscillators, modeling one of the basic features of biological systems, may generate truncated fractals: a truncated fractal pattern for basin boundaries appears in a simple mathematical model of two coupled nonlinear oscillators with weak dissipation. This fractal pattern can be considered as a particular hidden fractal property. At the level of sufficiently fine precision technique the truncated fractality acts as a simple structure, leading to predictability, but at a lower level of precision it is effectively fractal, limiting the predictability of the long-term behavior of biological systems. We point out to the generic nature of our result. Copyright 2001 Academic Press.

  16. 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.

  17. Electronic properties of fractal-glass models

    NASA Astrophysics Data System (ADS)

    Schwalm, William A.; Schwalm, Mizuho K.

    1989-06-01

    Analytic results are presented for four new fractal lattices. A basic similarity between fractals and homogeneous glassy networks is the fluctuating environments of the lattice sites. The fractals are classified in terms of their local bonding geometry by comparison with glassy networks: (1) amorphous graphite, (2) two-dimensional and (3) three-dimensional Zachariasen glasses of two components, and (4) a three-component, infinitely ramified glass model with fractal dimension d¯~=3 and spectral dimension d¯¯>2.5. Localization and size scaling of corner-to-corner propagation are investigated, and it is found that there is a transition from power-law to exponential dependence in the case of model (1) at a correlation length λ~=64. Edge states appear to play an important role in propagation over distances longer than λ. Effects of ring closure and site variety are studied by making two modifications to model (1). In the first, branch cuts unroll the ring structure into a Bethe lattice. In the second, the rings are severed, resulting in a fractal tree. Results suggest that noncontinuum spectral structure is more closely related to site variety than to connectedness or ring closure in these fractal-glass models. This is similar to Anderson localization in the homogeneous random case.

  18. Pulse regime in formation of fractal fibers

    NASA Astrophysics Data System (ADS)

    Smirnov, B. M.

    2016-11-01

    The pulse regime of vaporization of a bulk metal located in a buffer gas is analyzed as a method of generation of metal atoms under the action of a plasma torch or a laser beam. Subsequently these atoms are transformed into solid nanoclusters, fractal aggregates and then into fractal fibers if the growth process proceeds in an external electric field. We are guided by metals in which transitions between s and d-electrons of their atoms are possible, since these metals are used as catalysts and filters in interaction with gas flows. The resistance of metal fractal structures to a gas flow is evaluated that allows one to find optimal parameters of a fractal structure for gas flow propagation through it. The thermal regime of interaction between a plasma pulse or a laser beam and a metal surface is analyzed. It is shown that the basic energy from an external source is consumed on a bulk metal heating, and the efficiency of atom evaporation from the metal surface, that is the ratio of energy fluxes for vaporization and heating, is 10-3-10-4 for transient metals under consideration. A typical energy flux ( 106 W/cm2), a typical surface temperature ( 3000 K), and a typical pulse duration ( 1 μs) provide a sufficient amount of evaporated atoms to generate fractal fibers such that each molecule of a gas flow collides with the skeleton of fractal fibers many times.

  19. Pulse regime in formation of fractal fibers

    SciTech Connect

    Smirnov, B. M.

    2016-11-15

    The pulse regime of vaporization of a bulk metal located in a buffer gas is analyzed as a method of generation of metal atoms under the action of a plasma torch or a laser beam. Subsequently these atoms are transformed into solid nanoclusters, fractal aggregates and then into fractal fibers if the growth process proceeds in an external electric field. We are guided by metals in which transitions between s and d-electrons of their atoms are possible, since these metals are used as catalysts and filters in interaction with gas flows. The resistance of metal fractal structures to a gas flow is evaluated that allows one to find optimal parameters of a fractal structure for gas flow propagation through it. The thermal regime of interaction between a plasma pulse or a laser beam and a metal surface is analyzed. It is shown that the basic energy from an external source is consumed on a bulk metal heating, and the efficiency of atom evaporation from the metal surface, that is the ratio of energy fluxes for vaporization and heating, is 10{sup –3}–10{sup –4} for transient metals under consideration. A typical energy flux (~10{sup 6} W/cm{sup 2}), a typical surface temperature (~3000 K), and a typical pulse duration (~1 μs) provide a sufficient amount of evaporated atoms to generate fractal fibers such that each molecule of a gas flow collides with the skeleton of fractal fibers many times.

  20. Line graphs for fractals

    NASA Astrophysics Data System (ADS)

    Warchalowski, Wiktor; Krawczyk, Malgorzata J.

    2017-03-01

    We found the Lindenmayer systems for line graphs built on selected fractals. We show that the fractal dimension of such obtained graphs in all analysed cases is the same as for their original graphs. Both for the original graphs and for their line graphs we identified classes of nodes which reflect symmetry of the graph.

  1. Application of Fractal Dimension on Palsar Data

    NASA Astrophysics Data System (ADS)

    Singh, Dharmendra; Pant, Triloki

    viz. HH (Horizontal-Horizontal Polarization), VV (Vertical-Vertical Polarization) and HV (Horizontal-Vertical Polarization) are considered individually. First of all each polarized image is classified in an unsupervised way and various clusters, i.e., four clusters are identified with the help of reference data as Water, Urban and Agricultural Area. For each cluster, the fractal dimension is obtained from the fractal map. Based on the study the ranges of fractal dimension for three classes are Water: 2.0-2.17, Agricultural Area: 2.24-2.72, Urban Area: 2.63-2.92 for HH polarized image; Water: 2.0-2.21, Agricultural Area: 2.20-2.64, Urban; 2.58-2.94 for VV polarized image and Water: 2.0-2.14, Agricultural Area: 2.18-2.58, Urban: 2.46-2.94 for HV polarized image. Since the class Others represents a mixture of various classes, an explicit range of D for this class can not be determined. A closer look at the ranges of fractal dimension indicates that there is an overlapping of the values for different classes, despite of which the classes can be distinguished. Also, the class Water having low value of fractal dimension can be treated as smooth and Urban Area having higher values of fractal dimension can be considered rough in structure while the class Agricultural Area shows an intermediate roughness.

  2. Solid friction between soft filaments

    SciTech Connect

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

    2015-03-02

    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. In conclusion, 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.

  3. 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.

  4. Reversible S-glutathionylation of Cys 374 regulates actin filament formation by inducing structural changes in the actin molecule.

    PubMed

    Dalle-Donne, I; Giustarini, D; Rossi, R; Colombo, R; Milzani, A

    2003-01-01

    S-glutathionylation, the reversible formation of mixed disulphides of cysteinyl residues in target proteins with glutathione, occurs under conditions of oxidative stress; this could be a posttranslational mechanism through which protein function is regulated by the cellular redox status. A novel physiological relevance of actin polymerization regulated by glutathionylation of Cys(374) has been recently suggested. In the present study we showed that glutathionylated actin (GS-actin) has a decreased capacity to polymerize compared to native actin, filament elongation being the polymerization step actually inhibited. Actin polymerizability recovers completely after dethiolation, indicating that S-glutathionylation does not induce any protein denaturation and is therefore a reversible oxidative modification. The increased exposure of hydrophobic regions of protein surface observed upon S-glutathionylation indicates changes in actin conformation. Structural alterations are confirmed by the increased rate of ATP exchange as well as by the decreased susceptibility to proteolysis of the subtilisin cleavage site between Met(47) and Gly(48), in the DNase-I-binding loop of the actin subdomain 2. Structural changes in the surface loop 39-51 induced by S-glutathionylation could influence actin polymerization in view of the involvement of the N-terminal portion of this loop in intermonomer interactions, as predicted by the atomic models of F-actin.

  5. RESOLVED SHOCK STRUCTURE OF THE BALMER-DOMINATED FILAMENTS IN TYCHO'S SUPERNOVA REMNANT: COSMIC-RAY PRECURSOR?

    SciTech Connect

    Lee, Jae-Joon; Park, Sangwook; Raymond, John C.; Korreck, Kelly; Blair, William P.; Ghavamian, Parviz; Winkler, P. F.

    2010-06-01

    We report on the results from H{alpha} imaging observations of the eastern limb of Tycho's supernova remnant (SN1572) using the Wide Field Planetary Camera 2 on the Hubble Space Telescope. We resolve the detailed structure of the fast, collisionless shock wave into a delicate structure of nearly edge-on filaments. We find a gradual increase of H{alpha} intensity just ahead of the shock front, which we interpret as emission from the thin ({approx}1'') shock precursor. We find that a significant amount of the H{alpha} emission comes from the precursor and that this could affect the amount of temperature equilibration derived from the observed flux ratio of the broad and narrow H{alpha} components. The observed H{alpha} emission profiles are fit using simple precursor models, and we discuss the relevant parameters. We suggest that the precursor is likely due to cosmic rays and discuss the efficiency of cosmic-ray acceleration at this position.

  6. THE FORMATION AND ERUPTION OF A SMALL CIRCULAR FILAMENT DRIVEN BY ROTATING MAGNETIC STRUCTURES IN THE QUIET SUN

    SciTech Connect

    Yang, Bo; Jiang, Yunchun; Yang, Jiayan; Hong, Junchao; Xu, Zhe E-mail: yjy@ynao.ac.cn

    2015-04-20

    We present the first observation of the formation and eruption of a small circular filament driven by a rotating network magnetic field (RNF) in the quiet Sun. In the negative footpoint region of an inverse J-shaped dextral filament, the RNF was formed by the convergence to supergranular junctions of several magnetic flux patches of the same polarity, and it then rotated counterclockwise (CCW) for approximately 11 hr and showed up as a CCW rotating EUV cyclone, during which time the filament gradually evolved into a circular filament that surrounded the cyclone. When the calculated convergence and vortex flows appeared around the RNF during its formation and rotation phases, the injected magnetic helicity calculation also showed negative helicity accumulation during the RNF rotation that was consistent with the dextral chirality of the filament. Finally, the RNF rotation stopped and the cyclone disappeared, and, probably due to an emerging bipole and its forced cancellation with the RNF, the closure filament underwent an eruption along its axis in the (clockwise) direction opposite to the rotation directions of the RNF and cyclone. These observations suggest that the RNFs might play an important role in the formation of nearby small-scale circular filaments as they transport and inject magnetic energy and helicity, and the formation of the EUV cyclones may be a further manifestation of the helicity injected into the corona by the rotation of the RNFs in the photosphere. In addition, the new emerging bipole observed before the filament eruption might be responsible for destabilizing the system and triggering the magnetic reconnection which proves useful for the filament eruption.

  7. The Formation and Eruption of a Small Circular Filament Driven by Rotating Magnetic Structures in the Quiet Sun

    NASA Astrophysics Data System (ADS)

    Yang, Bo; Jiang, Yunchun; Yang, Jiayan; Hong, Junchao; Xu, Zhe

    2015-04-01

    We present the first observation of the formation and eruption of a small circular filament driven by a rotating network magnetic field (RNF) in the quiet Sun. In the negative footpoint region of an inverse J-shaped dextral filament, the RNF was formed by the convergence to supergranular junctions of several magnetic flux patches of the same polarity, and it then rotated counterclockwise (CCW) for approximately 11 hr and showed up as a CCW rotating EUV cyclone, during which time the filament gradually evolved into a circular filament that surrounded the cyclone. When the calculated convergence and vortex flows appeared around the RNF during its formation and rotation phases, the injected magnetic helicity calculation also showed negative helicity accumulation during the RNF rotation that was consistent with the dextral chirality of the filament. Finally, the RNF rotation stopped and the cyclone disappeared, and, probably due to an emerging bipole and its forced cancellation with the RNF, the closure filament underwent an eruption along its axis in the (clockwise) direction opposite to the rotation directions of the RNF and cyclone. These observations suggest that the RNFs might play an important role in the formation of nearby small-scale circular filaments as they transport and inject magnetic energy and helicity, and the formation of the EUV cyclones may be a further manifestation of the helicity injected into the corona by the rotation of the RNFs in the photosphere. In addition, the new emerging bipole observed before the filament eruption might be responsible for destabilizing the system and triggering the magnetic reconnection which proves useful for the filament eruption.

  8. 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.

  9. Surface manipulation of protein filaments

    NASA Astrophysics Data System (ADS)

    Kreplak, Laurent; Staple, Douglas; Loparic, Marko; Kreuzer, Hans-Juergen

    2009-03-01

    Within mammalian tissues, cells move by actively remodeling a dense network of collagen fibrils. In order to study this situation, we analyze the force response of two types of filamentous protein structures, desmin intermediate filaments 12 nm in diameter and collagen fibrils 80 nm in diameter. Both types of filaments were adsorbed at a solid-liquid interface and locally moved with an AFM tip at constant velocity against surface friction in the interfacial plane. In the case of collagen fibrils, that have an extensibility below 30% extension, we observed that microns long fibrils could be moved by the tip and deformed into shapes that could not be explain by the linear elastic theory for a stiff rod. In the case of desmin filaments that can be stretched up to 3.5 times there length, we observed local stretching of the filaments and discreet steps in the torsional force measured with the cantilever. In order to describe both types of filaments' behaviors, we described the protein filaments as a chain of beads of mass m linked together by a mass-less polymer linker. By solving the Newtonian equations of motions for the coupled beads in the presence of a point load and a viscous drag due to the surface-filament interactions we were able to reproduced our experimental data and extract information on friction.

  10. 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

  11. In-depth characterization and computational 3D reconstruction of flagellar filament protein layer structure based on in situ spectroscopic ellipsometry measurements

    NASA Astrophysics Data System (ADS)

    Kozma, Peter; Kozma, Daniel; Nemeth, Andrea; Jankovics, Hajnalka; Kurunczi, Sandor; Horvath, Robert; Vonderviszt, Ferenc; Fried, Miklos; Petrik, Peter

    2011-06-01

    In this study, we have reconstructed the statistical 3D structure of hundreds of nanometers thick surface immobilized flagellar filament protein layers in their native environment, in buffer solution. The protein deposition onto the surface activated Ta 2O 5 film was performed in a flow cell, and the immobilization process was followed by in situ spectroscopic ellipsometry. A multilayer optical model was developed, in that the protein layer was described by five effective medium sublayers. Applying this method, an in-depth analysis of the protein layer formation was performed. Based on the kinetics in the distribution of the surface mass density, the statistical properties of the filamentous film could be determined computationally as a function of the measurement time. It was also demonstrated that the 3D structure of the protein layer can be reconstructed based on the calculated in-depth mass density profile. The computational investigation revealed that the filaments can be classified into two individual groups in approximately equal ratio according to their orientation. In the first group the filaments are close to laying position, whereas in the second group they are in a standing position, resulting in a significantly denser sublayer close to the substrate than at a larger distance.

  12. 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.

  13. Fractal dimension and architecture of trabecular bone.

    PubMed

    Fazzalari, N L; Parkinson, I H

    1996-01-01

    The fractal dimension of trabecular bone was determined for biopsies from the proximal femur of 25 subjects undergoing hip arthroplasty. The average age was 67.7 years. A binary profile of the trabecular bone in the biopsy was obtained from a digitized image. A program written for the Quantimet 520 performed the fractal analysis. The fractal dimension was calculated for each specimen, using boxes whose sides ranged from 65 to 1000 microns in length. The mean fractal dimension for the 25 subjects was 1.195 +/- 0.064 and shows that in Euclidean terms the surface extent of trabecular bone is indeterminate. The Quantimet 520 was also used to perform bone histomorphometric measurements. These were bone volume/total volume (BV/TV) (per cent) = 11.05 +/- 4.38, bone surface/total volume (BS/TV) (mm2/mm3) = 1.90 +/- 0.51, trabecular thickness (Tb.Th) (mm) = 0.12 +/- 0.03, trabecular spacing (Tb.Sp) (mm) = 1.03 +/- 0.36, and trabecular number (Tb.N) (number/mm) = 0.95 +/- 0.25. Pearsons' correlation coefficients showed a statistically significant relationship between the fractal dimension and all the histomorphometric parameters, with BV/TV (r = 0.85, P < 0.0001), BS/TV (r = 0.74, P < 0.0001), Tb.Th (r = 0.50, P < 0.02), Tb.Sp (r = -0.81, P < 0.0001), and Tb.N (r = 0.76, P < 0.0001). This method for calculating fractal dimension shows that trabecular bone exhibits fractal properties over a defined box size, which is within the dimensions of a structural unit for trabecular bone. Therefore, the fractal dimension of trabecular bone provides a measure which does not rely on Euclidean descriptors in order to describe a complex geometry.

  14. Radiative transfer theory for the fractal structure and power-law decay characteristics of short-period seismograms

    NASA Astrophysics Data System (ADS)

    Sato, Haruo; Fukushima, Rintaro

    2013-12-01

    For short period S-wave seismograms of an earthquake, the maximum amplitude decreases according to a power of traveltime, and the coda amplitude also decreases according to a power of lapse time measured from the earthquake origin time. The radiative transfer theory has been often used for the envelope synthesis of complex seismograms composed of scattered waves due to random heterogeneities in the Earth medium; however, the conventional theory, which supposes uniform distributions of scatterers (heterogeneities) and intrinsic absorbers, predicts that both the ballistic term amplitude and the coda wave amplitude exponentially decrease with time increasing in addition to the geometrical decay. In order to explain their power-law characteristics, this paper proposes the radiative transfer theory for a fractally random and homogeneous distribution of isotropic scatterers and intrinsic absorbers with fractal dimension D ≤ 3 in the 3-D space: the number density of scatterers/absorbers in a sphere of radius r is proportional to rD - 3 for distance r ≫ rc but constant for r ≪ rc, where the corner distance rc is introduced to avoid divergence at a small r. The case of D = 3 corresponds to the conventional uniform distribution. For the case of D = 2, the theory well predicts that the mean square (MS) amplitude of the ballistic-wave decreases according to a power of traveltime and the MS amplitude of coda waves decreases according to a power of lapse time measured from the origin time, where each power is controlled by the scattering coefficient, intrinsic absorption coefficient and corner distance. For the case of D = 1, the ballistic-wave MS amplitude decay is the inverse square of time and the coda decay is much faster. As a preliminary work, fixing D = 2 as a priori choice, we analyse S-seismogram envelopes of a local earthquake in Japan. The case study shows that the radiative transfer theory for a fractal scattering medium is useful for the study of the

  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. Surface fractals in liposome aggregation.

    PubMed

    Roldán-Vargas, Sándalo; Barnadas-Rodríguez, Ramon; Quesada-Pérez, Manuel; Estelrich, Joan; Callejas-Fernández, José

    2009-01-01

    In this work, the aggregation of charged liposomes induced by magnesium is investigated. Static and dynamic light scattering, Fourier-transform infrared spectroscopy, and cryotransmission electron microscopy are used as experimental techniques. In particular, multiple intracluster scattering is reduced to a negligible amount using a cross-correlation light scattering scheme. The analysis of the cluster structure, probed by means of static light scattering, reveals an evolution from surface fractals to mass fractals with increasing magnesium concentration. Cryotransmission electron microscopy micrographs of the aggregates are consistent with this interpretation. In addition, a comparative analysis of these results with those previously reported in the presence of calcium suggests that the different hydration energy between lipid vesicles when these divalent cations are present plays a fundamental role in the cluster morphology. This suggestion is also supported by infrared spectroscopy data. The kinetics of the aggregation processes is also analyzed through the time evolution of the mean diffusion coefficient of the aggregates.

  17. 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.

  18. 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.

  19. Influence of buoyancy on drainage of a fractal porous medium

    NASA Astrophysics Data System (ADS)

    Huinink, H. P.; Michels, M. A.

    2002-10-01

    The influence of stabilizing hydrostatic pressure gradients on the drainage of a fractal porous medium is studied. The invasion process is treated with invasion percolation (IP) in a gradient. Fractality is mimicked by randomly closing bonds of a network. Two length scales govern the problem: the characteristic length of the pore structure ξs and a length scale ξg above which buoyancy determines the structure of the cluster. When ξs<ξg the local structure of the invading cluster is governed by the interplay of capillarity and the fractal properties of the pore space. Only parts of the backbone of the pore structure can be invaded. Therefore, the obtained fractal dimension for small systems L<ξs is much lower (1.40) than the one for ordinary IP (1.82). On larger length scales, ξsfractality of the pore space is no longer important and the cluster grows as in ordinary IP. When L>ξg, gravity becomes important and ξg scales with the bond number B as ξg~B-0.57, as in ordinary IP, while the fractal dimension becomes equal to the Euclidean one. When ξg<ξs gravity is already important on length scales where the fractality of the medium has to be considered too. On small scales L<ξg, where only capillarity and fractality play a role the cluster structure is again characterized by the fractal dimension of 1.40. On larger length scales, ξgfractal dimension of 1.52 is found. The length scale ξg no longer follows ordinary IP scaling: ξg~B-0.69. When L>ξs the fractal dimension of the invading cluster equals the Euclidean one and ξg~B-0.69.

  20. 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

  1. Cluster Monte Carlo dynamics for the Ising model on fractal structures in dimensions between one and two

    NASA Astrophysics Data System (ADS)

    Monceau, P.; Hsiao, P.-Y.

    2003-02-01

    We study the cluster size distributions generated by the Wolff algorithm in the framework of the Ising model on Sierpinski fractals with Hausdorff dimension Df between 1 and 2. We show that these distributions exhibit a scaling property involving the magnetic exponent yh associated with one of the eigen-direction of the renormalization flows. We suggest that a single cluster tends to invade the whole lattice as Df tends towards the lower critical dimension of the Ising model, namely 1. The autocorrelation times associated with the Wolff and Swendsen-Wang algorithms enable us to calculate dynamical exponents; the cluster algorithms are shown to be more efficient in reducing the critical slowing down when Df is lowered.

  2. Thermodynamics of fractal universe

    NASA Astrophysics Data System (ADS)

    Sheykhi, Ahmad; Teimoori, Zeinab; Wang, Bin

    2013-01-01

    We investigate the thermodynamical properties of the apparent horizon in a fractal universe. We find that one can always rewrite the Friedmann equation of the fractal universe in the form of the entropy balance relation δQ=ThdSh, where δQ and Th are the energy flux and Unruh temperature seen by an accelerated observer just inside the apparent horizon. We find that the entropy Sh consists two terms, the first one which obeys the usual area law and the second part which is the entropy production term due to nonequilibrium thermodynamics of fractal universe. This shows that in a fractal universe, a treatment with nonequilibrium thermodynamics of spacetime may be needed. We also study the generalized second law of thermodynamics in the framework of fractal universe. When the temperature of the apparent horizon and the matter fields inside the horizon are equal, i.e. T=Th, the generalized second law of thermodynamics can be fulfilled provided the deceleration and the equation of state parameters ranges either as -1⩽q<0, -1⩽w<-1/3 or as q<-1, w<-1 which are consistent with recent observations. We also find that for Th=bT, with b<1, the GSL of thermodynamics can be secured in a fractal universe by suitably choosing the fractal parameter β.

  3. SOC and Fractal Geometry

    NASA Astrophysics Data System (ADS)

    McAteer, R. T. J.

    2013-06-01

    When Mandelbrot, the father of modern fractal geometry, made this seemingly obvious statement he was trying to show that we should move out of our comfortable Euclidean space and adopt a fractal approach to geometry. The concepts and mathematical tools of fractal geometry provides insight into natural physical systems that Euclidean tools cannot do. The benet from applying fractal geometry to studies of Self-Organized Criticality (SOC) are even greater. SOC and fractal geometry share concepts of dynamic n-body interactions, apparent non-predictability, self-similarity, and an approach to global statistics in space and time that make these two areas into naturally paired research techniques. Further, the iterative generation techniques used in both SOC models and in fractals mean they share common features and common problems. This chapter explores the strong historical connections between fractal geometry and SOC from both a mathematical and conceptual understanding, explores modern day interactions between these two topics, and discusses how this is likely to evolve into an even stronger link in the near future.

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

    SciTech Connect

    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.; Spies, Maria

    2016-07-22

    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. In conclusion, our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.

  5. 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

  6. 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.

  7. Immobilization of functional light antenna structures derived from the filamentous green bacterium Chloroflexus aurantiacus.

    PubMed

    Sridharan, Arati; Muthuswamy, Jit; Labelle, Jeffrey T; Pizziconi, Vincent B

    2008-08-05

    The integration of highly efficient, natural photosynthetic light antenna structures into engineered systems while their biophotonic capabilities are maintained has been an elusive goal in the design of biohybrid photonic devices. In this study, we report a novel technique to covalently immobilize nanoscaled bacterial light antenna structures known as chlorosomes from Chloroflexus aurantiacus on both conductive and nonconductive glass while their energy transducing functionality was maintained. Chlorosomes without their reaction centers (RCs) were covalently immobilized on 3-aminoproyltriethoxysilane (APTES) treated surfaces using a glutaraldehyde linker. AFM techniques verified that the chlorosomes maintained their native ellipsoidal ultrastructure upon immobilization. Results from absorbance and fluorescence spectral analysis (where the Stokes shift to 808/810 nm was observed upon 470 nm blue light excitation) in conjunction with confocal microscopy confirm that the functional integrity of immobilized chlorosomes was also preserved. In addition, experiments with electrochemical impedance spectroscopy (EIS) suggested that the presence of chlorosomes in the electrical double layer of the electrode enhanced the electron transfer capacity of the electrochemical cell. Further, chronoamperometric studies suggested that the reduced form of the Bchl- c pigments found within the chlorosome modulate the conduction properties of the electrochemical cell, where the oxidized form of Bchl- c pigments impeded any current transduction at a bias of 0.4 V within the electrochemical cell. The results therefore demonstrate that the intact chlorosomes can be successfully immobilized while their biophotonic transduction capabilities are preserved through the immobilization process. These findings indicate that it is feasible to design biophotonic devices incorporating fully functional light antenna structures, which may offer significant performance enhancements to current silicon

  8. 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

  9. 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.

  10. Unwinding Motion of a Twisted Active Region Filament

    NASA Astrophysics Data System (ADS)

    Yan, X. L.; Xue, Z. K.; Liu, J. H.; Kong, D. F.; Xu, C. L.

    2014-12-01

    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.

  11. 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.

  12. On the fine structure of sunspot penumbrae. III. The vertical extension of penumbral filaments

    NASA Astrophysics Data System (ADS)

    Borrero, J. M.; Solanki, S. K.; Lagg, A.; Socas-Navarro, H.; Lites, B.

    2006-04-01

    In this paper we study the fine structure of the penumbra as inferred from the uncombed model (flux tube embedded in a magnetic surrounding) when applied to penumbral spectropolarimetric data from the neutral iron lines at 6300 Å. The inversion infers very similar radial dependences in the physical quantities (LOS velocity, magnetic field strength etc.) as those obtained from the inversion of the Fe I 1.56 μm lines. In addition, the large Stokes V area asymmetry exhibited by the visible lines helps to constrain the size of the penumbral flux tubes. As we demonstrate here, the uncombed model is able to reproduce the area asymmetry with striking accuracy, returning flux tubes as thick as 100-300 kilometers in the vertical direction, in good agreement with previous investigations.

  13. 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.

  14. 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