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Sample records for modeling semiflexible filaments

  1. Semiflexible filamentous composites

    NARCIS (Netherlands)

    Huisman, E.M.; Heussinger, C.; Storm, C.; Barkema, G.T.

    2010-01-01

    Inspired by the ubiquity of composite filamentous networks in nature, we investigate models of biopolymer networks that consist of interconnected floppy and stiff filaments. Numerical simulations carried out in three dimensions allow us to explore the microscopic partitioning of stresses and strains

  2. Theory of Semiflexible Filaments and Networks

    Directory of Open Access Journals (Sweden)

    Fanlong Meng

    2017-02-01

    Full Text Available We briefly review the recent developments in the theory of individual semiflexible filaments, and of a crosslinked network of such filaments, both permanent and transient. Starting from the free energy of an individual semiflexible chain, models on its force-extension relation and other mechanical properties such as Euler buckling are discussed. For a permanently crosslinked network of filaments, theories on how the network responds to deformation are provided, with a focus on continuum approaches. Characteristic features of filament networks, such as nonlinear stress-strain relation, negative normal stress, tensegrity, and marginal stability are discussed. In the new area of transient filament network, where the crosslinks can be dynamically broken and re-formed, we show some recent attempts for understanding the dynamics of the crosslinks, and the related rheological properties, such as stress relaxation, yield stress and plasticity.

  3. Semiflexible biopolymers: Microrheology and single filament condensation

    Science.gov (United States)

    Schnurr, Bernhard

    Polymers and their elementary subunits, called monomers, come in an immense variety of structures and sizes, and are of great importance for their material properties as well as a multitude of biological functions. The emphasis here is on semiflexible polymers, which are identified by their intermediate degree of stiffness. Their individual as well as their collective properties when assembled into entangled networks is a topic of great interest to polymer physics, materials science, and biology. Some of the most important semiflexible polymers are biopolymers, with such prominent examples as DNA, F-actin, and microtubules. Their functions range from their use as structural elements in the cytoskeleton of most plant and animal cells, to their role as transport tracks for molecular motors, and the storage of genetic information in their linear sequence. The two parts of this experimental and theoretical thesis address single filament aspects as well as network properties of solutions of semiflexible polymers. In the first part, we describe an optical technique for measuring the bulk properties of soft materials at the local scale. We apply it to a solution of entangled, filamentous actin, a particularly difficult material to characterize with conventional techniques. Beyond a description of measurements and apparatus, we also discuss, from a theoretical point of view, the interpretation and fundamental limitations of this and other microrheological techniques. In the second part, we describe the condensation dynamics of a single, semiflexible filament, induced by changing solvent conditions. A biologically important example of this phenomenon is the condensation of DNA into toroidal structures, which occurs, for instance, in viral capsids. Our observations of a molecular simulation motivate an unexpected pathway of collapse via a series of metastable intermediates we call ``racquet'' states. The analysis of the conformational energies of these structures in the

  4. A semi-flexible model prediction for the polymerization force exerted by a living F-actin filament on a fixed wall

    CERN Document Server

    Pierleoni, Carlo; Ryckaert, Jean-Paul

    2015-01-01

    We consider a single living semi-flexible filament with persistence length l_p in chemical equilibrium with an ideal solution of free monomers at fixed monomer chemical potential mu_1 and fixed temperature T. While one end of the filament is chemically active with single monomer (de)polymerization steps, the other end is grafted normally to a rigid wall to mimick a rigid network from which the filament under consideration emerges. A second rigid wall, parallel to the grafting wall, is fixed at distance L<filament seed. In supercritical conditions the filament tends to grow and impinges onto the second surface which, in suitable conditions (non-escaping filament regime) stops the filament growth. We first establish the grand-potential and derive some general properties, in particular the filament size distribution and the force exerted by the living filament on the obstacle wall. We apply this formalism to the semi-flexible, living, discrete Wormlike chain (d-WLC) model with step size d and...

  5. Non-equilibrium fluctuations of a semi-flexible filament driven by active cross-linkers

    CERN Document Server

    Weber, Ines; Schehr, Grégory; Santen, Ludger

    2016-01-01

    The cytoskeleton is an inhomogeneous network of semi-flexible filaments, which are involved in a wide variety of active biological processes. Although the cytoskeletal filaments can be very stiff and embedded in a dense and cross-linked network, it has been shown that, in cells, they typically exhibit significant bending on all length scales. In this work we propose a model of a semi-flexible filament deformed by different types of cross-linkers for which one can compute and investigate the bending spectrum. Our model allows to couple the evolution of the deformation of the semi-flexible polymer with the stochastic dynamics of linkers which exert transversal forces onto the filament. We observe a $q^{-2}$ dependence of the bending spectrum for some biologically relevant parameters and in a certain range of wavenumbers $q$. However, generically, the spatially localized forcing and the non-thermal dynamics both introduce deviations from the thermal-like $q^{-2}$ spectrum.

  6. Conformations, hydrodynamic interactions, and instabilities of sedimenting semiflexible filaments

    CERN Document Server

    Saggiorato, G; Winkler, R G; Gompper, G

    2015-01-01

    The conformations and dynamics of semiflexible filaments subject to a homogeneous external (gravitational) field, e.g., in a centrifuge, are studied numerically and analytically. The competition between hydrodynamic drag and bending elasticity generates new shapes and dynamical features. We show that the shape of a semiflexible filament undergoes instabilities as the external field increases. We identify two transitions that correspond to the excitation of higher bending modes. In particular, for strong fields the filament stabilizes in a non-planar shape, resulting in a sideways drift or in helical trajectories. For two interacting filaments, we find the same transitions, with the important consequence that the new non-planar shapes have an effective hydrodynamic repulsion, in contrast to the planar shapes which attract themselves even when their osculating planes are rotated with respect to each other. For the case of planar filaments, we show analytically and numerically that the relative velocity is not n...

  7. Semiflexible filament networks viewed as fluctuating beam frames

    Science.gov (United States)

    Su, Tianxiang; Purohit, Prashant

    2012-02-01

    We present a new method combining structural and statistical mechanics to study the entropic elasticity of semiflexible filament networks. We view a filament network as a frame structure and use structural mechanics to determine its static equilibrium configuration under applied loads in the first step. To account for thermal motion around this static equilibrium state, we then approximate the potential energy of the deformed frame structure up to the second order in kinematic variables and obtaina deformation-dependent stiffness matrix characterizing the flexibility of the network. Using statistical mechanics, we then evaluate the partition function, free energy and thermo-mechanical properties of the network in terms of the stiffness matrix. We show that penalty methods commonly used in finite elements to account for constraints, are applicable even when statistical and structural mechanics are combined in our method. We apply our framework to understand the expansion, shear, uniaxial tension and compression behavior of some simple filament networks. We are able to capture the stress-stiffening behavior due to filament reorientation and stretching out of thermal fluctuations, as well as the reversible stress-softening behavior due to filament buckling.

  8. Elasticity of a semiflexible filament with a discontinuous tension due to a cross-link or a molecular motor

    CERN Document Server

    Razbin, Mohammadhosein; Zippelius, Annette

    2016-01-01

    We analyze the stretching elasticity of a wormlike chain with a tension discontinuity resulting from a Hookean spring connecting its backbone to a fixed point. The elasticity of isolated semiflexible filaments has been the subject in a significant body of literature, primarily because of its relevance to the mechanics of biological matter. In real systems, however, these filaments are usually part of supramolecular structures involving cross-linkers or molecular motors which cause tension discontinuities. Our model is intended as a minimal structural element incorporating such a discontinuity. We obtain analytical results in the weakly bending limit of the filament, concerning its force-extension relation and the response of the two parts in which the filament is divided by the spring. For a small tension discontinuity, the linear response of the filament extension to this discontinuity strongly depends on the external tension. For large external tension $f$, the spring force contributes a subdominant correct...

  9. Elasticity of a semiflexible filament with a discontinuous tension due to a cross-link or a molecular motor

    Science.gov (United States)

    Razbin, Mohammadhosein; Benetatos, Panayotis; Zippelius, Annette

    2016-05-01

    We analyze the stretching elasticity of a wormlike chain with a tension discontinuity resulting from a Hookean spring connecting its backbone to a fixed point. The elasticity of isolated semiflexible filaments has been the subject in a significant body of literature, primarily because of its relevance to the mechanics of biological matter. In real systems, however, these filaments are usually part of supramolecular structures involving cross-linkers or molecular motors, which cause tension discontinuities. Our model is intended as a minimal structural element incorporating such a discontinuity. We obtain analytical results in the weakly bending limit of the filament, concerning its force-extension relation and the response of the two parts in which the filament is divided by the spring. For a small tension discontinuity, the linear response of the filament extension to this discontinuity strongly depends on the external tension. For large external tension f , the spring force contributes a subdominant correction ˜1 /f3 /2 to the well-known ˜1 /√{f } -dependence of the end-to-end extension.

  10. Elasticity of a semiflexible filament with a discontinuous tension due to a cross-link or a molecular motor

    OpenAIRE

    Razbin, Mohammadhosein; Benetatos, Panayotis; Zippelius, Annette

    2016-01-01

    We analyze the stretching elasticity of a wormlike chain with a tension discontinuity resulting from a Hookean spring connecting its backbone to a fixed point. The elasticity of isolated semiflexible filaments has been the subject in a significant body of literature, primarily because of its relevance to the mechanics of biological matter. In real systems, however, these filaments are usually part of supramolecular structures involving cross-linkers or molecular motors which cause tension dis...

  11. Collective stringlike motion of semiflexible filamentous particles in columnar liquid crystalline phases

    NARCIS (Netherlands)

    Naderi, S.; van der Schoot, P. P. A. M.

    2013-01-01

    We study, by means of Brownian dynamics simulations, heterogeneous dynamics in a dense columnar phase of monodisperse hard filamentous particles, and find that in a background of barely moving particles, some particles occasionally engage in a fast coherent string-type motion similar to what is

  12. Mechanistic modelling of weak interlayers in flexible and semi-flexible road pavements: Part 2

    CSIR Research Space (South Africa)

    De Beer, Morris

    2012-04-01

    Full Text Available This paper (Part 2 of a two-part set of papers) discusses models and illustrates the adverse effects of weak layers, interlayers, laminations and/or weak interfaces in flexible and semi-flexible pavements, also incorporating lightly cemented layers...

  13. Stiffening of semiflexible biopolymers and cross-linked networks

    CERN Document Server

    Van Dillen, T; Van der Giessen, E

    2006-01-01

    We study the mechanical stiffening behavior in two-dimensional (2D) cross-linked networks of semiflexible biopolymer filaments under simple shear. Filamental constituents immersed in a fluid undergo thermally excited bending motions. Pulling out these undulations results in an increase in the axial stiffness. We analyze this stiffening behavior of 2D semiflexible filaments in detail: we first investigate the average, {static} force-extension relation by considering the initially present undulated configuration that is pulled straight under a tensile force, and compare this result with the average response in which undulation dynamics is allowed during pulling, as derived earlier by MacKintosh and coworkers. We will show that the resulting mechanical behavior is rather similar, but with the axial stiffness being a factor 2 to 4 larger in the dynamic model. Furthermore, we study the stretching contribution in case of extensible filaments and show that, for 2D filaments, the mechanical response is dominated by {...

  14. A new bead-spring model for simulation of semi-flexible macromolecules

    Science.gov (United States)

    Saadat, Amir; Khomami, Bamin

    2016-11-01

    A bead-spring model for semi-flexible macromolecules is developed to overcome the deficiencies of the current coarse-grained bead-spring models. Specifically, model improvements are achieved through incorporation of a bending potential. The new model is designed to accurately describe the correlation along the backbone of the chain, segmental length, and force-extension behavior of the macromolecule even at the limit of 1 Kuhn step per spring. The relaxation time of different Rouse modes is used to demonstrate the capabilities of the new model in predicting chain dynamics.

  15. Orientational relaxation in semiflexible dendrimers.

    Science.gov (United States)

    Kumar, Amit; Biswas, Parbati

    2013-12-14

    The orientational relaxation dynamics of semiflexible dendrimers are theoretically calculated within the framework of optimized Rouse-Zimm formalism. Semiflexibility is modeled through appropriate restrictions in the direction and orientation of the respective bond vectors, while the hydrodynamic interactions are included via the preaveraged Oseen tensor. The time autocorrelation function M(i)(1)(t) and the second order orientational autocorrelation function P(i)(2)(t) are analyzed as a function of the branch-point functionality and the degree of semiflexibility. Our approach of calculating M(i)(1)(t) is completely different from that of the earlier studies (A. Perico and M. Guenza J. Chem. Phys., 1985, 83, 3103; J. Chem. Phys., 1986, 84, 510), where the expression of M(i)(1)(t) obtained from earlier studies does not demarcate the flexible dendrimers from the semiflexible ones. The component of global motion of the time autocorrelation function exhibits a strong dependence on both degree of semiflexibility and branch-point functionality, while the component of pulsation motion depends only on the degree of semiflexibility. But it is difficult to distinguish the difference in the extent of pulsation motion among the compressed (0 qualitative behavior of P(i)(2)(t) obtained from our calculations closely matches with the expression for P(exact)(2)(t) in the earlier studies. Theoretically calculated spectral density, J(ω), is found to depend on the degree of semiflexibility and the branch-point functionality for the compressed and expanded conformations of semiflexible dendrimers as a function of frequency, especially in the high frequency regime, where J(ω) decays with frequency for both compressed and expanded conformations of semiflexible dendrimers. This decay of the spectral density occurs after displaying a cross-over behavior with the variation in the degree of semiflexibility in the intermediate frequency regime. The characteristic area increases with the

  16. Current filamentation model for the Weibel/Filamentation instabilities

    Science.gov (United States)

    Ryu, Chang-Mo; Huynh, Cong Tuan; Kim, Chul Min

    2016-10-01

    A current filamentaion model for a nonrelativistic plasma with e +/e- beam has been presented together with PIC simulations, which can explain the mangetic field enhancement during the Weibel/ Filamentation instabilities. This filament model assumes the Hammer-Rostoker equilibrium. In addition, this model predicts preferential acceleration/deceleration for electron-ion plasmas depending on the injected beam to be e +/e-.

  17. Lattice model of linear telechelic polymer melts. I. Inclusion of chain semiflexibility in the lattice cluster theory

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Wen-Sheng, E-mail: wsxu@uchicago.edu [James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States); Freed, Karl F., E-mail: freed@uchicago.edu [James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States); Department of Chemistry, The University of Chicago, Chicago, Illinois 60637 (United States)

    2015-07-14

    The lattice cluster theory (LCT) for the thermodynamics of polymer systems has recently been reformulated to treat strongly interacting self-assembling polymers composed of fully flexible linear telechelic chains [J. Dudowicz and K. F. Freed, J. Chem. Phys. 136, 064902 (2012)]. Here, we further extend the LCT for linear telechelic polymer melts to include a description of chain semiflexibility, which is treated by introducing a bending energy penalty whenever a pair of consecutive bonds from a single chain lies along orthogonal directions. An analytical expression for the Helmholtz free energy is derived for the model of semiflexible linear telechelic polymer melts. The extension provides a theoretical tool for investigating the influence of chain stiffness on the thermodynamics of self-assembling telechelic polymers, and for further exploring the influence of self-assembly on glass formation in such systems.

  18. A Simple Analytical Model for Predicting the Collapsed State of Self-Attractive Semiflexible Polymers

    Directory of Open Access Journals (Sweden)

    Wenjun Huang

    2016-07-01

    Full Text Available We develop an analytical model to predict the collapse conformation for a single semiflexible polymer chain in solution, given its length, diameter, stiffness, and self-attractiveness. We construct conformational phase diagrams containing three collapsed states, namely torus, bundle, and globule over a range of dimensionless ratios of the three energy parameters, namely solvent-water surface energy ( γ s , energy of bundle end folds ( γ e , and bending energy per unit length in a torus ( γ b . Our phase diagram captures the general phase behavior of a single long chain (>10 Kuhn lengths at moderately high (order unity dimensionless temperature, which is the ratio of thermal energy to the attractive interaction between neighboring monomers. We find that the phase behavior approaches an asymptotic limit when the dimensionless chain length to diameter ratio (L* exceeds 300. We successfully validate our analytical results with Brownian Dynamics (BD simulations, using a mapping of the simulation parameters to those used in the phase diagram. We evaluate the effect of three different bending potentials in the range of moderately high dimensionless temperature, a regime not been previously explored by simulations, and find qualitative agreement between the model and simulation results. We, thus, demonstrate that a rather simplified analytical model can be used to qualitatively predict the final collapsed state of a given polymer chain.

  19. Microstructure of Sheared Entangled Solutions of Semiflexible Polymers

    Directory of Open Access Journals (Sweden)

    Marc Lämmel

    2016-09-01

    Full Text Available We study the influence of finite shear deformations on the microstructure and rheology of solutions of entangled semiflexible polymers theoretically and by numerical simulations and experiments with filamentous actin. Based on the tube model of semiflexible polymers, we predict that large finite shear deformations strongly affect the average tube width and curvature, thereby exciting considerable restoring stresses. In contrast, the associated shear alignment is moderate, with little impact on the average tube parameters, and thus expected to be long-lived and detectable after cessation of shear. Similarly, topologically preserved hairpin configurations are predicted to leave a long-lived fingerprint in the shape of the distributions of tube widths and curvatures. Our numerical and experimental data support the theory.

  20. Star forming filaments in warm dark models

    CERN Document Server

    Gao, Liang; Springel, Volker

    2014-01-01

    We performed a hydrodynamical cosmological simulation of the formation of a Milky Way-like galaxy in a warm dark matter (WDM) cosmology. Smooth and dense filaments, several co-moving mega parsec long, form generically above z 2 in this model. Atomic line cooling allows gas in the centres of these filaments to cool to the base of the cooling function, resulting in a very striking pattern of extended Lyman-limit systems (LLSs). Observations of the correlation function of LLSs might hence provide useful limits on the nature of the dark matter. We argue that the self-shielding of filaments may lead to a thermal instability resulting in star formation. We implement a sub-grid model for this, and find that filaments rather than haloes dominate star formation until z 6. Reionisation decreases the gas density in filaments, and the more usual star formation in haloes dominates below z 6, although star formation in filaments continues until z=2. Fifteen per cent of the stars of the z=0 galaxy formed in filaments. At hi...

  1. Multi-scale strain-stiffening of semiflexible bundle networks

    CERN Document Server

    Piechocka, I K; Broedersz, C P; Kurniawan, N A; MacKintosh, F C; Koenderink, G H

    2015-01-01

    Bundles of polymer filaments are responsible for the rich and unique mechanical behaviors of many biomaterials, including cells and extracellular matrices. In fibrin biopolymers, whose nonlinear elastic properties are crucial for normal blood clotting, protofibrils self-assemble and bundle to form networks of semiflexible fibers. Here we show that the extraordinary strain-stiffening response of fibrin networks is a direct reflection of the hierarchical architecture of the fibrin fibers. We measure the rheology of networks of unbundled protofibrils and find excellent agreement with an affine model of extensible wormlike polymers. By direct comparison with these data, we show that physiological fibrin networks composed of thick fibers can be modeled as networks of tight protofibril bundles. We demonstrate that the tightness of coupling between protofibrils in the fibers can be tuned by the degree of enzymatic intermolecular crosslinking by the coagulation Factor XIII. Furthermore, at high stress, the protofibri...

  2. Buckling a Semiflexible Polymer Chain under Compression

    Directory of Open Access Journals (Sweden)

    Ekaterina Pilyugina

    2017-03-01

    Full Text Available Instability and structural transitions arise in many important problems involving dynamics at molecular length scales. Buckling of an elastic rod under a compressive load offers a useful general picture of such a transition. However, the existing theoretical description of buckling is applicable in the load response of macroscopic structures, only when fluctuations can be neglected, whereas membranes, polymer brushes, filaments, and macromolecular chains undergo considerable Brownian fluctuations. We analyze here the buckling of a fluctuating semiflexible polymer experiencing a compressive load. Previous works rely on approximations to the polymer statistics, resulting in a range of predictions for the buckling transition that disagree on whether fluctuations elevate or depress the critical buckling force. In contrast, our theory exploits exact results for the statistical behavior of the worm-like chain model yielding unambiguous predictions about the buckling conditions and nature of the buckling transition. We find that a fluctuating polymer under compressive load requires a larger force to buckle than an elastic rod in the absence of fluctuations. The nature of the buckling transition exhibits a marked change from being distinctly second order in the absence of fluctuations to being a more gradual, compliant transition in the presence of fluctuations. We analyze the thermodynamic contributions throughout the buckling transition to demonstrate that the chain entropy favors the extended state over the buckled state, providing a thermodynamic justification of the elevated buckling force.

  3. Semiflexible particles in isotropic turbulence

    Science.gov (United States)

    Ali, Aamir; Plan, Emmanuel Lance Christopher Medillo, VI; Ray, Samriddhi Sankar; Vincenzi, Dario

    2016-12-01

    The Lagrangian dynamics of semiflexible particles in homogeneous and isotropic turbulent flows is studied by means of analytically solvable stochastic models and direct numerical simulations. The stationary statistics of the bending angle shows a strong dependence on the dimension of the flow. In two-dimensional turbulence, particles are found in either a fully extended or a fully folded configuration; in three dimensions, the predominant configuration is the fully extended one. Such a sensitivity of the bending statistics on the dimensionality of the flow is peculiar to fluctuating flows and is not observed in laminar stretching flows.

  4. Modelling the morphology of filamentous microorganisms

    DEFF Research Database (Denmark)

    Nielsen, Jens Bredal

    1996-01-01

    The rapid development in image analysis techniques has made it possible to study the growth kinetics of filamentous microorganisms in more detail than previously, However, owing to the many different processes that influence the morphology it is important to apply mathematical models to extract...

  5. Dynamics of semiflexible regular hyperbranched polymers

    Science.gov (United States)

    Fürstenberg, Florian; Dolgushev, Maxim; Blumen, Alexander

    2013-01-01

    We study the dynamics of semiflexible Vicsek fractals (SVF) following the framework established by Dolgushev and Blumen [J. Chem. Phys. 131, 044905 (2009), 10.1063/1.3184797], a scheme which allows to model semiflexible treelike polymers of arbitrary architecture. We show, extending the methods used in the treatment of semiflexible dendrimers by Fürstenberg et al. [J. Chem. Phys. 136, 154904 (2012), 10.1063/1.3703757], that in this way the Langevin-dynamics of SVF can be treated to a large part analytically. For this we show for arbitrary Vicsek fractals (VF) how to construct complete sets of eigenvectors; these reduce considerably the diagonalization problem of the corresponding equations of motion. In fact, such eigenvector sets arise naturally from a hierarchical procedure which follows the iterative construction of the VF. We use the obtained eigenvalues to calculate the loss moduli G″(ω) of SVF for different degrees of stiffness of the junctions. Finally, we compare the results for SVF to those found for semiflexible dendrimers.

  6. Rheology of semiflexible bundle networks with transient linkers.

    Science.gov (United States)

    Müller, Kei W; Bruinsma, Robijn F; Lieleg, Oliver; Bausch, Andreas R; Wall, Wolfgang A; Levine, Alex J

    2014-06-13

    We present a theoretical and computational analysis of the rheology of networks made up of bundles of semiflexible filaments bound by transient cross-linkers. Such systems are ubiquitous in the cytoskeleton and can be formed in vitro using filamentous actin and various cross-linkers. We find that their high-frequency rheology is characterized by a scaling behavior that is quite distinct from that of networks of the well-studied single semiflexible filaments. This regime can be understood theoretically in terms of a length-scale-dependent bending modulus for bundles. Next, we observe new dissipative dynamics associated with the shear-induced disruption of the network at intermediate frequencies. Finally, at low frequencies, we encounter a region of non-Newtonian rheology characterized by power-law scaling. This regime is dominated by bundle dissolution and large-scale rearrangements of the network driven by equilibrium thermal fluctuations.

  7. Self-assembly of semiflexible-flexible block copolymers

    Science.gov (United States)

    Kumar, Arun; Ganesan, Venkat

    2012-02-01

    We apply self-consistent Brownian dynamics simulations to study the self-assembly behavior of semiflexible-flexible block copolymers. A Maier-Saupe interaction model was applied for the orientational interactions between the semiflexible polymers, while the enthalpic interactions between semiflexible and flexible polymers were modeled through a standard Flory-Huggins approach. To develop a physical understanding of the phases and their regimes of occurrence as a function of varying persistence length of the semiflexible block, we computed the 2D phase diagram for our model. We quantify the progression of the self-assembly morphologies in transitioning from coil-coil block copolymers on the one hand to rod-coil block copolymers on the other hand. The results obtained are in qualitative agreement with the existing experimental and numerical results.

  8. Laser filamentation mathematical methods and models

    CERN Document Server

    Lorin, Emmanuel; Moloney, Jerome

    2016-01-01

    This book is focused on the nonlinear theoretical and mathematical problems associated with ultrafast intense laser pulse propagation in gases and in particular, in air. With the aim of understanding the physics of filamentation in gases, solids, the atmosphere, and even biological tissue, specialists in nonlinear optics and filamentation from both physics and mathematics attempt to rigorously derive and analyze relevant non-perturbative models. Modern laser technology allows the generation of ultrafast (few cycle) laser pulses, with intensities exceeding the internal electric field in atoms and molecules (E=5x109 V/cm or intensity I = 3.5 x 1016 Watts/cm2 ). The interaction of such pulses with atoms and molecules leads to new, highly nonlinear nonperturbative regimes, where new physical phenomena, such as High Harmonic Generation (HHG), occur, and from which the shortest (attosecond - the natural time scale of the electron) pulses have been created. One of the major experimental discoveries in this nonlinear...

  9. Filament winding cylinders. I - Process model

    Science.gov (United States)

    Lee, Soo-Yong; Springer, George S.

    1990-01-01

    A model was developed which describes the filament winding process of composite cylinders. The model relates the significant process variables such as winding speed, fiber tension, and applied temperature to the thermal, chemical and mechanical behavior of the composite cylinder and the mandrel. Based on the model, a user friendly code was written which can be used to calculate (1) the temperature in the cylinder and the mandrel, (2) the degree of cure and viscosity in the cylinder, (3) the fiber tensions and fiber positions, (4) the stresses and strains in the cylinder and in the mandrel, and (5) the void diameters in the cylinder.

  10. Modelling the chemistry of star forming filaments

    CERN Document Server

    Seifried, D

    2015-01-01

    We present simulations of star forming filaments incorporating - to our knowledge - the largest chemical network used to date on-the-fly in a 3D-MHD simulation. The network contains 37 chemical species and about 300 selected reaction rates. For this we use the newly developed package KROME (Grassi et al. 2014). We combine the KROME package with an algorithm which allows us to calculate the column density and attenuation of the interstellar radiation field necessary to properly model heating and ionisation rates. Our results demonstrate the feasibility of using such a complex chemical network in 3D-MHD simulations on modern supercomputers. We perform simulations with different strengths of the interstellar radiation field and the cosmic ray ionisation rate. We find that towards the centre of the filaments there is gradual conversion of hydrogen from H^+ over H to H_2 as well as of C^+ over C to CO. Moreover, we find a decrease of the dust temperature towards the centre of the filaments in agreement with recent...

  11. Conformation and intramolecular relaxation dynamics of semiflexible randomly hyperbranched polymers

    Science.gov (United States)

    Kumar, Amit; Rai, Gobind Ji; Biswas, Parbati

    2013-03-01

    The conformational and dynamic properties of semiflexible randomly hyperbranched polymers are investigated in dilute solutions within the framework of optimized Rouse-Zimm formalism. Semiflexibility is incorporated by restricting the directions and orientations of the respective bond vectors, while hydrodynamic interactions are modeled through the preaveraged Oseen tensor. The effect of semiflexibility is typically reflected in the intermediate frequency regime of the viscoelastic relaxation moduli where the bond orientation angle restores the characteristic power-law scaling in fractal structures, as in randomly hyperbranched polymers. Despite the absence of this power-law scaling regime in flexible randomly hyperbranched polymers and in earlier models of semiflexible randomly branched polymers due to weak disorder [C. von Ferber and A. Blumen, J. Chem. Phys. 116, 8616 (2002)], 10.1063/1.1470198, this power-law behavior may be reinstated by explicitly modeling hyperbranched polymers as a Vicsek fractals. The length of this power-law zone in the intermediate frequency region is a combined function of the number of monomers and the degree of semiflexibility. A clear conformational transition from compact to open structures is facilitated by changing the bond orientation angle, where the compressed conformations are compact, while the expanded ones are relatively non-compact. The extent of compactness in the compressed conformations are much less compared to the semiflexible dendrimers, which resemble hard spheres. The fractal dimensions of the compressed and expanded conformations calculated from the Porod's scaling law vary as a function of the bond orientation angle, spanning the entire range of three distinct scaling regimes of linear polymers in three-dimensions. The results confirm that semiflexibility exactly accounts for the excluded volume interactions which are expected to be significant for such polymers with complex topologies.

  12. Validation of the filament winding process model

    Science.gov (United States)

    Calius, Emilo P.; Springer, George S.; Wilson, Brian A.; Hanson, R. Scott

    1987-01-01

    Tests were performed toward validating the WIND model developed previously for simulating the filament winding of composite cylinders. In these tests two 24 in. long, 8 in. diam and 0.285 in. thick cylinders, made of IM-6G fibers and HBRF-55 resin, were wound at + or - 45 deg angle on steel mandrels. The temperatures on the inner and outer surfaces and inside the composite cylinders were recorded during oven cure. The temperatures inside the cylinders were also calculated by the WIND model. The measured and calculated temperatures were then compared. In addition, the degree of cure and resin viscosity distributions inside the cylinders were calculated for the conditions which existed in the tests.

  13. Modelling the chemistry of star-forming filaments - II. Testing filament characteristics with synthetic observations

    Science.gov (United States)

    Seifried, D.; Sánchez-Monge, Á.; Suri, S.; Walch, S.

    2017-06-01

    We present synthetic continuum and 13CO and C18O line emission observations of dense and cold filaments. The filaments are dynamically evolved using 3D-magnetohydrodynamic simulations that include one of the largest on-the-fly chemical networks used to date, which models the detailed evolution of H2 and CO. We investigate the reliability of observable properties, in particular filament mass and width, under different simulation conditions like magnetic field orientation and cosmic ray ionization rate. We find that filament widths of ˜0.1 pc can be probed with both line and continuum emission observations with a high accuracy (deviations ≤20 per cent). However, the width of more narrow filaments can be significantly overestimated by up to a factor of a few. Masses obtained via the dust emission are accurate within a few per cent whereas the masses inferred from molecular line emission observations deviate from the actual mass by up to a factor of 10 and show large differences for different J transitions. The inaccurate estimate of filament masses and widths of narrow filaments using molecular line observations can be attributed to (i) the non-isothermal state of the filaments, (ii) optical depth effects and (iii) the subthermally excited state of CO, while inclination effects and opacity correction only influence the obtained masses and widths by less than 50 per cent. Both, mass and width estimates, can be improved by using two isotopes to correct for the optical depth. Since gas and dust temperatures generally differ (by up to 25 K), the filaments appear more gravitationally unstable if the (too low) dust temperature is used for the stability analysis.

  14. Relaxation Dynamics of Semiflexible Fractal Macromolecules

    Directory of Open Access Journals (Sweden)

    Jonas Mielke

    2016-07-01

    Full Text Available We study the dynamics of semiflexible hyperbranched macromolecules having only dendritic units and no linear spacers, while the structure of these macromolecules is modeled through T-fractals. We construct a full set of eigenmodes of the dynamical matrix, which couples the set of Langevin equations. Based on the ensuing relaxation spectra, we analyze the mechanical relaxation moduli. The fractal character of the macromolecules reveals itself in the storage and loss moduli in the intermediate region of frequencies through scaling, whereas at higher frequencies, we observe the locally-dendritic structure that is more pronounced for higher stiffness.

  15. Adsorption of finite semiflexible polymers and their loop and tail distributions

    Science.gov (United States)

    Kampmann, Tobias A.; Kierfeld, Jan

    2017-07-01

    We discuss the adsorption of semiflexible polymers to a planar attractive wall and focus on the questions of the adsorption threshold for polymers of finite length and their loop and tail distributions using both Monte Carlo simulations and analytical arguments. For the adsorption threshold, we find three regimes: (i) a flexible or Gaussian regime if the persistence length is smaller than the adsorption potential range, (ii) a semiflexible regime if the persistence length is larger than the potential range, and (iii) for finite polymers, a novel crossover to a rigid rod regime if the deflection length exceeds the contour length. In the flexible and semiflexible regimes, finite size corrections arise because the correlation length exceeds the contour length. In the rigid rod regime, however, it is essential how the global orientational or translational degrees of freedom are restricted by grafting or confinement. We discuss finite size corrections for polymers grafted to the adsorbing surface and for polymers confined by a second (parallel) hard wall. Based on these results, we obtain a method to analyze adsorption data for finite semiflexible polymers such as filamentous actin. For the loop and tail distributions, we find power laws with an exponential decay on length scales exceeding the correlation length. We derive and confirm the loop and tail power law exponents for flexible and semiflexible polymers. This allows us to explain that, close to the transition, semiflexible polymers have significantly smaller loops and both flexible and semiflexible polymers desorb by expanding their tail length. The tail distribution allows us to extract the free energy per length of adsorption for actin filaments from experimental data [D. Welch et al., Soft Matter 11, 7507 (2015)].

  16. Forced desorption of semiflexible polymers, adsorbed and driven by molecular motors

    CERN Document Server

    Chaudhuri, Abhishek

    2014-01-01

    We formulate and characterize a model to describe dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the filament. The stochastic binding-unbinding of the motor proteins and their ability to move along the polymer, generates active forces. As the pulling force reaches a threshold value, the polymer eventually desorbs from the substrate. We present a mean field theory that predicts increase in desorption force with polymer bending rigidity, active velocity and processivity of the motor proteins. Performing molecular dynamics simulations of the polymer in presence of a Langevin heat bath, and stochastic motor activity we obtain desorption phase diagrams that show good agreement with theory. With increase in pulling force, the polymer undergoes a first order phase transition from mostly adsorbed to fully desorbed state via a regime of coexistence where the steady state dynamics of the polyme...

  17. Direct visualization of flow-induced conformational transitions of single actin filaments in entangled solutions

    CERN Document Server

    Kirchenbuechler, Inka; Kurniawan, Nicholas A; Koenderink, Gijsje H; Lettinga, M Paul

    2015-01-01

    While semi-flexible polymers and fibers are an important class of material due to their rich mechanical properties, it remains unclear how these properties relate to the microscopic conformation of the polymers. Actin filaments constitute an ideal model polymer system due to their micron-sized length and relatively high stiffness that allow imaging at the single filament level. Here we study the effect of entanglements on the conformational dynamics of actin filaments in shear flow. We directly measure the full three-dimensional conformation of single actin filaments, using confocal microscopy in combination with a counter-rotating cone-plate shear cell. We show that initially entangled filaments form disentangled orientationally ordered hairpins, confined in the flow-vorticity plane. In addition, shear flow causes stretching and shear alignment of the hairpin tails, while the filament length distribution remains unchanged. These observations explain the strain-softening and shear-thinning behavior of entangl...

  18. Filamentous Phages As a Model System in Soft Matter Physics.

    Science.gov (United States)

    Dogic, Zvonimir

    2016-01-01

    Filamentous phages have unique physical properties, such as uniform particle lengths, that are not found in other model systems of rod-like colloidal particles. Consequently, suspensions of such phages provided powerful model systems that have advanced our understanding of soft matter physics in general and liquid crystals in particular. We described some of these advances. In particular we briefly summarize how suspensions of filamentous phages have provided valuable insight into the field of colloidal liquid crystals. We also describe recent experiments on filamentous phages that have elucidated a robust pathway for assembly of 2D membrane-like materials. Finally, we outline unique structural properties of filamentous phages that have so far remained largely unexplored yet have the potential to further advance soft matter physics and material science.

  19. Current state of genome-scale modeling in filamentous fungi

    DEFF Research Database (Denmark)

    Brandl, Julian; Andersen, Mikael Rørdam

    2015-01-01

    The group of filamentous fungi contains important species used in industrial biotechnology for acid, antibiotics and enzyme production. Their unique lifestyle turns these organisms into a valuable genetic reservoir of new natural products and biomass degrading enzymes that has not been used to full...... testing them in vivo. The increasing availability of high quality models and molecular biological tools for manipulating filamentous fungi renders the model-guided engineering of these fungal factories possible with comprehensive metabolic networks. A typical fungal model contains on average 1138 unique...... metabolic reactions and 1050 ORFs, making them a vast knowledge-base of fungal metabolism. In the present review we focus on the current state as well as potential future applications of genome-scale models in filamentous fungi....

  20. Dynamics of Actin Filament Ends in a Network

    Science.gov (United States)

    Yang, Le; Sept, David; Carlsson, Anders

    2004-03-01

    The formation of filopodia-like bundles in vitro from a dendritic actin network has been observed(D. Vignjevic et al, J. Cell Biol. 160, 951 (2003)) to occur as a result of a nucleation process. We study the dynamics of the actin filament ends in such a network in order to evaluate the dynamics of the bundle nucleation process. Our model treats two semiflexible actin filaments fixed at one end and free at the other, moving according to Brownian dynamics. The initial filament positions are chosen according to a thermal distribution, and we evaluate the time for the filaments to come close enough to each other to interact and bind. The capture criterion is based either on the distance between filaments, or on a combination of distance and relative orientation. We evaluate the dependence of the capture time on the filament length and radius, and the distance between the filament bases. Since treating the movement of the individual monomers in filaments is computationally unwieldy, we treat the filament motion using a normal mode analysis which permits use of a much longer timestep. We find that this method yields rapid convergence even when only the few longest-wavelength modes are included.

  1. Yeast and filamentous fungi as model organisms in microbody research

    NARCIS (Netherlands)

    Klei, Ida J. van der; Veenhuis, Marten

    2006-01-01

    Yeast and filamentous fungi are important model organisms in microbody research. The value of these organisms as models for higher eukaryotes is underscored by the observation that the principles of various aspects of microbody biology are strongly conserved from lower to higher eukaryotes. This has

  2. Analytical & Numerical Modelings of Elliptical Superconducting Filament Magnetization

    CERN Document Server

    Bottura, L; Bouillault, F; Devred, Arnaud

    2005-01-01

    This paper deals with the two-dimensional computation of magnetization in an elliptic superconducting filament by using numerical and analytical methods. The numerical results are obtained from the finite element method and by using Bean's model. This model is well adapted for Low Tc superconductor studies. We observe the effect of the axis ratio and of the field angle to the magnetic moment per unit length at saturation, and also to the cycle of magnetization. Moreover, the current density and the distribution of the electromagnetic fields in the superconducting filament are also studied.

  3. Semiflexible Biopolymers in Bundled Arrangements

    Directory of Open Access Journals (Sweden)

    Jörg Schnauß

    2016-07-01

    Full Text Available Bundles and networks of semiflexible biopolymers are key elements in cells, lending them mechanical integrity while also enabling dynamic functions. Networks have been the subject of many studies, revealing a variety of fundamental characteristics often determined via bulk measurements. Although bundles are equally important in biological systems, they have garnered much less scientific attention since they have to be probed on the mesoscopic scale. Here, we review theoretical as well as experimental approaches, which mainly employ the naturally occurring biopolymer actin, to highlight the principles behind these structures on the single bundle level.

  4. Modeling the Galactic Center Nonthermal Filaments as Magnetized Wake

    CERN Document Server

    Dahlburg, R B; La Rosa, T N; Shore, S N; Dahlburg, Russell B.; Einaudi, Giorgio; Shore, Steven N.

    2001-01-01

    We simulate the Galactic Center nonthermal filaments as magnetized wakes formed dynamically from amplification of a weak (tens of $\\mu$G) global magnetic field through the interaction of molecular clouds with a Galactic Center wind. One of the key issues in this cometary model is the stability of the filament against dynamical disruption. Here we show 2-dimensional MHD simulations for interstellar conditions that are appropriate for the Galactic Center. The structures eventually disrupt through a shear driven nonlinear instability but maintain coherence for lengths up to 100 times their width as observed. The final instability, which destroys the filament through shredding and plasmoid formation, grows quickly in space (and time) and leads to an abrupt end to the structure, in accord with observations. As a by-product, the simulation shows that emission should peak well downstream from the cloud-wind interaction site.

  5. Stretching a Semiflexible Polymer in a Tube

    Directory of Open Access Journals (Sweden)

    Runhua Li

    2016-09-01

    Full Text Available How the statistical behavior of semiflexible polymer chains may be affected by force stretching and tube confinement is a classical unsolved problem in polymer physics. Based on the Odijk deflection theory and normal mode decomposition in terms of Fourier expansion, we have derived a new compact formula for the extension of a wormlike chain of finite length strongly confined in a tube and simultaneously stretched by an external force. We have also suggested a new deflection length, which together with the force-extension relation is valid for a very extended range of the tube-diameter/persistence-length ratio comparing to the classic Odijk theory. The newly derived formula has no adjustable fitting parameters for the whole deflection regime; in contrast, the classic Odijk length needs different prefactors to fit the free energy and average extension, respectively. Brownian dynamics simulations based on the Generalized Bead-Rod (GBR model were extensively performed, which justified the theoretical predictions.

  6. Adiabatic Floquet model for the optical response in femtosecond filaments

    CERN Document Server

    Hofmann, Michael

    2016-01-01

    The standard model of femtosecond filamentation is based on phenomenological assumptions which suggest that the ionization-induced carriers can be treated as free according to the Drude model, while the nonlinear response of the bound carriers follows the all-optical Kerr effect. Here, we demonstrate that the additional plasma generated at a multiphoton resonance dominates the saturation of the nonlinear refractive index. Since resonances are not captured by the standard model, we propose a modification of the latter in which ionization enhancements can be accounted for by an ionization rate obtained from non-Hermitian Floquet theory. In the adiabatic regime of long pulse envelopes, this augmented standard model is in excellent agreement with direct quantum mechanical simulations. Since our proposal maintains the structure of the standard model, it can be easily incorporated into existing codes of filament simulation.

  7. A Magnetic Ribbon Model for Star-Forming Filaments

    CERN Document Server

    Auddy, Sayantan; Kudoh, Takahiro

    2016-01-01

    We develop a magnetic ribbon model for molecular cloud filaments. These result from turbulent compression in a molecular cloud in which the background magnetic field sets a preferred direction. We argue that this is a natural model for filaments and is based on the interplay between turbulence, strong magnetic fields, and gravitationally-driven ambipolar diffusion, rather than pure gravity and thermal pressure. An analytic model for the formation of magnetic ribbons that is based on numerical simulations is used to derive a lateral width of a magnetic ribbon. This differs from the thickness along the magnetic field direction, which is essentially the Jeans scale. We use our model to calculate a synthetic observed relation between apparent width in projection versus observed column density. The relationship is relatively flat, similar to observations, and unlike the simple expectation based on a Jeans length argument.

  8. A Magnetic Ribbon Model for Star-forming Filaments

    Science.gov (United States)

    Auddy, Sayantan; Basu, Shantanu; Kudoh, Takahiro

    2016-11-01

    We develop a magnetic ribbon model for molecular cloud filaments. These result from turbulent compression in a molecular cloud in which the background magnetic field sets a preferred direction. We argue that this is a natural model for filaments and is based on the interplay between turbulence, strong magnetic fields, and gravitationally driven ambipolar diffusion, rather than pure gravity and thermal pressure. An analytic model for the formation of magnetic ribbons that is based on numerical simulations is used to derive a lateral width of a magnetic ribbon. This differs from the thickness along the magnetic field direction, which is essentially the Jeans scale. We use our model to calculate a synthetic observed relation between apparent width in projection versus observed column density. The relationship is relatively flat, similar to observations, and unlike the simple expectation based on a Jeans length argument.

  9. Jamming of Semiflexible Polymers

    Science.gov (United States)

    Hoy, Robert S.

    2017-02-01

    We study jamming in model freely rotating polymers as a function of chain length N and bond angle θ0. The volume fraction at jamming ϕJ(θ0) is minimal for rigid-rodlike chains (θ0=0 ), and increases monotonically with increasing θ0≤π /2 . In contrast to flexible polymers, marginally jammed states of freely rotating polymers are highly hypostatic, even when bond and angle constraints are accounted for. Large-aspect-ratio (small θ0) chains behave comparably to stiff fibers: resistance to large-scale bending plays a major role in their jamming phenomenology. Low-aspect-ratio (large θ0) chains behave more like flexible polymers, but still jam at much lower densities due to the presence of frozen-in three-body correlations corresponding to the fixed bond angles. Long-chain systems jam at lower ϕ and are more hypostatic at jamming than short-chain systems. Implications of these findings for polymer solidification are discussed.

  10. On semiflexible, flexible and pie algebras

    CERN Document Server

    Bourke, John

    2011-01-01

    We introduce the notion of pie algebra for a 2-monad, these bearing the same relationship to the flexible and semiflexible algebras as pie limits do to flexible and semiflexible ones. We see that in many cases, the pie algebras are precisely those "free at the level of objects" in a suitable sense; so that, for instance, a strict monoidal category is pie just when its underlying monoid of objects is free. Pie algebras are contrasted with flexible and semiflexible algebras via a series of characterisations of each class; particular attention is paid to the case of pie, flexible and semiflexible weights, these being characterised in terms of the behaviour of the corresponding weighted limit functors.

  11. Current state of genome-scale modeling in filamentous fungi.

    Science.gov (United States)

    Brandl, Julian; Andersen, Mikael R

    2015-06-01

    The group of filamentous fungi contains important species used in industrial biotechnology for acid, antibiotics and enzyme production. Their unique lifestyle turns these organisms into a valuable genetic reservoir of new natural products and biomass degrading enzymes that has not been used to full capacity. One of the major bottlenecks in the development of new strains into viable industrial hosts is the alteration of the metabolism towards optimal production. Genome-scale models promise a reduction in the time needed for metabolic engineering by predicting the most potent targets in silico before testing them in vivo. The increasing availability of high quality models and molecular biological tools for manipulating filamentous fungi renders the model-guided engineering of these fungal factories possible with comprehensive metabolic networks. A typical fungal model contains on average 1138 unique metabolic reactions and 1050 ORFs, making them a vast knowledge-base of fungal metabolism. In the present review we focus on the current state as well as potential future applications of genome-scale models in filamentous fungi.

  12. Thin Filament Structure and the Steric Blocking Model.

    Science.gov (United States)

    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.

  13. Discontinuous bundling transition in semiflexible polymer networks induced by Casimir interactions

    Science.gov (United States)

    Kachan, Devin; Müller, Kei W.; Wall, Wolfgang A.; Levine, Alex J.

    2016-09-01

    Fluctuation-induced interactions are an important organizing principle in a variety of soft matter systems. We investigate the role of fluctuation-based or thermal Casimir interactions between cross linkers in a semiflexible network. One finds that, by integrating out the polymer degrees of freedom, there is an attractive logarithmic potential between nearest-neighbor cross linkers in a bundle, with a significantly weaker next-nearest-neighbor interaction. Here we show that a one-dimensional gas of these strongly interacting linkers in equilibrium with a source of unbound ones admits a discontinuous phase transition between a sparsely and a densely bound bundle. This discontinuous transition induced by the long-ranged nature of the Casimir interaction allows for a similarly abrupt structural transition in semiflexible filament networks between a low cross linker density isotropic phase and a higher cross link density bundle network. We support these calculations with the results of finite element Brownian dynamics simulations of semiflexible filaments and transient cross linkers.

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

    Energy Technology Data Exchange (ETDEWEB)

    Splettstoesser, Thomas [University of Heidelberg; Holmes, Kenneth [Max Planck Institute, Heidelberg, Germany; Noe, Frank [DFG Research Center Matheon, FU Berlin, Germany; Smith, Jeremy C [ORNL

    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.

  15. Modeling of the growth of filamentous fungi in artificial microstructures

    Science.gov (United States)

    Nicolau, Dan V., Jr.; Hanson, Kristi; Nicolau, Dan V.

    2006-01-01

    We present a stochastic and spatial Monte Carlo model for the growth of a fungal colony in microstructures. This model is based on an "L-system-like" representation of filaments as individual objects. Each of these can both grow in space (and be diverted by obstacles) and can send new branches. All parameters in the model such as filament dimensions, the growth speed, behavior at and around obstacles, branching angle and frequency and others are obtained from experimental studies of growth in artificial microstructures. We investigate four different possible "strategies" the colony might use to achieve the tasks of (a) filling the available space and (2) finding its way out of the structures. The simulation results indicate that a combination of directional memory and a stop-and-branch behavior at corners gives the best results and observe that in fact this is similar to the experimentally observed behavior of the fungi. The model is expected to be of use in studying the colonization of microstructures by fungi and in the design of devices either using fungal growth or aiming to inhibit it.

  16. Filament winding cylinders. II - Validation of the process model

    Science.gov (United States)

    Calius, Emilio P.; Lee, Soo-Yong; Springer, George S.

    1990-01-01

    Analytical and experimental studies were performed to validate the model developed by Lee and Springer for simulating the manufacturing process of filament wound composite cylinders. First, results calculated by the Lee-Springer model were compared to results of the Calius-Springer thin cylinder model. Second, temperatures and strains calculated by the Lee-Springer model were compared to data. The data used in these comparisons were generated during the course of this investigation with cylinders made of Hercules IM-6G/HBRF-55 and Fiberite T-300/976 graphite-epoxy tows. Good agreement was found between the calculated and measured stresses and strains, indicating that the model is a useful representation of the winding and curing processes.

  17. Ordered quasi-two-dimensional structure of nanoparticles in semiflexible ring polymer brushes under compression

    Science.gov (United States)

    Hua, Yunfeng; Deng, Zhenyu; Jiang, Yangwei; Zhang, Linxi

    2017-06-01

    Molecular dynamics simulations of a coarse-grained bead-spring model of ring polymer brushes under compression are presented. Flexible polymer brushes are always disordered during compression, whereas semiflexible polymer brushes tend to be ordered under sufficiently strong compression. Further, the polymer monomer density of the semiflexible polymer brush is very high near the brush surface, inducing a peak value of the free energy near the surface. Therefore, when nanoparticles are compressed in semiflexible ring polymer brushes, they tend to exhibit a closely packed single-layer structure between the brush surface and the impenetrable wall, and a quasi-two-dimensional ordered structure near the brush surface is formed under strong compression. These findings provide a new approach to designing responsive applications.

  18. The Breakout Model for Coronal Jets with Filaments

    Science.gov (United States)

    Wyper, Peter; DeVore, C. Richard; Antiochos, Spiro K.

    2016-05-01

    Coronal jets are impulsive, collimated plasma outflows originating low in the solar corona. Many of these events exhibit broad, curtain-like morphologies with helical structure and motions. Recently, Sterling et al. (2015) [doi:10.1038/nature14556] reported that such jets are associated with the eruption of small filaments and, therefore, are miniature versions of corona mass ejections (CMEs). This account differs from the traditional picture of jets, in that internal flare reconnection, rather than interchange reconnection with the external ambient magnetic field, creates the bright loops observed at the jet base. We present 3D simulations, performed with the Adaptively Refined MHD Solver (ARMS), which demonstrate how the magnetic breakout mechanism generates mini-CME-type jets in a compact bipolar region energized by simple footpoint motions. Our numerical model captures the formation of the strongly sheared pre-jet filament structure, the post-jet flare-like loops and ribbons, and the curtain-like untwisting dynamics observed higher in the corona. We will discuss the significance of our new results for understanding solar EUV and X-ray jets and CMEs in general. NASA supported this research by awards to the NASA Postdoctoral Program (P.F.W.) and the LWS TR&T and H-SR programs (C.R.D. & S.K.A.).

  19. Bending dynamics of semi-flexible macromolecules in isotropic turbulence

    CERN Document Server

    Ali, Aamir; Vincenzi, Dario

    2014-01-01

    We study the Lagrangian dynamics of semi-flexible macromolecules in laminar as well as in homogeneous and isotropic turbulent flows by means of analytically solvable stochastic models and direct numerical simulations. The statistics of the bending angle is qualitatively different in laminar and turbulent flows and exhibits a strong dependence on the topology of the velocity field. In particular, in two-dimensional turbulence, particles are either found in a fully extended or in a fully folded configuration; in three dimensions, the predominant configuration is the fully extended one.

  20. Tetrahedral collapse: a rotational toy model of simultaneous dark-matter halo, filament and wall formation

    Science.gov (United States)

    Neyrinck, Mark C.

    2016-07-01

    We discuss an idealized model of halo formation, in which a collapsing halo node is tetrahedral, with a filament extruding from each of its four faces, and with a wall connecting each pair of filaments. In the model, filaments generally spin when they form, and the halo spins if and only if there is some rotation in filaments. This is the simplest possible fully three-dimensional halo collapse in the `origami approximation', in which voids are irrotational, and the dark-matter sheet out of which dark-matter structures form is allowed to fold in position-velocity phase space, but not stretch (i.e. it cannot vary in density along a stream). Up to an overall scaling, the four filament directions, and only three other quantities, such as filament spins, suffice to determine all of the collapse's properties: the shape, mass, and spin of the halo; the densities per unit length and spins of all filaments; and masses per unit area of the walls. If the filaments are arranged regular-tetrahedrally, filament properties obey simple laws, reminiscent of angular-momentum conservation. The model may be most useful in understanding spin correlations between neighbouring galaxies joined by filaments; these correlations would give intrinsic alignments between galaxies, essential to understand for accurate cosmological weak-lensing measurements.

  1. A two-segment model for thin filament architecture in skeletal muscle.

    Science.gov (United States)

    Gokhin, David S; Fowler, Velia M

    2013-02-01

    Correct specification of myofilament length is essential for efficient skeletal muscle contraction. The length of thin actin filaments can be explained by a novel 'two-segment' model, wherein the thin filaments consist of two concatenated segments, which are of either constant or variable length. This is in contrast to the classic 'nebulin ruler' model, which postulates that thin filaments are uniform structures, the lengths of which are dictated by nebulin. The two-segment model implicates position-specific microregulation of actin dynamics as a general principle underlying actin filament length and stability.

  2. Biomass density and filament length synergistically affect activated sludge settling: systematic quantification and modeling.

    Science.gov (United States)

    Jassby, D; Xiao, Y; Schuler, A J

    2014-01-01

    Settling of the biomass produced during biological treatment of wastewater is a critical and often problematic process. Filamentous bacteria content is the best-known factor affecting biomass settleability in activated sludge wastewater treatment systems, and varying biomass density has recently been shown to play an important role as well. The objective of this study was to systematically determine how filament content and biomass density combine to affect microbial biomass settling, with a focus on density variations over the range found in full-scale systems. A laboratory-scale bioreactor system was operated to produce biomass with a range of filamentous bacterium contents. Biomass density was systematically varied in samples from this system by addition of synthetic microspheres to allow separation of filament content and density effects on settleability. Fluorescent in-situ hybridization indicated that the culture was dominated by Sphaerotilus natans, a common contributor to poor settling in full-scale systems. A simple, image-based metric of filament content (filament length per floc area) was linearly correlated with the more commonly used filament length per dry biomass measurement. A non-linear, semi-empirical model of settleability as a function of filament content and density was developed and evaluated, providing a better understanding of how these two parameters combine to affect settleability. Filament content (length per dry biomass weight) was nearly linearly related to sludge volume index (SVI) values, with a slightly decreasing differential, and biomass density exhibited an asymptotic relationship with SVI. The filament content associated with bulking was shown to be a function of biomass density. The marginal effect of filament content on settleability increased with decreasing biomass density (low density biomass was more sensitive to changes in filament content than was high density biomass), indicating a synergistic relationship between these

  3. Different approaches to modeling the LANSCE H- ion source filament performance

    Science.gov (United States)

    Draganic, I. N.; O'Hara, J. F.; Rybarcyk, L. J.

    2016-02-01

    An overview of different approaches to modeling of hot tungsten filament performance in the Los Alamos Neutron Science Center (LANSCE) H- surface converter ion source is presented. The most critical components in this negative ion source are two specially shaped wire filaments heated up to the working temperature range of 2600 K-2700 K during normal beam production. In order to prevent catastrophic filament failures (creation of hot spots, wire breaking, excessive filament deflection towards source body, etc.) and to improve understanding of the material erosion processes, we have simulated the filament performance using three different models: a semi-empirical model, a thermal finite-element analysis model, and an analytical model. Results of all three models were compared with data taken during LANSCE beam production. The models were used to support the recent successful transition from the beam pulse repetition rate of 60 Hz-120 Hz.

  4. Current-vortex filament model of nonlinear Alfven perturbations in a finite-pressure plasma

    NARCIS (Netherlands)

    Lakhin, V. P.; Schep, T. J.; Westerhof, E.

    1998-01-01

    A low-beta, two-fluid model is shown to possess solutions in the form of current-vortex filaments. The model can be viewed as that of reduced magnetohydrodynamics, extended with electron inertia, the Hall term and parallel electron pressure. These drift-Alfven filaments are the plasma analogs of poi

  5. Phase Diagram and Effective Shape of Semiflexible Colloidal Rods and Biopolymers

    NARCIS (Netherlands)

    Dennison, M; Dijkstra, M.; van Roij, R.H.H.G.

    2011-01-01

    We study suspensions of semiflexible colloidal rods and biopolymers using an Onsager-type second-virial functional for a segmented-chain model. For mixtures of thin and thick fd virus particles, we calculate full phase diagrams, finding quantitative agreement with experimental observations. We show

  6. A Monte Carlo study of excluded volume effects in wormlike micelles and semiflexible polymers

    DEFF Research Database (Denmark)

    Pedersen, J.S.; Laso, M.; Schurtenberger, P.

    1996-01-01

    An off-lattice pseudocontinuous model for semiflexible polymerlike micelles with excluded volume interactions is presented. Expansion factors are determined for the radius of gyration squared and for three different characteristic point-point distances squared. They are found to scale with an exp...

  7. Multiscale modeling and mechanics of filamentous actin cytoskeleton.

    Science.gov (United States)

    Yamaoka, Hidetaka; Matsushita, Shinji; Shimada, Yoshitaka; Adachi, Taiji

    2012-03-01

    The adaptive structure and functional changes of the actin cytoskeleton are induced by its mechanical behavior at various temporal and spatial scales. In particular, the mechanical behaviors at different scales play important roles in the mechanical functions of various cells, and these multiscale phenomena require clarification. To establish a milestone toward achieving multiscale modeling and simulation, this paper reviews mathematical analyses and simulation methods applied to the mechanics of the filamentous actin cytoskeleton. The actin cytoskeleton demonstrates characteristic behaviors at every temporal and spatial scale, and mathematical models and simulation methods can be applied to each level of actin cytoskeletal structure ranging from the molecular to the network level. This paper considers studies on mathematical models and simulation methods based on the molecular dynamics, coarse-graining, and continuum dynamics approaches. Every temporal and spatial scale of actin cytoskeletal structure is considered, and it is expected that discrete and continuum dynamics ranging from functional expression at the molecular level to macroscopic functional expression at the whole cell level will be developed and applied to multiscale modeling and simulation.

  8. Tetrahedral collapse: a rotational toy model of simultaneous dark-matter halo, filament and wall formation

    CERN Document Server

    Neyrinck, Mark C

    2015-01-01

    We discuss an idealized model of halo formation, in which a collapsing halo node is tetrahedral, with a filament extruding from each of its four faces, and with a wall connecting each pair of filaments. In the model, filaments generally spin when they form, and the halo spins if and only if there is some rotation in filaments. This is the simplest-possible fully three-dimensional halo collapse in the 'origami approximation,' in which voids are irrotational, and the dark-matter sheet out of which dark-matter structures form is allowed to fold in position-velocity phase space, but not stretch (i.e., it cannot vary in density along a stream). Up to an overall scaling, the four filament directions, and only three other quantities, such as filament spins, suffice to determine all of the collapse's properties: the shape, mass, and spin of the halo; the densities per unit length and spins of all filaments; and masses per unit area of the walls. If the filaments are arranged regular-tetrahedrally, filament properties...

  9. A novel three-filament model of force generation in eccentric contraction of skeletal muscles.

    Directory of Open Access Journals (Sweden)

    Gudrun Schappacher-Tilp

    Full Text Available We propose and examine a three filament model of skeletal muscle force generation, thereby extending classical cross-bridge models by involving titin-actin interaction upon active force production. In regions with optimal actin-myosin overlap, the model does not alter energy and force predictions of cross-bridge models for isometric contractions. However, in contrast to cross-bridge models, the three filament model accurately predicts history-dependent force generation in half sarcomeres for eccentric and concentric contractions, and predicts the activation-dependent forces for stretches beyond actin-myosin filament overlap.

  10. A Model of Filamentous Cyanobacteria Leading to Reticulate Pattern Formation

    Directory of Open Access Journals (Sweden)

    Carlos Tamulonis

    2014-09-01

    Full Text Available The filamentous cyanobacterium, Pseudanabaena, has been shown to produce reticulate patterns that are thought to be the result of its gliding motility. Similar fossilized structures found in the geological record constitute some of the earliest signs of life on Earth. It is difficult to tie these fossils, which are billions of years old, directly to the specific microorganisms that built them. Identifying the physicochemical conditions and microorganism properties that lead microbial mats to form macroscopic structures can lead to a better understanding of the conditions on Earth at the dawn of life. In this article, a cell-based model is used to simulate the formation of reticulate patterns in cultures of Pseudanabaena. A minimal system of long and flexible trichomes capable of gliding motility is shown to be sufficient to produce stable patterns consisting of a network of streams. Varying model parameters indicate that systems with little to no cohesion, high trichome density and persistent movement are conducive to reticulate pattern formation, in conformance with experimental observations.

  11. Glassy dynamics of nanoparticles in semiflexible ring polymer nanocomposite melts

    Science.gov (United States)

    Zhou, Xiaolin; Jiang, Yangwei; Deng, Zhenyu; Zhang, Linxi

    2017-03-01

    By employing molecular dynamics simulations, we explore the dynamics of NPs in semiflexible ring polymer nanocomposite melts. A novel glass transition is observed for NPs in semiflexible ring polymer melts as the bending energy (Kb) of ring polymers increases. For NPs in flexible ring polymer melts (Kb = 0), NPs move in the classic diffusive behavior. However, for NPs in semiflexible ring polymer melts with large bending energy, NPs diffuse very slowly and exhibit the glassy state in which the NPs are all irreversibly caged be the neighbouring semiflexible ring polymers. This glass transition occurs well above the classical glass transition temperature at which microscopic mobility is lost, and the topological interactions of semiflexible ring polymers play an important role in this non-classical glass transition. This investigation can help us understand the nature of the glass transition in polymer systems.

  12. Glassy dynamics of nanoparticles in semiflexible ring polymer nanocomposite melts

    Science.gov (United States)

    Zhou, Xiaolin; Jiang, Yangwei; Deng, Zhenyu; Zhang, Linxi

    2017-01-01

    By employing molecular dynamics simulations, we explore the dynamics of NPs in semiflexible ring polymer nanocomposite melts. A novel glass transition is observed for NPs in semiflexible ring polymer melts as the bending energy (Kb) of ring polymers increases. For NPs in flexible ring polymer melts (Kb = 0), NPs move in the classic diffusive behavior. However, for NPs in semiflexible ring polymer melts with large bending energy, NPs diffuse very slowly and exhibit the glassy state in which the NPs are all irreversibly caged be the neighbouring semiflexible ring polymers. This glass transition occurs well above the classical glass transition temperature at which microscopic mobility is lost, and the topological interactions of semiflexible ring polymers play an important role in this non-classical glass transition. This investigation can help us understand the nature of the glass transition in polymer systems. PMID:28290546

  13. Polymerization and oscillation stuttering in a filamentous model of the subcellular Min oscillation

    Science.gov (United States)

    Rutenberg, Andrew; Sengupta, Supratim; Sain, Anirban; Derr, Julien

    2011-03-01

    We present a computational model of the E. coli Min oscillation that involves polymerization of MinD filaments followed by depolymerization stimulated by filament-end zones of MinE. Our stochastic model is fully three-dimensional, and tracks the diffusion and interactions of every MinD and MinE molecule. We recover self-organized Min oscillations. We investigate the experimental phenomenon of oscillation stuttering, which we relate to the disruption of MinE tip-binding at the filament scale.

  14. Structural Transition of Actin Filament in a Cell-Sized Water Droplet with a Phospholipid Membrane

    CERN Document Server

    Hase, M

    2005-01-01

    Actin filament, F-actin, is a semiflexible polymer with a negative charge, and is one of the main constituents on 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 6 mM Mg2+, while between 6 and 12 mM Mg2+, actin filaments are adsorbed onto the inner membrane surface. With PE, actin filaments are uniformly adsorbed onto the inner membrane surface between 2 and 12 mM Mg2+. With both PS and PE membranes, at Mg2+ concentrations higher than 12 mM, thick bundles are formed in the...

  15. The Bean model of the critical state in a magnetically shielded superconductor filament

    Energy Technology Data Exchange (ETDEWEB)

    Yampolskii, S V [Institut fuer Materialwissenschaft, Technische Universitaet Darmstadt, 64287 Darmstadt (Germany); Genenko, Y A [Institut fuer Materialwissenschaft, Technische Universitaet Darmstadt, 64287 Darmstadt (Germany); Rauh, H [Institut fuer Materialwissenschaft, Technische Universitaet Darmstadt, 64287 Darmstadt (Germany); Snezhko, A V [Materials Science Division, Argonne National Laboratory, Argonne, IL 60439 (United States)

    2006-06-01

    We study the magnetization of a cylindrical type-II superconductor filament covered by a coaxial soft-magnet sheath and exposed to an applied transverse magnetic field. Examining penetration of magnetic flux into the superconductor core of the filament on the basis of the Bean model of the critical state, we find that the presence of a non-hysteretic magnetic sheath can strongly enhance the field of full penetration of magnetic flux. The average magnetization of the superconductor/magnet heterostructure under consideration and hysteresis AC losses in the core of the filament are calculated as well.

  16. Vortex filament dynamics in computational models of ventricular fibrillation in the heart

    Science.gov (United States)

    Clayton, Richard H.

    2008-12-01

    In three-dimensional cardiac tissue, the re-entrant waves that sustain ventricular fibrillation rotate around a line of phase singularity or vortex filament. The aim of this study was to investigate how the behavior of these vortex filaments is influenced by membrane kinetics, initial conditions, and tissue geometry in computational models of excitable tissue. A monodomain model of cardiac tissue was used, with kinetics described by a three-variable simplified ionic model (3V-SIM). Two versions of 3V-SIM were used, one with steep action potential duration restitution, and one with reduced excitability. Re-entrant fibrillation was then simulated in three tissue geometries: a cube, a slab, and an anatomically detailed model of rabbit ventricles. Filaments were identified using a phase-based method, and the number, size, origin, and orientation of filaments was tracked throughout each simulation. The main finding of this study is that kinetics, initial conditions, geometry, and anisotropy all affected the number, proliferation, and orientation of vortex filaments in re-entrant fibrillation. An important finding of this study was that the behavior of vortex filaments in simplified slab geometry representing part of the ventricular wall did not necessarily predict behavior in an anatomically detailed model of the rabbit ventricles.

  17. Sequence-Dependent Effects on the Properties of Semiflexible Biopolymers

    CERN Document Server

    Zicong, Bela

    2008-01-01

    Using path integral technique, we show exactly that for a semiflexible biopolymer in constant extension ensemble, no matter how long the polymer and how large the external force, the effects of short range correlations in the sequence-dependent spontaneous curvatures and torsions can be incorporated into a model with well-defined mean spontaneous curvature and torsion as well as a renormalized persistence length. Moreover, for a long biopolymer with large mean persistence length, the sequence-dependent persistence lengths can be replaced by their mean. However, for a short biopolymer or for a biopolymer with small persistence lengths, inhomogeneity in persistence lengths tends to make physical observables very sensitive to details and therefore less predictable.

  18. Particle-Based Modeling of Living Actin Filaments in an Optical Trap

    Directory of Open Access Journals (Sweden)

    Thomas A. Hunt

    2016-09-01

    Full Text Available We report a coarse-grained molecular dynamics simulation study of a bundle of parallel actin filaments under supercritical conditions pressing against a loaded mobile wall using a particle-based approach where each particle represents an actin unit. The filaments are grafted to a fixed wall at one end and are reactive at the other end, where they can perform single monomer (depolymerization steps and push on a mobile obstacle. We simulate a reactive grand canonical ensemble in a box of fixed transverse area A, with a fixed number of grafted filaments N f , at temperature T and monomer chemical potential μ 1 . For a single filament case ( N f = 1 and for a bundle of N f = 8 filaments, we analyze the structural and dynamical properties at equilibrium where the external load compensates the average force exerted by the bundle. The dynamics of the bundle-moving-wall unit are characteristic of an over-damped Brownian oscillator in agreement with recent in vitro experiments by an optical trap setup. We analyze the influence of the pressing wall on the kinetic rates of (depolymerization events for the filaments. Both static and dynamic results compare reasonably well with recent theoretical treatments of the same system. Thus, we consider the proposed model as a good tool to investigate the properties of a bundle of living filaments.

  19. Helicity and internal twist within the vortex filament model

    CERN Document Server

    Hietala, N; Salman, H

    2016-01-01

    For ideal fluids, besides energy, kinetic helicity is the only other known quadratic invariant of the Euler equations besides energy and is understood to be inherently linked to the degree of knotting of vortex lines within the fluid. For vortices arising in superfluid $^4$He, the vorticity is concentrated along vortex filaments. In this setting, helicity would be expected to acquire its simplest form. However, the lack of a core structure for vortex filaments appears to result in a helicity that does not retain its key attribute as a quadratic invariant. By defining the spanwise vector to coincide with the Seifert framing, we are able to introduce twist and henceforth recover the key properties of helicity. Through a detailed analysis of the velocity field induced in the vicinity of the superfluid vortices we are able to express our choice of the spanwise vector in terms of the tangential component of velocity along the filament. Since adding an arbitrary tangential velocity does not alter the configuration ...

  20. Self-organization of actin filament orientation in the dendritic-nucleation/array-treadmilling model.

    Science.gov (United States)

    Schaus, Thomas E; Taylor, Edwin W; Borisy, Gary G

    2007-04-24

    The dendritic-nucleation/array-treadmilling model provides a conceptual framework for the generation of the actin network driving motile cells. We have incorporated it into a 2D, stochastic computer model to study lamellipodia via the self-organization of filament orientation patterns. Essential dendritic-nucleation submodels were incorporated, including discretized actin monomer diffusion, Monte-Carlo filament kinetics, and flexible filament and plasma membrane mechanics. Model parameters were estimated from the literature and simulation, providing values for the extent of the leading edge-branching/capping-protective zone (5.4 nm) and the autocatalytic branch rate (0.43/sec). For a given set of parameters, the system evolved to a steady-state filament count and velocity, at which total branching and capping rates were equal only for specific orientations; net capping eliminated others. The standard parameter set evoked a sharp preference for the +/-35 degree filaments seen in lamellipodial electron micrographs, requiring approximately 12 generations of successive branching to adapt to a 15 degree change in protrusion direction. This pattern was robust with respect to membrane surface and bending energies and to actin concentrations but required protection from capping at the leading edge and branching angles >60 degrees. A +70/0/-70 degree pattern was formed with flexible filaments approximately 100 nm or longer and with velocities < approximately 20% of free polymerization rates.

  1. Composite Pressure Vessel Variability in Geometry and Filament Winding Model

    Science.gov (United States)

    Green, Steven J.; Greene, Nathanael J.

    2012-01-01

    Composite pressure vessels (CPVs) are used in a variety of applications ranging from carbon dioxide canisters for paintball guns to life support and pressurant storage on the International Space Station. With widespread use, it is important to be able to evaluate the effect of variability on structural performance. Data analysis was completed on CPVs to determine the amount of variation that occurs among the same type of CPV, and a filament winding routine was developed to facilitate study of the effect of manufacturing variation on structural response.

  2. Modelling the chemical evolution of star forming filaments

    Science.gov (United States)

    Seifried, D.; Walch, S.

    2016-05-01

    We present simulations of star forming filaments incorporating - to our knowledge - the largest chemical network used to date on-the-fly in a 3D-MHD simulation. The network contains 37 chemical species and about 300 selected reaction rates. For this we use the newly developed package KROME (Grassi et al. [4]). Our results demonstrate the feasibility of using such a complex chemical network in 3D-MHD simulations on modern supercomputers. We perform simulations with different strengths of the interstellar radiation field and the cosmic ray ionisation rate and find chemical and physical results in accordance with observations and other recent numerical work.

  3. Modelling the chemical evolution of star forming filaments

    CERN Document Server

    Seifried, D

    2015-01-01

    We present simulations of star forming filaments incorporating - to our knowledge - the largest chemical network used to date on-the-fly in a 3D-MHD simulation. The network contains 37 chemical species and about 300 selected reaction rates. For this we use the newly developed package KROME (Grassi et al. 2014). Our results demonstrate the feasibility of using such a complex chemical network in 3D-MHD simulations on modern supercomputers. We perform simulations with different strengths of the interstellar radiation field and the cosmic ray ionisation rate and find chemical and physical results in accordance with observations and other recent numerical work.

  4. Computational and theoretical modeling of intermediate filament networks:Structure, mechanics and disease

    Institute of Scientific and Technical Information of China (English)

    Zhao Qin; Markus J. Buehler

    2012-01-01

    Intermediate filaments,in addition to microtubules and actin microfilaments,are one of the three major components of the cytoskeleton in eukaryotic cells.It was discovered during the recent decades that in most cells,intermediate filament proteins play key roles to reinforce cells subjected to large-deformation,and that they participate in signal transduction,and it was proposed that their nanomechanical properties are critical to perform those functions.However,it is still poorly understood how the nanoscopic structure,as well as the combination of chemical composition,molecular structure and interfacial properties of these protein molecules contribute to the biomechanical properties of filaments and filament networks. Here we review recent progress in computational and theoretical studies of the intermediate filaments network at various levels in the protein's structure. A multiple scale method is discussed,used to couple molecular modeling with atomistic detail to larger-scale material properties of the networked material. It is shown that a finer-trains-coarser methodology as discussed here provides a useful tool in understanding the biomechanical property and disease mechanism of intermediate filaments,coupling experiment and simulation. It further allows us to improve the understanding of associated disease mechanisms and lays the foundation for engineering the mechanical properties of biomaterials.

  5. Communication: Self-assembly of semiflexible-flexible block copolymers

    Science.gov (United States)

    Kumar, N. Arun; Ganesan, Venkat

    2012-03-01

    We apply the methodology of self-consistent Brownian dynamics simulations to study the self-assembly behavior in melts of semiflexible-flexible diblock copolymers as a function of the persistence length of the semiflexible block. Our results reveal a novel progression of morphologies in transitioning from the case of flexible-coil to rod-coil copolymers. At even moderate persistence lengths, the morphologies in the semiflexible-block rich region of the phase diagram transform to liquid crystalline phases. In contrast, the phases in the flexible-block rich region of the phase diagram persist up to much larger persistence lengths. Our analysis suggests that the development of orientational order in the semiflexible block to be a critical factor influencing the morphologies of self-assembly.

  6. Effects of branched O-glycosylation on a semiflexible peptide linker.

    Science.gov (United States)

    Johnson, Quentin R; Lindsay, Richard J; Raval, Sherin R; Dobbs, Jeremy S; Nellas, Ricky B; Shen, Tongye

    2014-02-27

    Glycosylation is an essential modification of proteins and lipids by the addition of carbohydrate residues. These attached carbohydrates range from single monomers to elaborate branched glycans. Here, we examine how the level of glycosylation affects the conformation of a semiflexible peptide linker using the example of the hinge peptide from immunoglobulin A. Three sets of atomistic models of this hinge peptide with varying degrees of glycosylation are constructed to probe how glycosylation affects the physical properties of the linker. We found that glycosylation greatly altered the predominant conformations of the peptide, causing it to become elongated in reference to the unglycosylated form. Furthermore, glycosylation restricts the conformational exploration of the peptide. At the residue level, glycans are found to introduce a bias for the formation of more extended secondary structural elements for glycosylated serines. Additionally, the flexibility of this semiflexible proline-rich peptide is significantly reduced by glycosylation.

  7. Force distribution in a semiflexible loop

    CERN Document Server

    Waters, James T

    2016-01-01

    Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in terms of free energy, an average quantity, but it may also be impacted by local fluctuating forces acting within these systems. The full distribution of these forces can thus give us insights into mechanochemistry beyond the predictive capability of thermodynamics. In this paper, we study the force exerted by an inextensible semiflexible polymer constrained in a looped state. By using a novel simulation method termed "phase-space sampling", we generate the equilibrium distribution of chain conformations in both position and momentum space. We compute the constraint forces between the two ends of the loop in this chain ensemble using Lagrangian mechanics, and show that the mean of these forces is equal to the thermodynamic force. By analyzing kinetic and potential contribution...

  8. Microthrix parvicella abundance associates with activated sludge settling velocity and rheology - Quantifying and modelling filamentous bulking.

    Science.gov (United States)

    Wágner, Dorottya S; Ramin, Elham; Szabo, Peter; Dechesne, Arnaud; Plósz, Benedek Gy

    2015-07-01

    The objective of this work is to identify relevant settling velocity and rheology model parameters and to assess the underlying filamentous microbial community characteristics that can influence the solids mixing and transport in secondary settling tanks. Parameter values for hindered, transient and compression settling velocity functions were estimated by carrying out biweekly batch settling tests using a novel column setup through a four-month long measurement campaign. To estimate viscosity model parameters, rheological experiments were carried out on the same sludge sample using a rotational viscometer. Quantitative fluorescence in-situ hybridisation (qFISH) analysis, targeting Microthrix parvicella and phylum Chloroflexi, was used. This study finds that M. parvicella - predominantly residing inside the microbial flocs in our samples - can significantly influence secondary settling through altering the hindered settling velocity and yield stress parameter. Strikingly, this is not the case for Chloroflexi, occurring in more than double the abundance of M. parvicella, and forming filaments primarily protruding from the flocs. The transient and compression settling parameters show a comparably high variability, and no significant association with filamentous abundance. A two-dimensional, axi-symmetrical computational fluid dynamics (CFD) model was used to assess calibration scenarios to model filamentous bulking. Our results suggest that model predictions can significantly benefit from explicitly accounting for filamentous bulking by calibrating the hindered settling velocity function. Furthermore, accounting for the transient and compression settling velocity in the computational domain is crucial to improve model accuracy when modelling filamentous bulking. However, the case-specific calibration of transient and compression settling parameters as well as yield stress is not necessary, and an average parameter set - obtained under bulking and good settling

  9. Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

    Energy Technology Data Exchange (ETDEWEB)

    McCluskey, Kevin; Baker, Scott E.

    2017-02-17

    Filamentous fungi have been important as model organisms since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycete filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Similarly, shared data has contributed to the success of model systems. The scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.

  10. Large-Scale Patterns of Filament Channels and Filaments

    Science.gov (United States)

    Mackay, Duncan

    2016-07-01

    In this review the properties and large-scale patterns of filament channels and filaments will be considered. Initially, the global formation locations of filament channels and filaments are discussed, along with their hemispheric pattern. Next, observations of the formation of filament channels and filaments are described where two opposing views are considered. Finally, the wide range of models that have been constructed to consider the formation of filament channels and filaments over long time-scales are described, along with the origin of the hemispheric pattern of filaments.

  11. Modelling the Global Solar Corona II: Coronal Evolution and Filament Chirality Comparison

    CERN Document Server

    Yeates, A R; Van Ballegooijen, A A

    2007-01-01

    The hemispheric pattern of solar filaments is considered using newly-developed simulations of the real photospheric and 3D coronal magnetic fields over a 6-month period, on a global scale. The magnetic field direction in the simulation is compared directly with the chirality of observed filaments, at their observed locations. In our model the coronal field evolves through a continuous sequence of nonlinear force-free equilibria, in response to the changing photospheric boundary conditions and the emergence of new magnetic flux. In total 119 magnetic bipoles with properties matching observed active regions are inserted. These bipoles emerge twisted and inject magnetic helicity into the solar atmosphere. When we choose the sign of this active-region helicity to match that observed in each hemisphere, the model produces the correct chirality for up to 96% of filaments, including exceptions to the hemispheric pattern. If the emerging bipoles have zero helicity, or helicity of the opposite sign, then this percenta...

  12. Crosslink dynamics in a model of two filaments of actin under shear

    Science.gov (United States)

    Boerma, Arjan; van der Giessen, Erik; Papanikolaou, Stefanos

    2015-03-01

    We seek to elucidate the dynamic mechanisms underlying the stress dependent effects of the cellular cytoskeleton, as they are observed in the storage and loss modulus as a function of frequency and cross-linker concentration. We report on the statistical behavior of the effects originating from cross-linker dynamics in the basic constituent of a cytoskeleton network: two mutually cross-linked filaments. We model each of the filaments and the cross-linkers in terms of elastic finite elements. Unbinding of individual cross-linkers takes place through a realistic constitutive model and re-binding may occur to maintain the average cross-linker density. Our approach provides a direct analysis of the athermal interplay of the elastic filament interactions with the dynamics of the cross-linking molecules.

  13. A coarse-grained model to study calcium activation of the cardiac thin filament

    Science.gov (United States)

    Zhang, Jing; Schwartz, Steven

    2015-03-01

    Familial hypertrophic cardiomyopathy (FHC) is one of the most common heart disease caused by genetic mutations. Cardiac muscle contraction and relaxation involve regulation of crossbridge binding to the cardiac thin filament, which regulates actomyosin interactions through calcium-dependent alterations in the dynamics of cardiac troponin (cTn) and tropomyosin (Tm). An atomistic model of cTn complex interacting with Tm has been studied by our group. A more realistic model requires the inclusion of the dynamics of actin filament, which is almost 6 times larger than cTn and Tm in terms of atom numbers, and extensive sampling of the model becomes very resource-demanding. By using physics-based protein united-residue force field, we introduce a coarse-grained model to study the calcium activation of the thin filament resulting from cTn's allosteric regulation of Tm dynamics on actin. The time scale is much longer than that of all-atom molecular dynamics simulation because of the reduction of the degrees of freedom. The coarse-grained model is a good template for studying cardiac thin filament mutations that cause FHC, and reduces the cost of computational resources.

  14. A metabolic model for the 0092 morphotype associated with filamentous bulking problems in wastewater treatment plants

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Karst, Søren Michael; Nierychlo, Marta

    Overgrowth of filamentous bacteria in activated sludge wastewater treatment plants (WWTPs) leads to impaired sludge settleability, a condition known as bulking, which is a common operational problem worldwide. The B45 genus-level-taxon, exhibiting the Eikelboom 0092 bulking filament morphotype...... was constructed, based on annotation of its genome, showing its ability to generate energy by aerobic respiration, utilizing oxygen, nitrite, or nitrous oxide as electron acceptors, or by fermentation of sugars. This model was validated partially in situ. This study represents the first detailed information...

  15. Prestellar core modeling in the presence of a filament. The dense heart of L1689B

    Science.gov (United States)

    Steinacker, J.; Bacmann, A.; Henning, Th.; Heigl, S.

    2016-08-01

    Context. Lacking a paradigm for the onset of star formation, it is important to derive basic physical properties of prestellar cores and filaments like density and temperature structures. Aims: We aim to disentangle the spatial variation in density and temperature across the prestellar core L1689B, which is embedded in a filament. We want to determine the range of possible central densities and temperatures that are consistent with the continuum radiation data. Methods: We apply a new synergetic radiative transfer method: the derived 1D density profiles are both consistent with a cut through the Herschel PACS/SPIRE and JCMT SCUBA-2 continuum maps of L1689B and with a derived local interstellar radiation field. Choosing an appropriate cut along the filament major axis, we minimize the impact of the filament emission on the modeling. Results: For the bulk of the core (5000-20 000 au) an isothermal sphere model with a temperature of around 10 K provides the best fits. We show that the power law index of the density profile, as well as the constant temperature can be derived directly from the radial surface brightness profiles. For the inner region (transfer methods also avoids the loss of information owing to smearing of all maps to the coarsest spatial resolution. We find the central core region to be colder and denser than estimated in recent inverse radiative transfer modeling, possibly indicating the start of star formation in L1689B.

  16. Automated quantification and sizing of unbranched filamentous cyanobacteria by model-based object-oriented image analysis.

    Science.gov (United States)

    Zeder, Michael; Van den Wyngaert, Silke; Köster, Oliver; Felder, Kathrin M; Pernthaler, Jakob

    2010-03-01

    Quantification and sizing of filamentous cyanobacteria in environmental samples or cultures are time-consuming and are often performed by using manual or semiautomated microscopic analysis. Automation of conventional image analysis is difficult because filaments may exhibit great variations in length and patchy autofluorescence. Moreover, individual filaments frequently cross each other in microscopic preparations, as deduced by modeling. This paper describes a novel approach based on object-oriented image analysis to simultaneously determine (i) filament number, (ii) individual filament lengths, and (iii) the cumulative filament length of unbranched cyanobacterial morphotypes in fluorescent microscope images in a fully automated high-throughput manner. Special emphasis was placed on correct detection of overlapping objects by image analysis and on appropriate coverage of filament length distribution by using large composite images. The method was validated with a data set for Planktothrix rubescens from field samples and was compared with manual filament tracing, the line intercept method, and the Utermöhl counting approach. The computer program described allows batch processing of large images from any appropriate source and annotation of detected filaments. It requires no user interaction, is available free, and thus might be a useful tool for basic research and drinking water quality control.

  17. Orientation of semiflexible polymers at a liquid/liquid interface

    Science.gov (United States)

    ten Bosch, Alexandra

    2001-03-01

    The formation and control of ordered liquid layers at an interface is of fundamental and practical interest and useful in the many applications of lubricants and coatings and in the preparation of self assembled liquids. Orientational order is observed in polymer systems in the immediate vicinity of a surface or interface. Semiflexible polymers resist deformation perpendicular to the monomer and the anchoring force at the surface fixes the direction of preferred orientation by coupling the direction of the molecular axis and the surface plane. When a second incompatible liquid is added to the system, a sharp interface between the two liquids forms at a given distance from the supporting substrate. By changing the nature of the second liquid, this second constraint can control the order and force the polymer in the ordered surface layer to assume different conformations. The wormlike chain model is used to calculate the orientational order parameter, the extent of the ordered surface layer and the anisotropic chain conformation and the parameters are determined for which an extended or contracted conformation will occur.

  18. Dynamics of single semiflexible polymers in dilute solution

    Science.gov (United States)

    Nikoubashman, Arash; Milchev, Andrey; Binder, Kurt

    2016-12-01

    We study the dynamics of a single semiflexible chain in solution using computer simulations, where we systematically investigate the effect of excluded volume, chain stiffness, and hydrodynamic interactions. We achieve excellent agreement with previous theoretical considerations, but find that the crossover from the time τb, up to which free ballistic motion of the monomers describes the chain dynamics, to the times W-1 or τ0, where anomalous monomer diffusion described by Rouse-type and Zimm-type models sets in, requires two decades of time. While in the limit of fully flexible chains the visibility of the anomalous diffusion behavior is thus rather restricted, the t3/4 power law predicted for stiff chains without hydrodynamic interactions is verified. Including hydrodynamics, evidence for the predicted [tln (t ) ] 3 /4 behavior is obtained. Similar good agreement with previous theoretical predictions is found for the decay of the bond autocorrelation functions and the end-to-end vector correlation. Finally, several predictions on the variation of characteristic relaxation times with persistence length describing the chain stiffness are tested.

  19. Fracture behavior of filament in Nb{sub 3}Sn strands with crack-bridging model

    Energy Technology Data Exchange (ETDEWEB)

    Yong, Huadong, E-mail: yonghd@lzu.edu.cn; Yang, Penglei; Xue, Cun; Zhou, Youhe

    2016-01-15

    Highlights: • The crack-bridging model is used to study the fracture behavior of filaments. • Two different fracture modes are characterized by the number of bridging bronzes. • Short twist pitch has better mechanical stability for the tensile loadings. • The widths of bridging bronze and filament have different effects for the central crack and two collinear cracks. - Abstract: The Nb{sub 3}Sn strands which have high critical field are used in cable-in-conduit conductors (CICCs). The superconducting strands are twisted multistage and experience complex thermal and electromagnetic loadings. Due to their brittleness, the cracking of the Nb{sub 3}Sn filaments will occur under mechanical loading. In this paper, based on the linear elastic fracture theory, we study the effects of tension loading on the fracture behavior of central crack firstly. The strain energy release rates for different twist pitches and cabling stages are presented. As the triplet is subjected to the uniaxial strain, the cracking probability will increase with the twist pitch. The crack number increases with the applied strain, and wider filament or bronze can lead to smaller crack number under the same applied strain. In addition, multistage cabling has better mechanical stability. Next, the two collinear crack problem is considered. The variations of microcrack number show that the wider bronze can provide more resistance for the propagating of the large cracks. We can conclude that the bronze plays an important role in improving the stability and strength.

  20. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.

    Science.gov (United States)

    Saladin, Adrien; Amourda, Christopher; Poulain, Pierre; Férey, Nicolas; Baaden, Marc; Zacharias, Martin; Delalande, Olivier; Prévost, Chantal

    2010-10-01

    Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson-Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.

  1. Guiding-center models for edge plasmas and numerical simulations of isolated plasma filaments

    DEFF Research Database (Denmark)

    Madsen, Jens

    The work presented in this thesis falls into two categories: development of reduced dynamical models applicable to edge turbulence in magnetically confined fusion plasmas and numerical simulations of isolated plasma filaments in the scrape-off layer region investigating the influence of finite...... models are presented that overcome some of the difficulties associated with the development of reduced dynamical models applicable to the edge. Second order guiding-center coordinates are derived using the phasespace Lie transform method. Using a variational principle the corresponding Vlasov......-Maxwell equations in a more tractable form, which could be relevant for direct numerical simulations of edge plasma turbulence. Finally, an investigation of the influence of finite Larmor radius effects on the radial transport of isolated plasma filaments (blobs) in the scrape-off region of fusion plasmas...

  2. Force distribution in a semiflexible loop

    Science.gov (United States)

    Waters, James T.; Kim, Harold D.

    2017-01-01

    Loops undergoing thermal fluctuations are prevalent in nature. Ringlike or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in terms of free energy, an average quantity, but it may also be impacted by local fluctuating forces acting within these systems. The full distribution of these forces can thus give us insights into mechanochemistry beyond the predictive capability of thermodynamics. In this paper, we study the force exerted by an inextensible semiflexible polymer constrained in a looped state. By using a simulation method termed “phase-space sampling,” we generate the equilibrium distribution of chain conformations in both position and momentum space. We compute the constraint forces between the two ends of the loop in this chain ensemble using Lagrangian mechanics, and show that the mean of these forces is equal to the thermodynamic force. By analyzing kinetic and potential contributions to the forces, we find that the mean force acts in the direction of increasing extension not because of bending stress, but in spite of it. Furthermore, we obtain a distribution of constraint forces as a function of chain length, extension, and stiffness. Notably, increasing contour length decreases the average force, but the additional freedom allows fluctuations in the constraint force to increase. The force distribution is asymmetric and falls off less sharply than a Gaussian distribution. Our work exemplifies a system where large-amplitude fluctuations occur in a way unforeseen by a purely thermodynamic framework, and offers computational tools useful for efficient, unbiased simulation of a constrained system. PMID:27176436

  3. Modelling of helical current filaments induced by LHW on EAST

    Energy Technology Data Exchange (ETDEWEB)

    Rack, Michael; Denner, Peter; Liang, Yunfeng [Institute of Energy and Climate Research - Plasma Physics, Forschungszentrum Juelich GmbH, Association EURATOM-FZJ, Partner in the Trilateral Euregio Cluster, D-52425 Juelich (Germany); Zeng, Long [Institute of Energy and Climate Research - Plasma Physics, Forschungszentrum Juelich GmbH, Association EURATOM-FZJ, Partner in the Trilateral Euregio Cluster, D-52425 Juelich (Germany); Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Gong, Xianzu; Gan, Kaifu; Wang, Liang; Liu, Fukun; Qian, Jinping; Shen, Biao; Li, Jiangang [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Gauthier, Eric [Association EURATOM-CEA, IRFM, F-13108 Saint-Paul-lez-Durance (France); Collaboration: the EAST Team

    2013-07-01

    Helical radiation belts have been observed in the scrape-off layer (SOL) of the plasma during the application of lower hybrid wave (LHW) heating at the superconducting tokamak EAST. Modelled SOL field lines, starting in-front of the LHW antennas, show agreement in position and pitch angle to the experimental observed radiation belts. A splitting of the strike-line can be observed on the outer divertor plates during the application of LHW heating. Agreement in the comparison of the Mirnov coil signals and a modelled electric current flow along these SOL field lines was found. A lower hybrid current drive can induce such an electric current flow near the plasma edge. This electric current flow causes a change of the plasma topology which could result in the splitting of the strike-line as known from the application of resonant magnetic perturbation fields. Comparisons of modelled footprint structures and experimental observed heat load patterns in the divertor region are discussed.

  4. A novel model-based control strategy for aerobic filamentous fungal fed-batch fermentation processes

    DEFF Research Database (Denmark)

    Mears, Lisa; Stocks, Stuart M.; Albaek, Mads O.

    2017-01-01

    A novel model-based control strategy has been developed for filamentous fungal fed-batch fermentation processes. The system of interest is a pilot scale (550 L) filamentous fungus process operating at Novozymes A/S. In such processes, it is desirable to maximize the total product achieved...... in a batch in a defined process time. In order to achieve this goal, it is important to maximize both the product concentration, and also the total final mass in the fed-batch system. To this end, we describe the development of a control strategy which aims to achieve maximum tank fill, while avoiding oxygen...... limited conditions. This requires a two stage approach: (i) calculation of the tank start fill; and (ii) on-line control in order to maximize fill subject to oxygen transfer limitations. First, a mechanistic model was applied off-line in order to determine the appropriate start fill for processes...

  5. Experimental validation of a filament transport model in turbulent magnetized plasmas

    CERN Document Server

    Carralero, D; Aho-Mantila, L; Birkenmeier, G; Brix, M; Groth, M; Müller, H W; Stroth, U; Vianello, N; Wolfrum, E; Contributors, JET

    2015-01-01

    In a wide variety of natural and laboratory magnetized plasmas, filaments appear as a result of interchange instability. These convective structures substantially enhance transport in the direction perpendicular to the magnetic field. According to filament models, their propagation may follow different regimes depending on the parallel closure of charge conservation. This is of paramount importance in magnetic fusion plasmas, as high collisionality in the scrape-off layer may trigger a regime transition leading to strongly enhanced perpendicular particle fluxes. This work reports for the first time on an experimental verification of this process, linking enhanced transport with a regime transition as predicted by models. Based on these results, a novel scaling for global perpendicular particle transport in reactor relevant tokamaks such as ASDEX-Upgrade and JET is found, leading to important implications for next generation fusion devices.

  6. Modeling filamentous cyanobacteria reveals the advantages of long and fast trichomes for optimizing light exposure.

    Science.gov (United States)

    Tamulonis, Carlos; Postma, Marten; Kaandorp, Jaap

    2011-01-01

    Cyanobacteria form a very large and diverse phylum of prokaryotes that perform oxygenic photosynthesis. Many species of cyanobacteria live colonially in long trichomes of hundreds to thousands of cells. Of the filamentous species, many are also motile, gliding along their long axis, and display photomovement, by which a trichome modulates its gliding according to the incident light. The latter has been found to play an important role in guiding the trichomes to optimal lighting conditions, which can either inhibit the cells if the incident light is too weak, or damage the cells if too strong. We have developed a computational model for gliding filamentous photophobic cyanobacteria that allows us to perform simulations on the scale of a Petri dish using over 10(5) individual trichomes. Using the model, we quantify the effectiveness of one commonly observed photomovement strategy--photophobic responses--in distributing large populations of trichomes optimally over a light field. The model predicts that the typical observed length and gliding speeds of filamentous cyanobacteria are optimal for the photophobic strategy. Therefore, our results suggest that not just photomovement but also the trichome shape itself improves the ability of the cyanobacteria to optimize their light exposure.

  7. Modeling filamentous cyanobacteria reveals the advantages of long and fast trichomes for optimizing light exposure.

    Directory of Open Access Journals (Sweden)

    Carlos Tamulonis

    Full Text Available Cyanobacteria form a very large and diverse phylum of prokaryotes that perform oxygenic photosynthesis. Many species of cyanobacteria live colonially in long trichomes of hundreds to thousands of cells. Of the filamentous species, many are also motile, gliding along their long axis, and display photomovement, by which a trichome modulates its gliding according to the incident light. The latter has been found to play an important role in guiding the trichomes to optimal lighting conditions, which can either inhibit the cells if the incident light is too weak, or damage the cells if too strong. We have developed a computational model for gliding filamentous photophobic cyanobacteria that allows us to perform simulations on the scale of a Petri dish using over 10(5 individual trichomes. Using the model, we quantify the effectiveness of one commonly observed photomovement strategy--photophobic responses--in distributing large populations of trichomes optimally over a light field. The model predicts that the typical observed length and gliding speeds of filamentous cyanobacteria are optimal for the photophobic strategy. Therefore, our results suggest that not just photomovement but also the trichome shape itself improves the ability of the cyanobacteria to optimize their light exposure.

  8. Semi-flexible sockets for amputation below the knee.

    Science.gov (United States)

    Symington, D C; Lowe, P J; Mackay, S

    1975-09-01

    A semi-flexible socket fitted to a series of 47 consecutive below-knee amputees is evaluated, and the problems in assessing prosthetic components and appropriate methodology are discussed. The results suggest that this type of socket deserves wider use and further evaluation in active amputees, where comfort, perspiration control or the condition of the skin is interfering with the patient's function.

  9. A Gas Centric Model For Intergalactic Filament Development During the First Gigayear

    CERN Document Server

    Harford, A Gayler

    2016-01-01

    Using a cosmological simulation of the first gigayear of the universe, we find that the mass per unit length of reionizing intergalactic filaments is proportional to the square of the sound speed with a proportionality constant equal to that predicted for a gravitationally bound, isothermal cylinder. These cylinders contain both gas and dark matter, and the dark matter contributes to the gravitational field roughly in proportion to its abundance. The dark matter of each galaxy collapses according to the cycloid predicted for spherically symmetric collapse in an expanding universe. In contrast, the gas collapses more slowly into the centre of the galaxy. After reionization filaments persist and, in some cases, become enriched in either gas or dark matter. We have incorporated these findings into a unified model. A key feature of a gravitationally bound, isothermal cylinder is that the mass per unit length depends only upon the temperature and ionization state of the gas. This property suggests a lower limit on...

  10. NLTE modeling of a small active region filament observed with the VTT

    Science.gov (United States)

    Schwartz, P.; Balthasar, H.; Kuckein, C.; Koza, J.; Gömöry, P.; Rybák, J.; Heinzel, P.; Kučera, A.

    2016-11-01

    An active region mini-discretionary-filament was observed with the Vacuum Tower Telescope (VTT) in Tenerife simultaneously in the He I infrared triplet using the Tenerife Infrared Polarimeter 1 (TIP 1), in Hα with the TESOS Fabry-Pérot interferometer, and in Ca II 8542 Å with the VTT spectrograph. The spectropolarimetric data were inverted using the HAZEL code and Hα profiles were modelled by solving a NLTE radiative transfer in a simple isobaric and isothermal 2D slab irradiated both from its bottom and sides from the solar surface. It was found that the mini-discretionary-filament is composed of horizontal fluxtubes, along which the cool plasma of T˜10 000 K can flow with very large, even supersonic, velocities.

  11. An Integrative Approach for Modeling and Simulation of Heterocyst Pattern Formation in Cyanobacteria Filaments

    Science.gov (United States)

    Torres-Sánchez, Alejandro; Gómez-Gardeñes, Jesús; Falo, Fernando

    2015-01-01

    Heterocyst differentiation in cyanobacteria filaments is one of the simplest examples of cellular differentiation and pattern formation in multicellular organisms. Despite of the many experimental studies addressing the evolution and sustainment of heterocyst patterns and the knowledge of the genetic circuit underlying the behavior of single cyanobacterium under nitrogen deprivation, there is still a theoretical gap connecting these two macroscopic and microscopic processes. As an attempt to shed light on this issue, here we explore heterocyst differentiation under the paradigm of systems biology. This framework allows us to formulate the essential dynamical ingredients of the genetic circuit of a single cyanobacterium into a set of differential equations describing the time evolution of the concentrations of the relevant molecular products. As a result, we are able to study the behavior of a single cyanobacterium under different external conditions, emulating nitrogen deprivation, and simulate the dynamics of cyanobacteria filaments by coupling their respective genetic circuits via molecular diffusion. These two ingredients allow us to understand the principles by which heterocyst patterns can be generated and sustained. In particular, our results point out that, by including both diffusion and noisy external conditions in the computational model, it is possible to reproduce the main features of the formation and sustainment of heterocyst patterns in cyanobacteria filaments as observed experimentally. Finally, we discuss the validity and possible improvements of the model. PMID:25816286

  12. Modelling the chemistry of star-forming filaments - I. H2 and CO chemistry

    Science.gov (United States)

    Seifried, D.; Walch, S.

    2016-06-01

    We present simulations of star-forming filaments incorporating on of the largest chemical network used to date on-the-fly in a 3D-magnetohydrodynamic (MHD) simulation. The network contains 37 chemical species and about 300 selected reaction rates. For this, we use the newly developed package KROME (Grassi et al.). We combine the KROME package with an algorithm which allows us to calculate the column density and attenuation of the interstellar radiation field necessary to properly model heating and ionization rates. Our results demonstrate the feasibility of using such a complex chemical network in 3D-MHD simulations on modern supercomputers. We perform simulations with different strengths of the interstellar radiation field and the cosmic ray ionization rate. We find that, towards the centre of the filaments, there is gradual conversion of hydrogen from H to H2 as well as of C+ over C to CO. Moreover, we find a decrease of the dust temperature towards the centre of the filaments in agreement with recent HERSCHEL observations.

  13. Equilibrium properties of DNA and other semiflexible polymers confined in nanochannels

    Science.gov (United States)

    Muralidhar, Abhiram

    Recent developments in next-generation sequencing (NGS) techniques have opened the door for low-cost, high-throughput sequencing of genomes. However, these developments have also exposed the inability of NGS to track large scale genomic information, which are extremely important to understand the relationship between genotype and phenotype. Genome mapping offers a reliable way to obtain information about large-scale structural variations in a given genome. A promising variant of genome mapping involves confining single DNA molecules in nanochannels whose cross-sectional dimensions are approximately 50 nm. Despite the development and commercialization of nanochannel-based genome mapping technology, the polymer physics of DNA in confinement is only beginning to be understood. Apart from its biological relevance, DNA is also used as a model polymer in experiments by polymer physicists. Indeed, the seminal experiments by Reisner et al. (2005) of DNA confined in nanochannels of different widths revealed discrepancies with the classical theories of Odijk and de Gennes for polymer confinement. Picking up from the conclusions of the dissertation of Tree (2014), this dissertation addresses a number of key outstanding problems in the area of nanoconfined DNA. Adopting a Monte Carlo chain growth technique known as the pruned-enriched Rosenbluth method, we examine the equilibrium and near-equilibrium properties of DNA and other semiflexible polymers in nanochannel confinement. We begin by analyzing the dependence of molecular weight on various thermodynamic properties of confined semiflexible polymers. This allows us to point out the finite size effects that can occur when using low molecular weight DNA in experiments. We then analyze the statistics of backfolding and hairpin formation in the context of existing theories and discuss how our results can be used to engineer better conditions for genome mapping. Finally, we elucidate the diffusion behavior of confined

  14. Modeling the Scattering Polarization of the Hydrogen Ly-alpha Line Observed by CLASP in a Filament Channel

    Science.gov (United States)

    Stepan, J.; Trujillo Bueno, J.; Gunar, S.; del Pino Aleman, T.; Heinzel, P.; Kano, R.; Ishikawa, R.; Narukage, M.; Bando, T.; Winebarger, Amy; Kobayashi, K.; Auchere, F.

    2016-01-01

    The 400 arcsec spectrograph slit of CLASP crossed predominantly quiet regions of the solar chromosphere, from the limb towards the solar disk center. Interestingly, in the CLASP slit-jaw images and in the SDO images of the He I line at 304 A, we can identify a filament channel (FC) extending over more than 60 arcsec crossing the spectrograph slit. In order to interpret the peculiar spatial variation of the Q/1 and U/1 signals observed by CLASP in the hydrogen Ly-alpha line (1216 A) and in the Si Ill line (1206 A) in such a filament channel, it is necessary to perform multi-dimensional radiative transfer modeling. In this contribution, we show the first results of the two-dimensional calculations we are carrying out in given filament models, with the aim of determining the filament thermal and magnetic structure by comparing the theoretical and the observed polarization signals.

  15. Twist and Stretch of Helices Explained via the Kirchhoff-Love Rod Model of Elastic Filaments

    KAUST Repository

    Đuričković, Bojan

    2013-09-05

    In various single-molecule experiments, a chiral polymer, such as DNA, is simultaneously pulled and twisted. We address an elementary but fundamental question raised by various authors: does the molecule overwind or unwind under tension? We show that within the context of the classic Kirchhoff-Love rod model of elastic filaments, both behaviors are possible, depending on the precise constitutive relations of the polymer. More generally, our analysis provides an effective linear response theory for helical structures that relates axial force and axial torque to axial translation and rotation. © 2013 American Physical Society.

  16. Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers

    Directory of Open Access Journals (Sweden)

    Saeed Najafi

    2016-09-01

    Full Text Available Knots appear frequently in semiflexible (biopolymers, including double-stranded DNA, and their presence can affect the polymer’s physical and functional properties. In particular, it is possible and indeed often the case that multiple knots appear on a single chain, with effects which have only come under scrutiny in the last few years. In this manuscript, we study the interaction of two knots on a stretched semiflexible polymer, expanding some recent results on the topic. Specifically, we consider an idealization of a typical optical tweezers experiment and show how the bending rigidity of the chain—And consequently its persistence length—Influences the distribution of the entanglements; possibly more importantly, we observe and report how the relative chirality of the otherwise identical knots substantially modifies their interaction. We analyze the free energy of the chain and extract the effective interactions between embedded knots, rationalizing some of their pertinent features by means of simple effective models. We believe the salient aspect of the knot–knot interactions emerging from our study will be present in a large number of semiflexible polymers under tension, with important consequences for the characterization and manipulation of these systems—Be they artificial or biologica in origin—And for their technological application.

  17. Effect of intrinsic curvature on semiflexible polymers

    Science.gov (United States)

    Ghosh, Surya K.; Singh, Kulveer; Sain, Anirban

    2009-11-01

    Recently many important biopolymers have been found to possess intrinsic curvature. Tubulin protofilaments in animal cells, FtsZ filaments in bacteria and double stranded DNA are examples. We examine how intrinsic curvature influences the conformational statistics of such polymers. We give exact results for the tangent-tangent spatial correlation function C(r)=⟨t̂(s).t̂(s+r)⟩ , both in two and three dimensions. Contrary to expectation, C(r) does not show any oscillatory behavior, rather decays exponentially and the effective persistence length has strong length dependence for short polymers. We also compute the distribution function P(R) of the end to end distance R and show how curved chains can be distinguished from wormlike chains using loop formation probability.

  18. Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping

    Energy Technology Data Exchange (ETDEWEB)

    Giovan, Stefan M. [Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 (United States); Scharein, Robert G. [Hypnagogic Software, Vancouver, British Columbia V6K 1V6 (Canada); Hanke, Andreas [Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, Texas 78520 (United States); Levene, Stephen D., E-mail: sdlevene@utdallas.edu [Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 (United States); Department of Bioengineering, University of Texas at Dallas, Richardson, Texas 75083 (United States); Department of Physics, University of Texas at Dallas, Richardson, Texas 75083 (United States)

    2014-11-07

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.

  19. [Mechanisms and regulation of enzymatic hydrolysis of cellulose in filamentous fungi: classical cases and new models].

    Science.gov (United States)

    Gutiérrez-Rojas, Ivonne; Moreno-Sarmiento, Nubia; Montoya, Dolly

    2015-01-01

    Cellulose is the most abundant renewable carbon source on earth. However, this polymer structure comprises a physical and chemical barrier for carbon access, which has limited its exploitation. In nature, only a few percentage of microorganisms may degrade this polymer by cellulase expression. Filamentous fungi are one of the most active and efficient groups among these microorganisms. This review describes similarities and differences between cellulase activity mechanisms and regulatory mechanisms controlling gene expression for 3 of the most studied cellulolytic filamentous fungi models: Trichoderma reesei, Aspergillus niger and Aspergillus nidulans, and the recently described model Neurospora crassa. Unlike gene expression mechanisms, it was found that enzymatic activity mechanisms are similar for all the studied models. Understanding the distinctive elements of each system is essential for the development of strategies for the improvement of cellulase production, either by providing the optimum environment (fermentation conditions) or increasing gene expression in these microorganisms by genetic engineering. Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  20. Metabolic model for the filamentous ‘Candidatus Microthrix parvicella' based on genomic and metagenomic analyses

    Science.gov (United States)

    Jon McIlroy, Simon; Kristiansen, Rikke; Albertsen, Mads; Michael Karst, Søren; Rossetti, Simona; Lund Nielsen, Jeppe; Tandoi, Valter; James Seviour, Robert; Nielsen, Per Halkjær

    2013-01-01

    ‘Candidatus Microthrix parvicella' is a lipid-accumulating, filamentous bacterium so far found only in activated sludge wastewater treatment plants, where it is a common causative agent of sludge separation problems. Despite attracting considerable interest, its detailed physiology is still unclear. In this study, the genome of the RN1 strain was sequenced and annotated, which facilitated the construction of a theoretical metabolic model based on available in situ and axenic experimental data. This model proposes that under anaerobic conditions, this organism accumulates preferentially long-chain fatty acids as triacylglycerols. Utilisation of trehalose and/or polyphosphate stores or partial oxidation of long-chain fatty acids may supply the energy required for anaerobic lipid uptake and storage. Comparing the genome sequence of this isolate with metagenomes from two full-scale wastewater treatment plants with enhanced biological phosphorus removal reveals high similarity, with few metabolic differences between the axenic and the dominant community ‘Ca. M. parvicella' strains. Hence, the metabolic model presented in this paper could be considered generally applicable to strains in full-scale treatment systems. The genomic information obtained here will provide the basis for future research into in situ gene expression and regulation. Such information will give substantial insight into the ecophysiology of this unusual and biotechnologically important filamentous bacterium. PMID:23446830

  1. Prestellar core modeling in the presence of a filament - The dense heart of L1689B

    CERN Document Server

    Steinacker, Juergen; Henning, Thomas; Heigl, Stefan

    2016-01-01

    Short version: We apply a new synergetic radiative transfer method: the derived 1D density profiles are both consistent with a cut through the Herschel PACS/SPIRE and JCMT SCUBA-2 continuum maps of L1689B and with a derived local interstellar radiation field. Choosing an appropriate cut along the filament major axis, we minimize the impact of the filament emission on the modeling. For the bulk of the core (5000-20000 au) an isothermal sphere model with a temperature of around 10 K provides the best fits. We show that the power law index of the density profile, as well as the constant temperature can be derived directly from the radial surface brightness profiles. For the inner region (< 5000 au), we find a range of densities and temperatures that are consistent with the surface brightness profiles and the local interstellar radiation field. Based on our core models, we find that pixel-by-pixel single temperature spectral energy distribution fits are incapable of determining dense core properties. We conclu...

  2. Modeling of the motion of the actin filament on the myosin motility assays

    Science.gov (United States)

    Young, Yuan; Shelley, Mike

    2007-11-01

    In motility assays, cytoskeletal actin filaments (actin filaments) glide over a surface coated with motor proteins, and the different modes of motion provide a simple measure of the force exerted by the motor proteins (Bourdieu, 1995). Motivated by these experiments, we consider the actin filament as a slender, elastic filament immersed in Stokesian flow, driven by a tangential forcing that mimics the force by the motor proteins. We find qualitative agreement on several points between our analysis and simulations and experimental observations. Furthermore, we study the correlation between filament transport and the characteristics of motion with the spatial pattern of motor protein density.

  3. Persistence of strain in motor-filament assemblies

    CERN Document Server

    Gopinath, Arvind; Mahadevan, L

    2015-01-01

    Crosslinked semi-flexible and flexible filaments that are actively deformed by molecular motors occur in various natural settings, such as the ordered eukaryotic flagellum, and the disordered cytoskeleton. The deformation of these composite systems is driven by active motor forces and resisted by passive filament elasticity, and structural constraints due to permanent cross-links. Using a mean field theory for a one-dimensional ordered system, we show that the combination of motor activity and finite filament extensibility yields a characteristic persistence length scale over which active strain decays. This decay length is set by the ability of motors to respond to combination of the weak extensional elasticity, passive shear resistance and the viscoelastic properties of the motor assembly, and generalizes the notion of persistence in purely thermal filaments to active systems.

  4. A Molecular Perspective of Inter-filament Bonding in Fused Deposition Modeling 3-D Printing

    Science.gov (United States)

    Duranty, Edward; Spradlin, Brandon; Dadmun, Mark

    2015-03-01

    Fused deposition 3D printing is an important tool for low-cost and rapid prototyping of objects with complex geometries. 3D printed materials are composed of many filaments deposited on a heated substrate, requiring the bonding of neighboring filaments during the deposition process. Filament deposition often creates voids between filaments, which requires necking between them to create a robust sample. Therefore the amount of interfacial contact and interdiffusion between filaments become important parameters that control the macroscopic physical properties of the printed prototype. Our research focuses on quantifying the interfacial adhesion between ABS filaments and its impact on structural properties. The time evolution of the temperature profile near the heated substrate demonstrates that the deposited filaments are repeatedly heated above the Tg of ABS allowing interpenetration of the polymer chains between adjacent filaments. Results of DMA experiments on samples of different geometries have been correlated to microphotography that monitors the degree of necking between filaments and the thermal history. Results indicate that interfacial contact area between filaments and increased thermal energy are crucial to their mechanical properties.

  5. The role of filament length, finite-extensibility and motor force dispersity in stress relaxation and buckling mechanisms in non-sarcomeric active gels.

    Science.gov (United States)

    Córdoba, Andrés; Schieber, Jay D; Indei, Tsutomu

    2015-01-07

    After relaxing some assumptions we apply a single-chain mean-field mathematical model recently introduced [RSC Adv. (2014)] to describe the role of molecular motors in the mechanical properties of active gels. The model allows physics that are not available in models postulated on coarser levels of description. Moreover it proposes a level of description that allows the prediction of observables at time scales too difficult to achieve in multi-chain simulations for realistic filament lengths and densities. We model the semiflexible filaments that compose the active gel as bead-spring chains; molecular motors are accounted for by using a mean-field approach, in which filaments undergo transitions of one motor attachment state depending on the state of the probe filament. The level of description includes the end-to-end distance and attachment state of the filaments, and the motor-generated forces, as stochastic state variables which evolve according to a proposed differential Chapman-Kolmogorov equation. The motor-generated forces are drawn from a stationary distribution of motor stall forces. We consider bead-spring chains with multiple beads, explore the effect of finite-extensibility of the strands and incorporate into the model motor force distributions that have been measured experimentally. The model can no longer be solved analytically but is amenable to numerical simulation. This version of the model allows a more quantitative description of buckling dynamics [Lenz et. al. PRL, 2012, 108, 238107] and the dynamic modulus of active gels. The effect of finite extensibility of the filament strands on the dynamic modulus was also found to be in agreement with the microrheology experiments of Mizuno et. al., [Science, 2007, 315, 370-373].

  6. Molecular alignment and filamentation: comparison between weak and strong field models

    CERN Document Server

    Berti, N; Wolf, J -P; Faucher, O

    2014-01-01

    The impact of nonadiabatic laser-induced molecular alignment on filamentation is numerically studied. Weak and strong field model of impulsive molecular alignment are compared in the context of nonlinear pulse propagation. It is shown that the widely used weak field model describing the refractive index modification induced by impulsive molecular alignment accurately reproduces the propagation dynamics providing that only a single pulse is involved during the experiment. On the contrary, it fails at reproducing the nonlinear propagation experienced by an intense laser pulse traveling in the wake of a second strong laser pulse. The discrepancy depends on the relative delay between the two pulses and is maximal for delays corresponding to half the rotational period of the molecule.

  7. Microthrix parvicella abundance associates with activated sludge settling velocity and rheology - Quantifying and modelling filamentous bulking

    DEFF Research Database (Denmark)

    Wágner, Dorottya Sarolta; Ramin, Elham; Szabo, Peter;

    2015-01-01

    The objective of this work is to identify relevant settling velocity and rheology model parameters and to assess the underlying filamentous microbial community characteristics that can influence the solids mixing and transport in secondary settling tanks. Parameter values for hindered, transient...... viscometer. Quantitative fluorescence in-situ hybridisation (qFISH) analysis, targeting Microthrix parvicella and phylum Chloroflexi, was used. This study finds that M. parvicella - predominantly residing inside the microbial flocs in our samples - can significantly influence secondary settling through...... and compression settling velocity functions were estimated by carrying out biweekly batch settling tests using a novel column setup through a four-month long measurement campaign. To estimate viscosity model parameters, rheological experiments were carried out on the same sludge sample using a rotational...

  8. Powering of cool filaments in cluster cores by buoyant bubbles. I. Qualitative model

    CERN Document Server

    Churazov, E; Schekochihin, A

    2013-01-01

    Cool-core clusters (e.g., Perseus or M87) often possess a network of bright gaseous filaments, observed in radio, IR, optical and X-ray bands. We propose that these filaments are powered by the reconnection of the magnetic field in the wakes of buoyant bubbles. AGN-inflated bubbles of relativistic plasma rise buoyantly in the cluster atmosphere, stretching and amplifying the field in the wake to values of $\\beta =8\\pi P_{gas}/B^2\\sim 1$. The field lines in the wake have opposite directions and are forced together as the bubble motion stretches the filament. This setup bears strong similarity to the coronal loops on the Sun or the Earth magneto-tail. The reconnection process naturally explains both the required level of local dissipation rate in filaments and the overall luminosity of filaments. The original source of power for the filaments is the potential energy of buoyant bubbles, inflated by the central AGN.

  9. Including the effects of filamentous bulking sludge during the simulation of wastewater treatment plants using a risk assessment model

    DEFF Research Database (Denmark)

    Flores Alsina, Xavier; Comas, J.; Rodriquez-Roda, I.

    2009-01-01

    The main objective of this paper is to demonstrate how including the occurrence of filamentous bulking sludge in a secondary clarifier model will affect the predicted process performance during the simulation of WWTPs. The IWA Benchmark Simulation Model No. 2 (BSM2) is hereby used as a simulation...

  10. Filaments in the southern giant lobe of Centaurus A: constraints on nature and origin from modelling and GMRT observations

    CERN Document Server

    Wykes, Sarka; Hardcastle, Martin J; Achterberg, Abraham; Jones, Thomas W; Jerjen, Helmut; Orru, Emanuela; Lazarian, Alex; Shimwell, Timothy W; Wise, Michael W; Kronberg, Philipp P

    2014-01-01

    We present results from imaging of the radio filaments in the southern giant lobe of Centaurus A using data from GMRT observations at 325 and 235 MHz, and outcomes from filament modelling. The observations reveal a rich filamentary structure, largely matching the morphology at 1.4 GHz. We find no clear connection of the filaments to the jet. We seek to constrain the nature and origin of the vertex and vortex filaments associated with the lobe and their role in high-energy particle acceleration. We deduce that these filaments are at most mildly overpressured with respect to the global lobe plasma showing no evidence of large-scale efficient Fermi I-type particle acceleration, and persist for ~ 2-3 Myr. We demonstrate that the dwarf galaxy KK 196 (AM 1318-444) cannot account for the features, and that surface plasma instabilities, the internal sausage mode and radiative instabilities are highly unlikely. An internal tearing instability and the kink mode are allowed within the observational and growth time const...

  11. Modeling the Growth of Filamentous Fungi at the Particle Scale in Solid-State Fermentation Systems.

    Science.gov (United States)

    Sugai-Guérios, Maura Harumi; Balmant, Wellington; Furigo, Agenor; Krieger, Nadia; Mitchell, David Alexander

    2015-01-01

    Solid-state fermentation (SSF) with filamentous fungi is a promising technique for the production of a range of biotechnological products and has the potential to play an important role in future biorefineries. The performance of such processes is intimately linked with the mycelial mode of growth of these fungi: Not only is the production of extracellular enzymes related to morphological characteristics, but also the mycelium can affect bed properties and, consequently, the efficiency of heat and mass transfer within the bed. A mathematical model that describes the development of the fungal mycelium in SSF systems at the particle scale would be a useful tool for investigating these phenomena, but, as yet, a sufficiently complete model has not been proposed. This review presents the biological and mass transfer phenomena that should be included in such a model and then evaluates how these phenomena have been modeled previously in the SSF and related literature. We conclude that a discrete lattice-based model that uses differential equations to describe the mass balances of the components within the system would be most appropriate and that mathematical expressions for describing the individual phenomena are available in the literature. It remains for these phenomena to be integrated into a complete model describing the development of fungal mycelia in SSF systems.

  12. Effects of Stiffness on Short, Semiflexible Homopolymer Chains

    Science.gov (United States)

    Seaton, Daniel T.; Schnabel, Stefan; Bachmann, Michael; Landau, David P.

    2012-08-01

    Conformational and transition behavior of finite, semiflexible homopolymers is studied using an extension of the Wang-Landau algorithm. Generation of a flat distribution in the sampling parameters energy and stiffness allows for efficient investigation of transitions between various conformational phases. Of particular importance is the ability to predict behavior for a given stiffness value, where three classes of minimum energy conformations are expected: Solid-globular, rod-like and toroidal. We present first results highlighting the behavior of a single N = 20 length chain.

  13. Structure of human Rad51 protein filament from molecular modeling and site-specific linear dichroism spectroscopy

    KAUST Repository

    Reymer, A.

    2009-07-08

    To get mechanistic insight into the DNA strand-exchange reaction of homologous recombination, we solved a filament structure of a human Rad51 protein, combining molecular modeling with experimental data. We build our structure on reported structures for central and N-terminal parts of pure (uncomplexed) Rad51 protein by aid of linear dichroism spectroscopy, providing angular orientations of substituted tyrosine residues of Rad51-dsDNA filaments in solution. The structure, validated by comparison with an electron microscopy density map and results from mutation analysis, is proposed to represent an active solution structure of the nucleo-protein complex. An inhomogeneously stretched double-stranded DNA fitted into the filament emphasizes the strategic positioning of 2 putative DNA-binding loops in a way that allows us speculate about their possibly distinct roles in nucleo-protein filament assembly and DNA strand-exchange reaction. The model suggests that the extension of a single-stranded DNA molecule upon binding of Rad51 is ensured by intercalation of Tyr-232 of the L1 loop, which might act as a docking tool, aligning protein monomers along the DNA strand upon filament assembly. Arg-235, also sitting on L1, is in the right position to make electrostatic contact with the phosphate backbone of the other DNA strand. The L2 loop position and its more ordered compact conformation makes us propose that this loop has another role, as a binding site for an incoming double-stranded DNA. Our filament structure and spectroscopic approach open the possibility of analyzing details along the multistep path of the strand-exchange reaction.

  14. Wrapping transition and wrapping-mediated interactions for discrete binding along an elastic filament: An exact solution

    Science.gov (United States)

    Dean, David S.; Hammant, Thomas C.; Horgan, Ronald R.; Naji, Ali; Podgornik, Rudolf

    2012-10-01

    The wrapping equilibria of one and two adsorbing cylinders are studied along a semi-flexible filament (polymer) due to the interplay between elastic rigidity and short-range adhesive energy between the cylinder and the filament. We show that statistical mechanics of the system can be solved exactly using a path integral formalism which gives access to the full effect of thermal fluctuations, going thus beyond the usual Gaussian approximations which take into account only the contributions from the minimal energy configuration and small fluctuations about this minimal energy solution. We obtain the free energy of the wrapping-unwrapping transition of the filament around the cylinders as well as the effective interaction between two wrapped cylinders due to thermal fluctuations of the elastic filament. A change of entropy due to wrapping of the filament around the adsorbing cylinders as they move closer together is identified as an additional source of interactions between them. Such entropic wrapping effects should be distinguished from the usual entropic configuration effects in semi-flexible polymers. Our results may be relevant to the problem of adsorption of oriented nano-rods on semi-flexible polymers.

  15. Curvature-induced cross-hatched order in two-dimensional semiflexible polymer networks

    CERN Document Server

    Vrusch, Cyril

    2015-01-01

    A recurring motif in the organization of biological tissues are networks of long, fibrillar protein strands effectively confined to cylindrical surfaces. Often, the fibers in such curved, quasi-2D geometries adopt a characteristic order: the fibers wrap around the central axis at an angle which varies with radius and, in several cases, is strongly bimodally distributed. In this Letter, we investigate the general problem of a 2D crosslinked network of semiflexible fibers confined to a cylindrical substrate, and demonstrate that in such systems the trade-off between bending and stretching energies, very generically, gives rise to cross-hatched order. We discuss its general dependency on the radius of the confining cylinder, and present an intuitive model that illustrates the basic physical principle of curvature-induced order. Our findings shed new light on the potential origin of some curiously universal fiber orientational distributions in tissue biology, and suggests novel ways in which synthetic polymeric s...

  16. Guiding-center models for edge plasmas and numerical simulations of isolated plasma filaments

    Energy Technology Data Exchange (ETDEWEB)

    Madsen, Jens

    2010-09-15

    The work presented in this thesis falls into two categories: development of reduced dynamical models applicable to edge turbulence in magnetically confined fusion plasmas and numerical simulations of isolated plasma filaments in the scrape-off layer region investigating the influence of finite Larmor radius effects on the radial plasma transport. The coexistence of low-frequency fluctuations, having length scales comparable to the ion gyroradius, steep pressure gradients and strong E x B flows in the edge region of fusion plasmas violates the standard gyrokinetic ordering. In this thesis two models are presented that overcome some of the difficulties associated with the development of reduced dynamical models applicable to the edge. Second order guiding-center coordinates are derived using the phasespace Lie transform method. Using a variational principle the corresponding Vlasov-Maxwell equations expressed in guiding-center coordinates are derived including a local energy theorem. The second order terms describe lowest order finite Larmor radius effects. This set of equations might be relevant for edge plasmas due to the capability of capturing strong E x B flows and lowest order finite Larmor radius effects self-consistently. Next, an extension of the existing gyrokinetic formalism with strong flows is presented. In this work the background electric fields is dynamical, whereas earlier contributions did only incorporate a stationary electric field. In an ordering relevant for edge plasma turbulence, fully electromagnetic second order gyrokinetic coordinates and the corresponding gyrokinetic Vlasov-Maxwell equations are derived, including a local energy theorem. By taking the polarization and magnetization densities in the drift kinetic limit, we present the gyrokinetic Vlasov-Maxwell equations in a more tractable form, which could be relevant for direct numerical simulations of edge plasma turbulence. Finally, an investigation of the influence of finite Larmor

  17. Mesoscale simulation of semiflexible chains. II. Evolution dynamics and stability of fiber bundle networks

    Science.gov (United States)

    Groot, Robert D.

    2013-06-01

    Network formation of associative semiflexible fibers and mixtures of fibers and colloidal particles is simulated for the Johnson-Kendall-Roberts model of elastic contacts, and a phase diagram in terms of particle elasticity and surface energy is presented. When fibers self-assemble, they form a network for sufficiently large fiber-solvent surface energy. If the surface energy is above the value where single particles crystallize, the adhesion forces drive diffusion-limited aggregation. Two mechanisms contribute to coarsening: non-associated chains joining existing bundles, and fiber bundles merging. Coarsening stops when the length of the network connections is roughly the persistence length, independent of surface energy. If the surface energy is below the value where single particles crystallize, a network can still be formed but at a much slower (reaction limited) rate. Loose (liquid-like) assemblies between chains form when they happen to run more-or-less parallel. These assemblies grow by diffusion and aggregation and form a loose network, which sets in micro-phase separation, i.e., syneresis. Only when the clusters crystallize, the coarsening process stops. In this case, the length of the network connections is larger than the persistence length of a single chain, and depends on the value of the surface energy. All networks of semiflexible homopolymers in this study show syneresis. Mixtures of fibers and colloid particles also form fiber bundle networks, but by choosing the colloid volume fraction sufficiently low, swelling gels are obtained. Applications of this model are in biological systems where fibers self-assemble into cell walls and bone tissue.

  18. Semi-flexible bimetal-based thermal energy harvesters

    CERN Document Server

    Boisseau, S; Monfray, S; Puscasu, O; Skotnicki, T; 10.1088/0964-1726/22/2/025021

    2013-01-01

    This paper introduces a new semi-flexible device able to turn thermal gradients into electricity by using a curved bimetal coupled to an electret-based converter. In fact, a two-steps conversion is carried out: (i) a curved bimetal turns the thermal gradient into a mechanical oscillation that is then (ii) converted into electricity thanks to an electrostatic converter using electrets in Teflon (r). The semi-flexible and low cost design of these new energy converters pave the way to mass production over large areas of thermal energy harvesters. Raw output powers up to 13.46uW per device were reached on a hot source at 60{\\deg}C and forced convection. Then, a DC-to-DC flyback converter has been sized to turn the energy harvesters' raw output powers into a viable supply source for an electronic circuit (DC-3V). At the end, 10uW of directly usable output power were reached with 3 devices, which is compatible with Wireless Sensor Networks powering applications. Please cite as : S Boisseau et al 2013 Smart Mater. S...

  19. Dual conical conducting filament model in resistance switching TiO2 thin films.

    Science.gov (United States)

    Kim, Kyung Min; Park, Tae Hyung; Hwang, Cheol Seong

    2015-01-19

    The resetting behaviors of Pt/TiO2/Pt resistive switching (RS) cell in unipolar RS operations were studied in detail through an experiment and by modeling. The experiment showed that the apparently highly arbitrary resetting current-voltage (I-V) curves could be grouped into three types: normal, delayed, and abnormal behaviors. A dual conical conducting filament (CF) model was conceived, and their electrothermal behaviors were analytically described from the heat-balance and charge-transport equations. The almost spontaneous resetting behavior of the normal reset could be easily understood from the mutually constructive interference effect between the Joule heating and temperature-dependent resistance effect along the CF. The delayed reset could be explained by the time-dependent increase in the reset voltage during the rest process, which was most probably induced in the more conical-shaped CF. The abnormal reset could be understood from the temporal transfer of oxygen ions near the kink positions of the two different-diameter portions of the more cylindrical CFs, which temporally decreases the overall resistance immediately prior for the actual reset to occur. The accuracy of the dual conical CF model was further confirmed by adopting a more thorough electrothermal simulation package, COMSOL.

  20. Helical filaments

    Energy Technology Data Exchange (ETDEWEB)

    Barbieri, Nicholas; Lim, Khan; Durand, Magali; Baudelet, Matthieu; Richardson, Martin [Townes Laser Institute, CREOL—The College of Optics and Photonics, University of Central Florida, Orlando, Florida 32816 (United States); Hosseinimakarem, Zahra; Johnson, Eric [Micro-Photonics Laboratory – Center for Optical Material Science, Clemson, Anderson, South Carolina 29634 (United States)

    2014-06-30

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

  1. Modeling the effects of laser-beam smoothing on filamentation and stimulated Brillouin backscattering

    Energy Technology Data Exchange (ETDEWEB)

    Berger, R.L.; Kaiser, T.B.; Lasinski, B.F. [and others

    1996-06-01

    Using the three-dimensional code (F3D), the authors compute the filamentation and backscattering of laser light. The results show that filamentation can be controlled and stimulated Brillouin backscattering (SBBS) can be reduced by using random phase plates (RPP) and small f-numbers or smoothing by spectral dispersion (SSD) with large bandwidth. An interesting result is that, for uniform plasmas, the SBBS amplification takes place over several laser axial coherence lengths (coherence length = speckle length).

  2. Hot-melt extruded filaments based on pharmaceutical grade polymers for 3D printing by fused deposition modeling.

    Science.gov (United States)

    Melocchi, Alice; Parietti, Federico; Maroni, Alessandra; Foppoli, Anastasia; Gazzaniga, Andrea; Zema, Lucia

    2016-07-25

    Fused deposition modeling (FDM) is a 3D printing technique based on the deposition of successive layers of thermoplastic materials following their softening/melting. Such a technique holds huge potential for the manufacturing of pharmaceutical products and is currently under extensive investigation. Challenges in this field are mainly related to the paucity of adequate filaments composed of pharmaceutical grade materials, which are needed for feeding the FDM equipment. Accordingly, a number of polymers of common use in pharmaceutical formulation were evaluated as starting materials for fabrication via hot melt extrusion of filaments suitable for FDM processes. By using a twin-screw extruder, filaments based on insoluble (ethylcellulose, Eudragit(®) RL), promptly soluble (polyethylene oxide, Kollicoat(®) IR), enteric soluble (Eudragit(®) L, hydroxypropyl methylcellulose acetate succinate) and swellable/erodible (hydrophilic cellulose derivatives, polyvinyl alcohol, Soluplus(®)) polymers were successfully produced, and the possibility of employing them for printing 600μm thick disks was demonstrated. The behavior of disks as barriers when in contact with aqueous fluids was shown consistent with the functional application of the relevant polymeric components. The produced filaments were thus considered potentially suitable for printing capsules and coating layers for immediate or modified release, and, when loaded with active ingredients, any type of dosage forms.

  3. Tension-induced binding of semiflexible biopolymers

    CERN Document Server

    Benetatos, Panayotis; Zippelius, Annette

    2014-01-01

    We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with a sequence of inter-chain binding sites regularly spaced along the contours. Reversible cross-links attach and detach at the sites with an affinity controlled by a chemical potential. In a mean-field approach, we calculate the free energy of the system and find the emergence of a free-energy barrier which controls the reversible (un)binding. The tension affects the conformational entropy of the chains which competes with the binding energy of the cross-links. This competition gives rise to a sudden increase in the fraction of bound sites as the tension increases. We show that this transition is related to the cross-over between weak and strong localization of a directed polymer in a pinning potential. The cross-over to the strongly bound state can be interpreted as a mechan...

  4. Electrophoresis of semiflexible heteropolymers and the ``hydrodynamic Kuhn length''

    Science.gov (United States)

    Chubynsky, Mykyta V.; Slater, Gary W.

    Semiflexible polymers, such as DNA, are rodlike for short lengths and coil-like for long lengths. For purely geometric properties, such as the end-to-end distance, the crossover between these two behaviors occurs when the polymer length is on the order of the Kuhn length. On the other hand, for the hydrodynamic friction coefficient it is easy to see by comparing the expressions for a rod and a coil that the crossover should occur at the polymer length, termed by us the hydrodynamic Kuhn length, which is larger than the ordinary Kuhn length by a logarithmic factor that can be quite significant. We show that for the problem of electrophoresis of a heteropolymer consisting of several blocks of (in general) different stiffnesses, both of these length scales can be important depending on the details of the problem.

  5. Mesoscopic model for filament orientation in growing actin networks: the role of obstacle geometry

    CERN Document Server

    Weichsel, Julian; 10.1088/1367-2630/15/3/035006

    2013-01-01

    Propulsion by growing actin networks is a universal mechanism used in many different biological systems. Although the core molecular machinery for actin network growth is well preserved in most cases, the geometry of the propelled obstacle can vary considerably. In recent years, filament orientation distribution has emerged as an important observable characterizing the structure and dynamical state of the growing network. Here we derive several continuum equations for the orientation distribution of filaments growing behind stiff obstacles of various shapes and validate the predicted steady state orientation patterns by stochastic computer simulations based on discrete filaments. We use an ordinary differential equation approach to demonstrate that for flat obstacles of finite size, two fundamentally different orientation patterns peaked at either +35/-35 or +70/0/-70 degrees exhibit mutually exclusive stability, in agreement with earlier results for flat obstacles of very large lateral extension. We calculat...

  6. Slow Rise and Partial Eruption of a Double-Decker Filament. II. Modeling by a Double Flux Rope Equilibrium

    CERN Document Server

    Kliem, Bernhard; Titov, Viacheslav S; Lionello, Roberto; Linker, Jon A; Liu, Rui; Liu, Chang; Wang, Haimin

    2014-01-01

    Force-free equilibria containing two vertically arranged magnetic flux ropes of like chirality and current direction are considered as a model for split filaments/prominences and filament-sigmoid systems. Such equilibria are constructed analytically through an extension of the methods developed in Titov & D\\'emoulin (1999) and numerically through an evolutionary sequence including shear flows, flux emergence, and flux cancellation in the photospheric boundary. It is demonstrated that the analytical equilibria are stable if an external toroidal (shear) field component exceeding a threshold value is included. If this component decreases sufficiently, then both flux ropes turn unstable for conditions typical of solar active regions, with the lower rope typically being unstable first. Either both flux ropes erupt upward, or only the upper rope erupts while the lower rope reconnects with the ambient flux low in the corona and is destroyed. However, for shear field strengths staying somewhat above the threshold...

  7. Modeling filamentous cyanobacteria reveals the advantages of long and fast trichomes for optimizing light exposure

    NARCIS (Netherlands)

    C. Tamulonis; M. Postma; J. Kaandorp

    2011-01-01

    Cyanobacteria form a very large and diverse phylum of prokaryotes that perform oxygenic photosynthesis. Many species of cyanobacteria live colonially in long trichomes of hundreds to thousands of cells. Of the filamentous species, many are also motile, gliding along their long axis, and display phot

  8. Galaxy pairs align with galactic filaments

    CERN Document Server

    Tempel, Elmo

    2015-01-01

    Context. Gravitational collapse theory and numerical simulations suggest that the velocity field within large-scale galaxy filaments is dominated by motions along the filaments. Aims. Our aim is to check whether observational data reveal any preferred orientation of galaxy pairs with respect to the underlying filaments as a result of the expectedly anisotropic velocity field. Methods. We use galaxy pairs and galaxy filaments identified from the Sloan Digital Sky Survey data. For filament extraction, we use the Bisous model that is based the marked point process technique. During the filament detection, we use the centre point of each pair instead of the positions of galaxies to avoid a built-in influence of pair orientation on the filament construction. For pairs lying within filaments (3012 cases), we calculate the angle between the line connecting galaxies of each pair and their host filament. To avoid redshift-space distortions, the angle is measured in the plain of the sky. Results. The alignment analysis...

  9. Protein-Nanocrystal Conjugates Support a Single Filament Polymerization Model in R1 Plasmid Segregation

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Charina L.; Claridge, Shelley A.; Garner, Ethan C.; Alivisatos, A. Paul; Mullins, R. Dyche

    2008-07-15

    To ensure inheritance by daughter cells, many low-copy number bacterial plasmids, including the R1 drug-resistance plasmid, encode their own DNA segregation systems. The par operon of plasmid R1 directs construction of a simple spindle structure that converts free energy of polymerization of an actin-like protein, ParM, into work required to move sister plasmids to opposite poles of rod-shaped cells. The structures of individual components have been solved, but little is known about the ultrastructure of the R1 spindle. To determine the number of ParM filaments in a minimal R1 spindle, we used DNA-gold nanocrystal conjugates as mimics of the R1 plasmid. Wefound that each end of a single polar ParM filament binds to a single ParR/parC-gold complex, consistent with the idea that ParM filaments bind in the hollow core of the ParR/parC ring complex. Our results further suggest that multifilament spindles observed in vivo are associated with clusters of plasmidssegregating as a unit.

  10. Dose estimation outside radiation field using Pinpoint and Semiflex ionization chamber detectors

    Science.gov (United States)

    Abdelaal, Ahmed M.; Attalla, Ehab M.; Elshemey, Wael M.

    2017-10-01

    This work aims to provide a comparison between two important detectors (Pinpoint and Semiflex) that are frequently used in radiation dosimetery in radiotherapy. This is carried out through the employment of both detectors in a quantitative estimation of the change in out-of-field dose with important dosimetric parameters such as field size (from 5×5 cm2 to 30×30 cm2) and depth (from 1.5 cm to 30 cm) at two different energies (6 MV and 15 MV) and two different collimator angles (0-90°). The change in out-of-field dose with Source-Skin-Distance (SSD) from 80 to 115 cm is also studied using both detectors. Results show that, the Pinpoint and Semiflex detectors both reported an increase in out-of-field dose with field size, depth, energy and SSD. In almost all measurements, Pinpoint detector reported considerably higher out-of-field dose values compared to Semiflex. For 6 MV and 0° collimator angle, the out-of-field dose at field size of 30×30 cm2 and at a depth of 1.5 cm is 7.3% for Pinpoint detector compared to 4.3% for Semiflex. At collimator angle of 90°, the out-of-field dose is 6.5% for Pinpoint detector compared to 5.5% for semiflex. The out-of-field dose for a depth of 30 cm and field size of 10×10 cm is 7.9% for Pinpoint detector compared to 5.9% for Semiflex. For 15 MV and 0° collimator angle, the out-of-field dose at field size of 30×30 cm2 and at a depth of 1.5 cm is 7.5% for Pinpoint detector compared 5.1% for Semiflex. At 6 MV, field size of 10×10 cm2 and depth of 1.5 cm, the out-of-field dose at SSD 115 cm is 3.7% for Pinpoint detector compared to 3.4% for Semiflex. The considerably higher out-of-field dose values reported by Pinpoint detector compared to Semiflex may be attributed to the relatively higher sensitivity of Pinpoint detector for low doses (such as out-of-field doses). Therefore, for reliable out-of-field dose measurements a Pinpoint detector is highly recommended.

  11. Efficient simulation of semiflexible polymers with stiff bonds

    Science.gov (United States)

    Barkema, Gerard T.; van Leeuwen, J. M. J.

    2017-01-01

    We investigate the simulation of stiff (extensible) and rigid (inextensible) semiflexible polymers in solution. In particular, we focus on polymers represented as chains of beads, interconnected by bonds with a low to zero extensibility, and significant persistence in the bond orientations along the chain, whose dynamical behavior is described by the Langevin equation. We review the derivation of the pseudopotential needed for rigid bonds. The efficiency of a number of routines for such simulations is determined. We propose a routine for handling rigid bonds which is, for longer chains, substantially more efficient than the existing ones. We also show that for extensible polymers, the Rouse modes can be exploited to achieve highly efficient simulations. At realistic values for the extensibility, e.g., that of double-stranded DNA, the simulations are orders of magnitude faster than those for rigid bonds. With increasing stiffness, however, the allowable time step and hence the efficiency decreases, until a crossover point is reached below which the routines with rigid bonds are more efficient; we present a numerical estimate of this crossover point.

  12. Brushes of semiflexible polymers in equilibrium and under flow in super-hydrophobic regime

    CERN Document Server

    Speyer, Kevin

    2015-01-01

    We performed molecular dynamics simulations to study equilibrium and flow properties of a liquid in a nano-channel with confining surfaces coated with a layer of grafted semiflexible polymers. The coverage spans a wide range of grafting densities from essentially isolated chains to dense brushes. The end-grafted polymers were described by a bead spring model with an harmonic potential to include the bond stiffness of the chains. We varied the rigidity of the chains, from fully flexible polymers to rigid rods, in which the configurational entropy of the chains is negligible. The brush-liquid interaction was tuned to obtain a super-hydrophobic channel, in which the liquid did not penetrate the polymer brush, giving rise to a Cassie-Baxter state. Equilibrium properties such us brush height and bending energy were measured, varying the grafting density and the stiffness of the polymers. We studied also the characteristics of the brush-liquid interface and the morphology of the polymers chains supporting the liqui...

  13. Recent Advances in the Use of Drosophila melanogaster as a Model to Study Immunopathogenesis of Medically Important Filamentous Fungi

    Directory of Open Access Journals (Sweden)

    Georgios Hamilos

    2012-01-01

    Full Text Available Airborne opportunistic fungi, including Aspergillus and other less common saprophytic molds, have recently emerged as important causes of mortality in immunocompromised individuals. Understanding the molecular mechanisms of host-fungal interplay in robust experimental pathosystems is becoming a research priority for development of novel therapeutics to combat these devastating infections. Over the past decade, invertebrate hosts with evolutionarily conserved innate immune signaling pathways and powerful genetics, such as Drosophila melanogaster, have been employed as a means to overcome logistic restrains associated with the use mammalian models of fungal infections. Recent studies in Drosophila models of filamentous fungi demonstrated that several genes implicated in fungal virulence in mammals also play a similarly important pathogenic role in fruit flies, and important host-related aspects in fungal pathogenesis are evolutionarily conserved. In view of recent advances in Drosophila genetics, fruit flies will become an invaluable surrogate model to study immunopathogenesis of fungal diseases.

  14. Collisions of Vortex Filament Pairs

    Science.gov (United States)

    Banica, Valeria; Faou, Erwan; Miot, Evelyne

    2014-12-01

    We consider the problem of collisions of vortex filaments for a model introduced by Klein et al. (J Fluid Mech 288:201-248, 1995) and Zakharov (Sov Phys Usp 31(7):672-674, 1988, Lect. Notes Phys 536:369-385, 1999) to describe the interaction of almost parallel vortex filaments in three-dimensional fluids. Since the results of Crow (AIAA J 8:2172-2179, 1970) examples of collisions are searched as perturbations of antiparallel translating pairs of filaments, with initial perturbations related to the unstable mode of the linearized problem; most results are numerical calculations. In this article, we first consider a related model for the evolution of pairs of filaments, and we display another type of initial perturbation leading to collision in finite time. Moreover, we give numerical evidence that it also leads to collision through the initial model. We finally study the self-similar solutions of the model.

  15. Pavement structure mechanics response of flexible on semi-flexible overlay that based on the old cement concrete pavement damage

    Directory of Open Access Journals (Sweden)

    Jiang Ruinan

    2015-01-01

    Full Text Available The old cement pavement damage status directly affect the design of the paving renovation. Based on the state of the old road investigation, combined with the research data at home and abroad, use the control index that average deflection, deflection value and CBR value to determine the reasonable time to overlay. Draw up the typical pavement structure according to the principle of combination of old cement pavement overlay structure design, and calculated that the tensile stress and shear stress in asphalt layer ,semi-flexible layer and the tensile in the old cement pavement adopting BISA3.0 statics finite element analysis model when modulus in the old road was diminishing. Use the computed result to analyses the influence of old road damage condition the influence of pavement structure.

  16. Triggering filamentation using turbulence

    CERN Document Server

    Eeltink, D; Marchiando, N; Hermelin, S; Gateau, J; Brunetti, M; Wolf, J P; Kasparian, J

    2016-01-01

    We study the triggering of single filaments due to turbulence in the beam path for a laser of power below the filamenting threshold. Turbulence can act as a switch between the beam not filamenting and producing single filaments. This 'positive' effect of turbulence on the filament probability, combined with our observation of off-axis filaments suggests the underlying mechanism is modulation instability caused by transverse perturbations. We hereby experimentally explore the interaction of modulation instability and turbulence, commonly associated with multiple-filaments, in the single-filament regime.

  17. Attractive interactions among intermediate filaments determine network mechanics in vitro.

    Directory of Open Access Journals (Sweden)

    Paul Pawelzyk

    Full Text Available Mechanical and structural properties of K8/K18 and vimentin intermediate filament (IF networks have been investigated using bulk mechanical rheometry and optical microrheology including diffusing wave spectroscopy and multiple particle tracking. A high elastic modulus G0 at low protein concentration c, a weak concentration dependency of G0 (G0 ∼ c(0.5 ± 0.1 and pronounced strain stiffening are found for these systems even without external crossbridgers. Strong attractive interactions among filaments are required to maintain these characteristic mechanical features, which have also been reported for various other IF networks. Filament assembly, the persistence length of the filaments and the network mesh size remain essentially unaffected when a nonionic surfactant is added, but strain stiffening is completely suppressed, G0 drops by orders of magnitude and exhibits a scaling G0 ∼ c(1.9 ± 0.2 in agreement with microrheological measurements and as expected for entangled networks of semi-flexible polymers. Tailless K8Δ/K18ΔT and various other tailless filament networks do not exhibit strain stiffening, but still show high G0 values. Therefore, two binding sites are proposed to exist in IF networks. A weaker one mediated by hydrophobic amino acid clusters in the central rod prevents stretched filaments between adjacent cross-links from thermal equilibration and thus provides the high G0 values. Another strong one facilitating strain stiffening is located in the tail domain with its high fraction of hydrophobic amino acid sequences. Strain stiffening is less pronounced for vimentin than for K8/K18 due to electrostatic repulsion forces partly compensating the strong attraction at filament contact points.

  18. Cooperation of Mtmr8 with PI3K regulates actin filament modeling and muscle development in zebrafish.

    Directory of Open Access Journals (Sweden)

    Jie Mei

    Full Text Available BACKGROUND: It has been shown that mutations in at least four myotubularin family genes (MTM1, MTMR1, 2 and 13 are causative for human neuromuscular disorders. However, the pathway and regulative mechanism remain unknown. METHODOLOGY/PRINCIPAL FINDINGS: Here, we reported a new role for Mtmr8 in neuromuscular development of zebrafish. Firstly, we cloned and characterized zebrafish Mtmr8, and revealed the expression pattern predominantly in the eye field and somites during early somitogenesis. Using morpholino knockdown, then, we observed that loss-of-function of Mtmr8 led to defects in somitogenesis. Subsequently, the possible underlying mechanism and signal pathway were examined. We first checked the Akt phosphorylation, and observed an increase of Akt phosphorylation in the morphant embryos. Furthermore, we studied the PH/G domain function within Mtmr8. Although the PH/G domain deletion by itself did not result in embryonic defect, addition of PI3K inhibitor LY294002 did give a defective phenotype in the PH/G deletion morphants, indicating that the PH/G domain was essential for Mtmr8's function. Moreover, we investigated the cooperation of Mtmr8 with PI3K in actin filament modeling and muscle development, and found that both Mtmr8-MO1 and Mtmr8-MO2+LY294002 led to the disorganization of the actin cytoskeleton. In addition, we revealed a possible participation of Mtmr8 in the Hedgehog pathway, and cell transplantation experiments showed that Mtmr8 worked in a non-cell autonomous manner in actin modeling. CONCLUSION/SIGNIFICANCE: The above data indicate that a conserved functional cooperation of Mtmr8 with PI3K regulates actin filament modeling and muscle development in zebrafish, and reveal a possible participation of Mtmr8 in the Hedgehog pathway. Therefore, this work provides a new clue to study the physiological function of MTM family members.

  19. Perturbation growth in accreting filaments

    Science.gov (United States)

    Clarke, S. D.; Whitworth, A. P.; Hubber, D. A.

    2016-05-01

    We use smoothed particle hydrodynamic simulations to investigate the growth of perturbations in infinitely long filaments as they form and grow by accretion. The growth of these perturbations leads to filament fragmentation and the formation of cores. Most previous work on this subject has been confined to the growth and fragmentation of equilibrium filaments and has found that there exists a preferential fragmentation length-scale which is roughly four times the filament's diameter. Our results show a more complicated dispersion relation with a series of peaks linking perturbation wavelength and growth rate. These are due to gravo-acoustic oscillations along the longitudinal axis during the sub-critical phase of growth. The positions of the peaks in growth rate have a strong dependence on both the mass accretion rate onto the filament and the temperature of the gas. When seeded with a multiwavelength density power spectrum, there exists a clear preferred core separation equal to the largest peak in the dispersion relation. Our results allow one to estimate a minimum age for a filament which is breaking up into regularly spaced fragments, as well as an average accretion rate. We apply the model to observations of filaments in Taurus by Tafalla & Hacar and find accretion rates consistent with those estimated by Palmeirim et al.

  20. A vortex filament tracking method for the Gross-Pitaevskii model of a superfluid

    Science.gov (United States)

    Villois, Alberto; Krstulovic, Giorgio; Proment, Davide; Salman, Hayder

    2016-10-01

    We present an accurate and robust numerical method to track quantised vortex lines in a superfluid described by the Gross-Pitaevskii equation. By utilising the pseudo-vorticity field of the associated complex scalar order parameter of the superfluid, we are able to track the topological defects of the superfluid and reconstruct the vortex lines which correspond to zeros of the field. Throughout, we assume our field is periodic to allow us to make extensive use of the Fourier representation of the field and its derivatives in order to retain spectral accuracy. We present several case studies to test the precision of the method which include the evaluation of the curvature and torsion of a torus vortex knot, and the measurement of the Kelvin wave spectrum of a vortex line and a vortex ring. The method we present makes no a priori assumptions on the geometry of the vortices and is therefore applicable to a wide range of systems such as a superfluid in a turbulent state that is characterised by many vortex rings coexisting with sound waves. This allows us to track the positions of the vortex filaments in a dense turbulent vortex tangle and extract statistical information about the distribution of the size of the vortex rings and the inter-vortex separations. In principle, the method can be extended to track similar topological defects arising in other physical systems.

  1. Dynamic modeling and analysis of vortex filament motion using a novel curve-fitting method

    Directory of Open Access Journals (Sweden)

    Chang-Joo Kim

    2016-02-01

    Full Text Available Applications of a novel curve-fitting technique are presented to efficiently predict the motion of the vortex filament, which is trailed from a rigid body such as wings and rotors. The governing equations of the motion, when a Lagrangian approach with the present curve-fitting method is applied, can be transformed into an easily solvable form of the system of nonlinear ordinary differential equations. The applicability of Bézier curves, B-spline, and Lagrange interpolating polynomials is investigated. Local Lagrange interpolating polynomials with a shift operator are proposed as the best selection for applications, since it provides superior system characteristics with minimum computing time, compared to other methods. In addition, the Gauss quadrature formula with local refinement strategy has been developed for an accurate prediction of the induced velocity computed with the line integration of the Biot–Savart law. Rotary-wing problems including a vortex ring problem are analyzed to show the efficiency, accuracy, and flexibility in the applications of the proposed method.

  2. Thermo-mechanical Characterization of Metal/Polymer Composite Filaments and Printing Parameter Study for Fused Deposition Modeling in the 3D Printing Process

    Science.gov (United States)

    Hwang, Seyeon; Reyes, Edgar I.; Moon, Kyoung-sik; Rumpf, Raymond C.; Kim, Nam Soo

    2015-03-01

    New metal/polymer composite filaments for fused deposition modeling (FDM) processes were developed in order to observe the thermo-mechanical properties of the new filaments. The acrylonitrile butadiene styrene (ABS) thermoplastic was mixed with copper and iron particles. The percent loading of the metal powder was varied to confirm the effects of metal particles on the thermo-mechanical properties of the filament, such as tensile strength and thermal conductivity. The printing parameters such as temperature and fill density were also varied to see the effects of the parameters on the tensile strength of the final product which was made with the FDM process. As a result of this study, it was confirmed that the tensile strength of the composites is decreased by increasing the loading of metal particles. Additionally, the thermal conductivity of the metal/polymer composite filament was improved by increasing the metal content. It is believed that the metal/polymer filament could be used to print metal and large-scale 3-dimensional (3D) structures without any distortion by the thermal expansion of thermoplastics. The material could also be used in 3D printed circuits and electromagnetic structures for shielding and other applications.

  3. A fast platform for simulating semi-flexible fiber suspensions applied to cell mechanics

    Science.gov (United States)

    Nazockdast, Ehssan; Rahimian, Abtin; Zorin, Denis; Shelley, Michael

    2017-01-01

    We present a novel platform for the large-scale simulation of three-dimensional fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space in three dimensions. One of the main motivations for this work is to study the dynamics of fiber assemblies within biological cells. For this, we also incorporate the key biophysical elements that determine the dynamics of these assemblies, which include the polymerization and depolymerization kinetics of fibers, their interactions with molecular motors and other objects, their flexibility, and hydrodynamic coupling. This work, to our knowledge, is the first technique to include many-body hydrodynamic interactions (HIs), and the resulting fluid flows, in cellular assemblies of flexible fibers. We use non-local slender body theory to compute the fluid-structure interactions of the fibers and a second-kind boundary integral formulation for other rigid bodies and the confining boundary. A kernel-independent implementation of the fast multipole method is utilized for efficient evaluation of HIs. The deformation of the fibers is described by nonlinear Euler-Bernoulli beam theory and their polymerization is modeled by the reparametrization of the dynamic equations in the appropriate non-Lagrangian frame. We use a pseudo-spectral representation of fiber positions and implicit time-stepping to resolve large fiber deformations, and to allow time-steps not excessively constrained by temporal stiffness or fiber-fiber interactions. The entire computational scheme is parallelized, which enables simulating assemblies of thousands of fibers. We use our method to investigate two important questions in the mechanics of cell division: (i) the effect of confinement on the hydrodynamic mobility of microtubule asters; and (ii) the dynamics of the positioning of mitotic spindle in complex cell geometries. Finally to demonstrate the general applicability of the method, we simulate the sedimentation of a cloud of

  4. A fast platform for simulating semi-flexible fiber suspensions applied to cell mechanics

    Energy Technology Data Exchange (ETDEWEB)

    Nazockdast, Ehssan, E-mail: ehssan@cims.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Center for Computational Biology, Simons Foundation, New York, NY 10010 (United States); Rahimian, Abtin, E-mail: arahimian@acm.org [Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Zorin, Denis, E-mail: dzorin@cs.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Shelley, Michael, E-mail: shelley@cims.nyu.edu [Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Center for Computational Biology, Simons Foundation, New York, NY 10010 (United States)

    2017-01-15

    We present a novel platform for the large-scale simulation of three-dimensional fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space in three dimensions. One of the main motivations for this work is to study the dynamics of fiber assemblies within biological cells. For this, we also incorporate the key biophysical elements that determine the dynamics of these assemblies, which include the polymerization and depolymerization kinetics of fibers, their interactions with molecular motors and other objects, their flexibility, and hydrodynamic coupling. This work, to our knowledge, is the first technique to include many-body hydrodynamic interactions (HIs), and the resulting fluid flows, in cellular assemblies of flexible fibers. We use non-local slender body theory to compute the fluid–structure interactions of the fibers and a second-kind boundary integral formulation for other rigid bodies and the confining boundary. A kernel-independent implementation of the fast multipole method is utilized for efficient evaluation of HIs. The deformation of the fibers is described by nonlinear Euler–Bernoulli beam theory and their polymerization is modeled by the reparametrization of the dynamic equations in the appropriate non-Lagrangian frame. We use a pseudo-spectral representation of fiber positions and implicit time-stepping to resolve large fiber deformations, and to allow time-steps not excessively constrained by temporal stiffness or fiber–fiber interactions. The entire computational scheme is parallelized, which enables simulating assemblies of thousands of fibers. We use our method to investigate two important questions in the mechanics of cell division: (i) the effect of confinement on the hydrodynamic mobility of microtubule asters; and (ii) the dynamics of the positioning of mitotic spindle in complex cell geometries. Finally to demonstrate the general applicability of the method, we simulate the sedimentation of a

  5. 3D Simulations of Plasma Filaments in the Scrape Off Layer: A Comparison with Models of Reduced Dimensionality

    CERN Document Server

    Easy, Luke; Omotani, John; Dudson, Benjamin; Havlíčková, Eva; Tamain, Patrick; Naulin, Volker; Nielsen, Anders H

    2014-01-01

    This paper presents simulations of isolated 3D filaments in a slab geometry obtained using a 3D reduced fluid code. First, systematic scans were performed to investigate how the dynamics of a filament are affected by its amplitude, perpendicular size and parallel extent. The perpendicular size of the filament was found to have a strong influence on its motions, as it determined the relative importance of parallel currents to polarisation and viscous currents, whilst drift-wave instabilities were observed if the initial amplitude of the blob was increased sufficiently. Next, the 3D simulations were compared to 2D simulations using different parallel closures; namely, the sheath dissipation closure, which neglects parallel gradients, and the vorticity advection closure, which neglects the influence of parallel currents. The vorticity advection closure was found to not replicate the 3D perpendicular dynamics and overestimated the initial radial acceleration of all the filaments studied. In contrast, a more satis...

  6. Constriction model of actomyosin ring for cytokinesis by fission yeast using a two-state sliding filament mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Yong-Woon [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States); Mascagni, Michael, E-mail: Mascagni@fsu.edu [Departments of Computer Science, Mathematics and Scientific Computing, and Graduate Program in Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-4530 (United States)

    2014-09-28

    We developed a model describing the structure and contractile mechanism of the actomyosin ring in fission yeast, Schizosaccharomyces pombe. The proposed ring includes actin, myosin, and α-actinin, and is organized into a structure similar to that of muscle sarcomeres. This structure justifies the use of the sliding-filament mechanism developed by Huxley and Hill, but it is probably less organized relative to that of muscle sarcomeres. Ring contraction tension was generated via the same fundamental mechanism used to generate muscle tension, but some physicochemical parameters were adjusted to be consistent with the proposed ring structure. Simulations allowed an estimate of ring constriction tension that reproduced the observed ring constriction velocity using a physiologically possible, self-consistent set of parameters. Proposed molecular-level properties responsible for the thousand-fold slower constriction velocity of the ring relative to that of muscle sarcomeres include fewer myosin molecules involved, a less organized contractile configuration, a low α-actinin concentration, and a high resistance membrane tension. Ring constriction velocity is demonstrated as an exponential function of time despite a near linear appearance. We proposed a hypothesis to explain why excess myosin heads inhibit constriction velocity rather than enhance it. The model revealed how myosin concentration and elastic resistance tension are balanced during cytokinesis in S. pombe.

  7. Constriction model of actomyosin ring for cytokinesis by fission yeast using a two-state sliding filament mechanism

    Science.gov (United States)

    Jung, Yong-Woon; Mascagni, Michael

    2014-09-01

    We developed a model describing the structure and contractile mechanism of the actomyosin ring in fission yeast, Schizosaccharomyces pombe. The proposed ring includes actin, myosin, and α-actinin, and is organized into a structure similar to that of muscle sarcomeres. This structure justifies the use of the sliding-filament mechanism developed by Huxley and Hill, but it is probably less organized relative to that of muscle sarcomeres. Ring contraction tension was generated via the same fundamental mechanism used to generate muscle tension, but some physicochemical parameters were adjusted to be consistent with the proposed ring structure. Simulations allowed an estimate of ring constriction tension that reproduced the observed ring constriction velocity using a physiologically possible, self-consistent set of parameters. Proposed molecular-level properties responsible for the thousand-fold slower constriction velocity of the ring relative to that of muscle sarcomeres include fewer myosin molecules involved, a less organized contractile configuration, a low α-actinin concentration, and a high resistance membrane tension. Ring constriction velocity is demonstrated as an exponential function of time despite a near linear appearance. We proposed a hypothesis to explain why excess myosin heads inhibit constriction velocity rather than enhance it. The model revealed how myosin concentration and elastic resistance tension are balanced during cytokinesis in S. pombe.

  8. Examination of the pathogenic potential of Candida albicans filamentous cells in an animal model of haematogenously disseminated candidiasis.

    Science.gov (United States)

    Cleary, Ian A; Reinhard, Sara M; Lazzell, Anna L; Monteagudo, Carlos; Thomas, Derek P; Lopez-Ribot, Jose L; Saville, Stephen P

    2016-03-01

    The opportunistic fungal pathogen Candida albicans is an increasingly common threat to human health. Candida albicans grows in several morphologies and mutant strains locked in yeast or filamentous forms have attenuated virulence in the murine model of disseminated candidiasis. Thus, the ability to change shape is important for virulence. The transcriptional repressors Nrg1p and Tup1p are required for normal regulation of C. albicans morphology. Strains lacking either NRG1 or TUP1 are constitutively pseudohyphal under yeast growth conditions, and display attenuated virulence in the disseminated model. To dissect the relative importance of hyphae and pseudohyphae during an infection, we used strains in which the morphological transition could be externally manipulated through controlled expression of NRG1 or TUP1. Remarkably, hyphal form inocula retain the capacity to cause disease. Whilst induction of a pseudohyphal morphology through depletion of TUP1 did result in attenuated virulence, this was not due to a defect in the ability to escape the bloodstream. Instead, we observed that pseudohyphal cells are cleared from tissues much more efficiently than either hyphal (virulent) or yeast form (avirulent) cells, indicating that different C. albicans morphologies have distinct interactions with host cells during an infection.

  9. Miscibility of Semi-flexible Thermotropic Liquid Crystalline Copolyesteramide with Polyamide 66

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Liquid crystalline polymer-polyamide 66 (LCP/PA66) blends were compounded by usingaBrabender mixing followed by compression moulding. The LCP employed was a semi-flexible liquid crystalline copolyesteramide based on 30% (molar fraction) of p-amino benzoic acid (ABA)and 70% (molar fraction) of poly (ethylene terephthalate)(PET). The LCP/PA66 blends wereinvestigated in terms of the thermal and dynamic mechanical properties. It was found that PA66and LCP components of the blends are miscible in the molten state, but are partially miscible inthe solid state. The inclusion of the semi-flexible LCP into PA66 retards the crystallization rateof PA66. Furthermore, the melting temperature and the degree of crystallinity of PA66 are reduced considerably due to the LCP addition.

  10. Self-organization in suspensions of end-functionalized semiflexible polymers under shear flow

    Science.gov (United States)

    Myung, Jin Suk; Winkler, Roland G.; Gompper, Gerhard

    2015-12-01

    The nonequilibrium dynamical behavior and structure formation of end-functionalized semiflexible polymer suspensions under flow are investigated by mesoscale hydrodynamic simulations. The hybrid simulation approach combines the multiparticle collision dynamics method for the fluid, which accounts for hydrodynamic interactions, with molecular dynamics simulations for the semiflexible polymers. In equilibrium, various kinds of scaffold-like network structures are observed, depending on polymer flexibility and end-attraction strength. We investigate the flow behavior of the polymer networks under shear and analyze their nonequilibrium structural and rheological properties. The scaffold structure breaks up and densified aggregates are formed at low shear rates, while the structural integrity is completely lost at high shear rates. We provide a detailed analysis of the shear- rate-dependent flow-induced structures. The studies provide a deeper understanding of the formation and deformation of network structures in complex materials.

  11. Mechanosensing in myosin filament solves a 60 years old conflict in skeletal muscle modeling between high power output and slow rise in tension

    CERN Document Server

    Marcucci, Lorenzo

    2016-01-01

    Almost 60 years ago Andrew Huxley with his seminal paper \\cite{Huxley1957} laid the foundation of modern muscle modeling, linking chemical events to mechanical performance. He described mechanics and energetics of muscle contraction through the cyclical attachment and detachment of myosin motors to the actin filament with ad hoc assumptions on the dependence of the rate constants on the strain of the myosin motors. That relatively simple hypothesis is still present in recent models, even though with several modifications to adapt the model to the different experimental constraints which became subsequently available. However, already in that paper, one controversial aspect of the model became clear. Relatively high attachment and detachment rates of myosin to the actin filament were needed to simulate the high power output at intermediate velocity of contraction. However, these rates were incompatible with the relatively slow rise in tension after activation, despite the rise should be generated by the same r...

  12. Filamentation in Laser Wakefields

    Science.gov (United States)

    Los, Eva; Trines, Raoul; Silva, Luis; Bingham, Robert

    2016-10-01

    Laser filamentation instability is observed in plasma wakefields with sub-critical densities, and in high density inertial fusion plasmas. This leads to non-uniform acceleration or compression respectively. Here, we present simulation results on laser filamentation in plasma wakefields. The 2-D simulations are carried out using the particle-in-cell code Osiris. The filament intensity was found to increase exponentially before saturating. The maximum amplitude to which the highest intensity filament grew for a specific set of parameters was also recorded, and plotted against a corresponding parameter value. Clear, positively correlated linear trends were established between plasma density, transverse wavenumber k, laser pulse amplitude and maximum filament amplitude. Plasma density and maximum filament amplitude also showed a positive correlation, which saturated after a certain plasma density. Pulse duration and interaction length did not affect either filament intensity or transverse k value in a predictable manner. There was no discernible trend between pulse amplitude and filament width.

  13. The Formation of Fibrils by Intertwining of Filaments: Model and Application to Amyloid Aβ Protein

    Science.gov (United States)

    van Gestel, Jeroen; de Leeuw, Simon W.

    2007-01-01

    We outline a model that describes the interaction of rods that form intertwined bundles. In this simple model, we compare the elastic energy penalty that arises due to the deformation of the rods to the gain in binding energy upon intertwining. We find that, for proper values of the bending Young's modulus and the binding energy, a helical pitch may be found for which the energy of intertwining is most favorable. We apply our description to the problem of Alzheimer's Aβ protein fibrillization. If we forbid configurations that exhibit steric overlap between the protofilaments that make up a protein fibril, our model predicts that fibrils consisting of three protofilaments shall form. This agrees well with experimental results. Our model can also provide an estimate for the helical pitch of suitable fibrils. PMID:17114229

  14. Mechanical properties of branched actin filaments

    CERN Document Server

    Razbin, Mohammadhosein; Benetatos, Panayotis; Zippelius, Annette

    2015-01-01

    Cells moving on a two dimensional substrate generate motion by polymerizing actin filament networks inside a flat membrane protrusion. New filaments are generated by branching off existing ones, giving rise to branched network structures. We investigate the force-extension relation of branched filaments, grafted on an elastic structure at one end and pushing with the free ends against the leading edge cell membrane. Single filaments are modeled as worm-like chains, whose thermal bending fluctuations are restricted by the leading edge cell membrane, resulting in an effective force. Branching can increase the stiffness considerably; however the effect depends on branch point position and filament orientation, being most pronounced for intermediate tilt angles and intermediate branch point positions. We describe filament networks without cross-linkers to focus on the effect of branching. We use randomly positioned branch points, as generated in the process of treadmilling, and orientation distributions as measur...

  15. Automated alignment-based curation of gene models in filamentous fungi

    OpenAIRE

    2014-01-01

    Background Automated gene-calling is still an error-prone process, particularly for the highly plastic genomes of fungal species. Improvement through quality control and manual curation of gene models is a time-consuming process that requires skilled biologists and is only marginally performed. The wealth of available fungal genomes has not yet been exploited by an automated method that applies quality control of gene models in order to obtain more accurate genome annotations. Results We prov...

  16. Hydrodynamic interactions between nearby slender filaments

    CERN Document Server

    Man, Yi; Lauga, Eric

    2016-01-01

    Cellular biology abound with filaments interacting through fluids, from intracellular microtubules, to rotating flagella and beating cilia. While previous work has demonstrated the complexity of capturing nonlocal hydrodynamic interactions between moving filaments, the problem remains difficult theoretically. We show here that when filaments are closer to each other than their relevant length scale, the integration of hydrodynamic interactions can be approximately carried out analytically. This leads to a set of simplified local equations, illustrated on a simple model of two interacting filaments, which can be used to tackle theoretically a range of problems in biology and physics.

  17. Transient filament stretching rheometer II

    DEFF Research Database (Denmark)

    Kolte, Mette Irene; Rasmussen, Henrik K.; Hassager, Ole

    1997-01-01

    The Lagrangian sspecification is used to simulate the transient stretching filament rheometer. Simulations are performed for dilute PIB-solutions modeled as a four mode Oldroyd-B fluid and a semidilute PIB-solution modeled as a non-linear single integral equation. The simulations are compared...

  18. Modelling of secondary sedimentation under wet-weather and filamentous bulking conditions

    DEFF Research Database (Denmark)

    Ramin, Elham

    Secondary settling tanks (SSTs) are the most hydraulically sensitive unit operations in wastewater treatment plants (WWTPs). Performance of SSTs influences the solids inventory in the activated sludge unit and consequently impacts the biological treatment efficiency. Moreover, SSTs limit the maxi......Secondary settling tanks (SSTs) are the most hydraulically sensitive unit operations in wastewater treatment plants (WWTPs). Performance of SSTs influences the solids inventory in the activated sludge unit and consequently impacts the biological treatment efficiency. Moreover, SSTs limit......-model in second-order 1-D SST models in the future. A significant part of the thesis was dedicated to the development of a CFD model of a circular conical SST with the open source OpenFOAM CFD toolbox. The focus was mainly on identifying the settling and rheology submodels using data obtained from laboratory...

  19. Hand-Held Model of a Sarcomere to Illustrate the Sliding Filament Mechanism in Muscle Contraction

    Science.gov (United States)

    Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2009-01-01

    From our teaching of the contractile unit of the striated muscle, we have found limitations in using textbook illustrations of sarcomere structure and its related dynamic molecular physiological details. A hand-held model of a striated muscle sarcomere made from common items has thus been made by us to enhance students' understanding of the…

  20. Automated alignment-based curation of gene models in filamentous fungi

    NARCIS (Netherlands)

    Burgt, van der A.; Severing, E.I.; Collemare, J.A.R.; Wit, de P.J.G.M.

    2014-01-01

    Background Automated gene-calling is still an error-prone process, particularly for the highly plastic genomes of fungal species. Improvement through quality control and manual curation of gene models is a time-consuming process that requires skilled biologists and is only marginally performed. The

  1. Hand-Held Model of a Sarcomere to Illustrate the Sliding Filament Mechanism in Muscle Contraction

    Science.gov (United States)

    Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2009-01-01

    From our teaching of the contractile unit of the striated muscle, we have found limitations in using textbook illustrations of sarcomere structure and its related dynamic molecular physiological details. A hand-held model of a striated muscle sarcomere made from common items has thus been made by us to enhance students' understanding of the…

  2. Extracerebral Tissue Damage in the Intraluminal Filament Mouse Model of Middle Cerebral Artery Occlusion

    Science.gov (United States)

    Vaas, Markus; Ni, Ruiqing; Rudin, Markus; Kipar, Anja; Klohs, Jan

    2017-01-01

    Middle cerebral artery occlusion is the most common model of focal cerebral ischemia in the mouse. In the surgical procedure, the external carotid artery (ECA) is ligated; however, its effect on the tissue supplied by the vessel has not been described so far. C57BL/6 mice underwent 1 h of transient MCAO (tMCAO) or sham surgery. Multi-spectral optoacoustic tomography was employed at 30 min after surgery to assess oxygenation in the temporal muscles. Microstructural changes were assessed with magnetic resonance imaging and histological examination at 24 h and 48 h after surgery. Ligation of the ECA resulted in decreased oxygenation of the left temporal muscle in most sham-operated and tMCAO animals. Susceptible mice of both groups exhibited increased T2 relaxation times in the affected muscle with histological evidence of myofibre degeneration, interstitial edema, and neutrophil influx. Ligatures had induced an extensive neutrophil-dominated inflammatory response. ECA ligation leads to distinct hypoxic degenerative changes in the tissue of the ECA territory and to ligature-induced inflammatory processes. An impact on outcome needs to be considered in this stroke model. PMID:28348545

  3. Boolean gates on actin filaments

    Science.gov (United States)

    Siccardi, Stefano; Tuszynski, Jack A.; Adamatzky, Andrew

    2016-01-01

    Actin is a globular protein which forms long polar filaments in the eukaryotic cytoskeleton. Actin networks play a key role in cell mechanics and cell motility. They have also been implicated in information transmission and processing, memory and learning in neuronal cells. The actin filaments have been shown to support propagation of voltage pulses. Here we apply a coupled nonlinear transmission line model of actin filaments to study interactions between voltage pulses. To represent digital information we assign a logical TRUTH value to the presence of a voltage pulse in a given location of the actin filament, and FALSE to the pulse's absence, so that information flows along the filament with pulse transmission. When two pulses, representing Boolean values of input variables, interact, then they can facilitate or inhibit further propagation of each other. We explore this phenomenon to construct Boolean logical gates and a one-bit half-adder with interacting voltage pulses. We discuss implications of these findings on cellular process and technological applications.

  4. Spectral stability of Alfven filament chains

    NARCIS (Netherlands)

    Bergmans, J.; Kuvshinov, B. N.; Lakhin, V. P.; Schep, T. J.

    2000-01-01

    The two-fluid model of nonlinear Alfven perturbations has singular solutions in the form of current-vortex filaments. We investigate analytically and numerically the spectral stability of single and double rows of filaments. Staggered and non-staggered double rows (von Karman streets) are studied. I

  5. Solar Features - Prominences and Filaments - Filaments

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Filaments are formed in magnetic loops that hold relatively cool, dense gas suspended above the surface of the Sun (David Hathaway/NASA)

  6. Merging Rates of the First Objects and the Formation of First Mini-Filaments in Models with Massive Neutrinos

    CERN Document Server

    Song, Hyunmi

    2010-01-01

    We study the effect of massive neutrinos on the evolution of the early mini-halos (M~10^{6} M_{\\odot} at z~20) where the first stars may have formed. In the framework of the extended Press-Schechter formalism, we evaluate analytically the rates of merging of the mini-halos into zero-dimensional larger halos and one dimensional mini-filaments. It is shown that the halo-to-filament merging rate increases sharply with the neutrino mass fraction f_{\

  7. Towards filament free semiconductor lasers

    DEFF Research Database (Denmark)

    McInerney, John; O'Brien, Peter; Skovgaard, Peter M. W.

    2000-01-01

    We outline physical models and simulations for suppression of self-focusing and filamentation in large aperture semiconductor lasers. The principal technical objective is to generate multi-watt CW or quasi-CW outputs with nearly diffraction limited beams, suitable for long distance free space...... propagation structures in lasers and amplifiers which suppress lateral reflections....

  8. Molecular dynamics simulation of spin-lattice NMR relaxation in poly-L-lysine dendrimers: manifestation of the semiflexibility effect.

    Science.gov (United States)

    Markelov, Denis A; Falkovich, Stanislav G; Neelov, Igor M; Ilyash, Maxim Yu; Matveev, Vladimir V; Lähderanta, Erkki; Ingman, Petri; Darinskii, Anatolii A

    2015-02-07

    NMR relaxation experiments are widely used to investigate the local orientation mobility in dendrimers. In particular, the NMR method allows one to measure the spin-lattice relaxation rate, 1/T1, which is connected with the orientational autocorrelation function (ACF) of NMR active groups. We calculate the temperature (Θ) and frequency (ω) dependences of the spin-lattice NMR relaxation rates for segments and NMR active CH2 groups in poly-L-lysine (PLL) dendrimers in water, on the basis of full-atomic molecular dynamics simulations. It is shown that the position of the maximum of 1/T1(ω) depends on the location of the segments inside the dendrimer. This dependence of the maximum is explained by the restricted flexibility of the dendrimer. Such behavior has been predicted recently by the analytical theory based on the semiflexible viscoelastic model. The simulated temperature dependences of 1/T1 for terminal and inner groups in PLL dendrimers of n = 2 and n = 4 generations dissolved in water are in good agreement with the NMR experimental data, which have been obtained for these systems previously by us. It is shown that in the case of PLL dendrimers, the traditional procedure of the interpretation of NMR experimental data - when smaller values of 1/T1 correspond to higher orientation mobility - is applicable to the whole accessible frequency interval only for the terminal groups. For the inner groups, this procedure is valid only at low frequencies.

  9. Conformations, Transverse Fluctuations and Crossover Dynamics of a Semi-Flexible Chain in Two Dimensions

    CERN Document Server

    Huang, Aiqun; Binder, Kurt

    2014-01-01

    We present a unified scaling theory for the dynamics of monomers of a semiflexible chain under good solvent condition in the free draining limit. We consider both the cases where the contour length $L$ is comparable to the persistence length $\\ell_p$ and the case $L\\gg \\ell_p$. Our theory captures the early time monomer dynamics of a stiff chain characterized by $t^{3/4}$ dependence for the mean square displacement(MSD) of the monomers, but predicts a first crossover to the Rouse regime of $t^{2\

  10. High-resolution Observations of Sympathetic Filament Eruptions by NVST

    Science.gov (United States)

    Su, Yingna; Li, Shangwei; Zhou, Tuanhui; Van Ballegooijen, Adriaan A.; Sun, Xudong; Ji, Haisheng

    2017-08-01

    We investigate two sympathetic filament eruptions observed by the New Vacuum Solar Telescope (NVST) on 2015 October 15. The full picture of the eruptions is obtained from the corresponding SDO/AIA observations. The two filaments start from the east border of active region NOAA 12434 in the north and end in one large quiescent filament channel in the south. The left filament erupts firstly, followed by the right filament eruption about 10 minutes later. Clear twist structure and rotating motion are observed in both filaments during the eruption. Both eruptions are failed, since the filaments firstly rise up, then flow towards the south and merge into the southern large quiescent filament. We also observe repeating activations of mini filaments below the right filament after its eruption. Using magnetic field models constructed based on SDO/HMI magnetograms by flux rope insertion method, we find that the left filament eruption is likely to be triggered by kink instability, while weakening of overlying magnetic fields due to magnetic reconnection at an X-point between the two filament systems might play an important role in the onset of the right filament eruption.

  11. Withaferin A Targets Intermediate Filaments Glial Fibrillary Acidic Protein and Vimentin in a Model of Retinal Gliosis*

    OpenAIRE

    2010-01-01

    Gliosis is a biological process that occurs during injury repair in the central nervous system and is characterized by the overexpression of the intermediate filaments (IFs) glial fibrillary acidic protein (GFAP) and vimentin. A common thread in many retinal diseases is reactive Müller cell gliosis, an untreatable condition that leads to tissue scarring and even blindness. Here, we demonstrate that the vimentin-targeting small molecule withaferin A (WFA) is a novel chemical probe of GFAP. Usi...

  12. Proteomics of Filamentous Fungi

    NARCIS (Netherlands)

    Passel, van M.W.J.; Schaap, P.J.; Graaff, de L.H.

    2013-01-01

    Filamentous fungi, such as Aspergillus niger and Aspergillus oryzae traditionally have had an important role in providing enzymes and enzyme cocktails that are used in food industry. In recent years the genome sequences of many filamentous fungi have become available. This combined with

  13. Proteomics of Filamentous Fungi

    NARCIS (Netherlands)

    Passel, van M.W.J.; Schaap, P.J.; Graaff, de L.H.

    2013-01-01

    Filamentous fungi, such as Aspergillus niger and Aspergillus oryzae traditionally have had an important role in providing enzymes and enzyme cocktails that are used in food industry. In recent years the genome sequences of many filamentous fungi have become available. This combined with technologica

  14. Tungsten Filament Fire

    Science.gov (United States)

    Ruiz, Michael J.; Perkins, James

    2016-01-01

    We safely remove the outer glass bulb from an incandescent lamp and burn up the tungsten filament after the glass is removed. This demonstration dramatically illustrates the necessity of a vacuum or inert gas for the environment surrounding the tungsten filament inside the bulb. Our approach has added historical importance since the incandescent…

  15. Mechanical heterogeneity favors fragmentation of strained actin filaments.

    Science.gov (United States)

    De La Cruz, Enrique M; Martiel, Jean-Louis; Blanchoin, Laurent

    2015-05-05

    We present a general model of actin filament deformation and fragmentation in response to compressive forces. The elastic free energy density along filaments is determined by their shape and mechanical properties, which were modeled in terms of bending, twisting, and twist-bend coupling elasticities. The elastic energy stored in filament deformation (i.e., strain) tilts the fragmentation-annealing reaction free-energy profile to favor fragmentation. The energy gradient introduces a local shear force that accelerates filament intersubunit bond rupture. The severing protein, cofilin, renders filaments more compliant in bending and twisting. As a result, filaments that are partially decorated with cofilin are mechanically heterogeneous (i.e., nonuniform) and display asymmetric shape deformations and energy profiles distinct from mechanically homogenous (i.e., uniform), bare actin, or saturated cofilactin filaments. The local buckling strain depends on the relative size of the compliant segment as well as the bending and twisting rigidities of flanking regions. Filaments with a single bare/cofilin-decorated boundary localize energy and force adjacent to the boundary, within the compliant cofilactin segment. Filaments with small cofilin clusters were predicted to fragment within the compliant cofilactin rather than at boundaries. Neglecting contributions from twist-bend coupling elasticity underestimates the energy density and gradients along filaments, and thus the net effects of filament strain to fragmentation. Spatial confinement causes compliant cofilactin segments and filaments to adopt higher deformation modes and store more elastic energy, thereby promoting fragmentation. The theory and simulations presented here establish a quantitative relationship between actin filament fragmentation thermodynamics and elasticity, and reveal how local discontinuities in filament mechanical properties introduced by regulatory proteins can modulate both the severing efficiency

  16. Microstructural model for cyclic hardening in F-actin networks crosslinked by α-actinin

    Science.gov (United States)

    López-Menéndez, Horacio; Rodríguez, José Félix

    2016-06-01

    The rheology of F-actin networks has attracted a great attention during the last years. In order to gain a complete understanding of the rheological properties of these novel materials, it is necessary the study in a large deformations regime to alter their internal structure. In this sense, Schmoller et al. (2010) showed that the reconstituted networks of F-actin crosslinked with α-actinin unexpectedly harden when they are subjected to a cyclical shear. This observation contradicts the expected Mullins effect observed in most soft materials, such as rubber and living tissues, where a pronounced softening is observed when they are cyclically deformed. We think that the key to understand this stunning effect is the gelation process. To define it, the most relevant constituents are the chemical crosslinks - α-actinin -, the physical crosslinks - introduced by the entanglement of the semiflexible network - and the interaction between them. As a consequence of this interaction, a pre-stressed network emerges and introduces a feedback effect, where the pre-stress also regulates the adhesion energy of the α-actinin, setting the structure in a metastable reference configuration. Therefore, the external loads and the evolvement of the trapped stress drive the microstructural changes during the cyclic loading protocol. In this work, we propose a micromechanical model into the framework of nonlinear continuum mechanics. The mechanics of the F-actin filaments is modelled using the wormlike chain model for semiflexible filaments and the gelation process is modelled as mesoscale dynamics for the α-actinin and physical crosslink. The model has been validated with reported experimental results.

  17. Actin filament attachments for sustained motility in vitro are maintained by filament bundling.

    Directory of Open Access Journals (Sweden)

    Xiaohua Hu

    Full Text Available We reconstructed cellular motility in vitro from individual proteins to investigate how actin filaments are organized at the leading edge. Using total internal reflection fluorescence microscopy of actin filaments, we tested how profilin, Arp2/3, and capping protein (CP function together to propel thin glass nanofibers or beads coated with N-WASP WCA domains. Thin nanofibers produced wide comet tails that showed more structural variation in actin filament organization than did bead substrates. During sustained motility, physiological concentrations of Mg(2+ generated actin filament bundles that processively attached to the nanofiber. Reduction of total Mg(2+ abolished particle motility and actin attachment to the particle surface without affecting actin polymerization, Arp2/3 nucleation, or filament capping. Analysis of similar motility of microspheres showed that loss of filament bundling did not affect actin shell formation or symmetry breaking but eliminated sustained attachments between the comet tail and the particle surface. Addition of Mg(2+, Lys-Lys(2+, or fascin restored both comet tail attachment and sustained particle motility in low Mg(2+ buffers. TIRF microscopic analysis of filaments captured by WCA-coated beads in the absence of Arp2/3, profilin, and CP showed that filament bundling by polycation or fascin addition increased barbed end capture by WCA domains. We propose a model in which CP directs barbed ends toward the leading edge and polycation-induced filament bundling sustains processive barbed end attachment to the leading edge.

  18. Significance of settling model structures and parameter subsets in modelling WWTPs under wet-weather flow and filamentous bulking conditions.

    Science.gov (United States)

    Ramin, Elham; Sin, Gürkan; Mikkelsen, Peter Steen; Plósz, Benedek Gy

    2014-10-15

    Current research focuses on predicting and mitigating the impacts of high hydraulic loadings on centralized wastewater treatment plants (WWTPs) under wet-weather conditions. The maximum permissible inflow to WWTPs depends not only on the settleability of activated sludge in secondary settling tanks (SSTs) but also on the hydraulic behaviour of SSTs. The present study investigates the impacts of ideal and non-ideal flow (dry and wet weather) and settling (good settling and bulking) boundary conditions on the sensitivity of WWTP model outputs to uncertainties intrinsic to the one-dimensional (1-D) SST model structures and parameters. We identify the critical sources of uncertainty in WWTP models through global sensitivity analysis (GSA) using the Benchmark simulation model No. 1 in combination with first- and second-order 1-D SST models. The results obtained illustrate that the contribution of settling parameters to the total variance of the key WWTP process outputs significantly depends on the influent flow and settling conditions. The magnitude of the impact is found to vary, depending on which type of 1-D SST model is used. Therefore, we identify and recommend potential parameter subsets for WWTP model calibration, and propose optimal choice of 1-D SST models under different flow and settling boundary conditions. Additionally, the hydraulic parameters in the second-order SST model are found significant under dynamic wet-weather flow conditions. These results highlight the importance of developing a more mechanistic based flow-dependent hydraulic sub-model in second-order 1-D SST models in the future.

  19. Ordered structures of nanoro ds induced by the helixes of semiflexible p olymer chains%半刚性高分子链螺旋结构诱导纳米棒的有序结构∗

    Institute of Scientific and Technical Information of China (English)

    华昀峰; 张冬; 章林溪

    2015-01-01

    packed hexagonal arrays of NRs are produced. In this paper, by employing the coarse-grained model and molecular dynamics simulation, we explore the structures of nanocomposites in which a small number of NRs bind with semiflexible polymer chain. The morphology of NRs/polymer mixture is greatly affected by the bending energy b of semiflexible polymer and the binding energy D0 between NRs and semiflexible polymer. If the binding energy D0 is less than 1.1kBT , the NRs are almost free and a gas-like phase is observed. For a suitably large value of D0, three completely different morphologies of NRs/polymer mixtures are identified, namely, the side-to-side parallel aggregation of NRs, the end-to-end parallel aggregation of NRs, and the dispersion of NRs. For the flexible polymer chain (i.e., small bending energy b), the side-to-side parallel aggregation structure of NRs and the disordered conformation of adsorbed polymer chain are observed. In general, a typical equilibrium conformation of free flexible polymer chain is random coil, the binding energy between NRs and polymer can lead to the collapse of a random coil for flexible polymer chain, and the NRs aggregate in the manner of the side-to-side parallel to each other because the enthalpy is maximized through sharing the more polymer monomers between neighbor NRs. That is to say, the local aggregation of NRs can be found because the orientational entropy can make the aggregated NRs arrange in the side-to-side parallel manner. In the rigid polymer chain limit (very large bending energy), the rigid polymer chain is stretched and the NRs are well dispersed. As the rigid polymer holds a long persistence length, the NRs can move freely along the stretched polymer chain, and the dispersed conformation of NRs is formed. For the semiflexible polymer chain with a moderate bending energy, the NRs are aggregated in the end-to-end parallel arrangement. Meanwhile, the polymer monomers wrap around those NRs in a well-defined helical

  20. Driven transport on open filaments with interfilament switching processes

    Science.gov (United States)

    Ghosh, Subhadip; Pagonabarraga, Ignacio; Muhuri, Sudipto

    2017-02-01

    We study a two-filament driven lattice gas model with oppositely directed species of particles moving on two parallel filaments with filament-switching processes and particle inflow and outflow at filament ends. The filament-switching process is correlated with the occupation number of the adjacent site such that particles switch filaments with finite probability only when oppositely directed particles meet on the same filament. This model mimics some of the coarse-grained features observed in context of microtubule-(MT) based intracellular transport, wherein cellular cargo loaded and off-loaded at filament ends are transported on multiple parallel MT filaments and can switch between the parallel microtubule filaments. We focus on a regime where the filaments are weakly coupled, such that filament-switching rate of particles scale inversely as the length of the filament. We find that the interplay of (off-) loading processes at the boundaries and the filament-switching process of particles leads to some distinctive features of the system. These features includes occurrence of a variety of phases in the system with inhomogeneous density profiles including localized density shocks, density difference across the filaments, and bidirectional current flows in the system. We analyze the system by developing a mean field (MF) theory and comparing the results obtained from the MF theory with the Monte Carlo (MC) simulations of the dynamics of the system. We find that the steady-state density and current profiles of particles and the phase diagram obtained within the MF picture matches quite well with MC simulation results. These findings maybe useful for studying multifilament intracellular transport.

  1. Filamentous hydrous ferric oxide biosignatures in a pipeline carrying acid mine drainage at Iron Mountain Mine, California

    Science.gov (United States)

    Williams, Amy J.; Alpers, Charles N.; Sumner, Dawn Y.; Campbell, Kate M.

    2017-01-01

    A pipeline carrying acidic mine effluent at Iron Mountain, CA, developed Fe(III)-rich precipitate caused by oxidation of Fe(II)aq. The native microbial community in the pipe included filamentous microbes. The pipe scale consisted of microbial filaments, and schwertmannite (ferric oxyhydroxysulfate, FOHS) mineral spheres and filaments. FOHS filaments contained central lumina with diameters similar to those of microbial filaments. FOHS filament geometry, the geochemical environment, and the presence of filamentous microbes suggest that FOHS filaments are mineralized microbial filaments. This formation of textural biosignatures provides the basis for a conceptual model for the development and preservation of biosignatures in other environments.

  2. Elasticity of cross-linked semiflexible biopolymers under tension

    CERN Document Server

    von der Heydt, Alice; Benetatos, Panayotis; Zippelius, Annette

    2013-01-01

    Aiming at the mechanical properties of cross-linked biopolymers, we set up and analyze a model of two weakly bending wormlike chains subjected to a tensile force, with regularly spaced inter-chain bonds (cross-links) represented by harmonic springs. Within this model, we compute the force-extension curve and the differential stiffness exactly and discuss several limiting cases. Cross-links effectively stiffen the chain pair by reducing thermal fluctuations transverse to the force and alignment direction. The extra alignment due to cross-links increases both with growing number and with growing strength of the cross-links, and is most prominent for small force f. For large f, the additional, cross-link-induced extension is subdominant except for the case of linking the chains rigidly and continuously along their contour. In this combined limit, we recover asymptotically the elasticity of a weakly bending wormlike chain without constraints, stiffened by a factor four. The increase in differential stiffness can ...

  3. Elasticity of cross-linked semiflexible biopolymers under tension.

    Science.gov (United States)

    von der Heydt, Alice; Wilkin, Daniel; Benetatos, Panayotis; Zippelius, Annette

    2013-09-01

    Aiming at the mechanical properties of cross-linked biopolymers, we set up and analyze a model of two weakly bending wormlike chains subjected to a tensile force, with regularly spaced inter-chain bonds (cross-links) represented by harmonic springs. Within this model, we compute the force-extension curve and the differential stiffness exactly and discuss several limiting cases. Cross-links effectively stiffen the chain pair by reducing thermal fluctuations transverse to the force and alignment direction. The extra alignment due to cross-links increases both with growing number and with growing strength of the cross-links, and is most prominent for small force f. For large f, the additional, cross-link-induced extension is subdominant except for the case of linking the chains rigidly and continuously along their contour. In this combined limit, we recover asymptotically the elasticity of a weakly bending wormlike chain without constraints, stiffened by a factor of 4. The increase in differential stiffness can be as large as 100% for small f or large numbers of cross-links.

  4. Significance of settling model structures and parameter subsets in modelling WWTPs under wet-weather flow and filamentous bulking conditions

    DEFF Research Database (Denmark)

    Ramin, Elham; Sin, Gürkan; Mikkelsen, Peter Steen;

    2014-01-01

    Current research focuses on predicting and mitigating the impacts of high hydraulic loadings on centralized wastewater treatment plants (WWTPs) under wet-weather conditions. The maximum permissible inflow to WWTPs depends not only on the settleability of activated sludge in secondary settling tanks...... (SSTs) but also on the hydraulic behaviour of SSTs. The present study investigates the impacts of ideal and non-ideal flow (dry and wet weather) and settling (good settling and bulking) boundary conditions on the sensitivity of WWTP model outputs to uncertainties intrinsic to the one-dimensional (1-D...... of settling parameters to the total variance of the key WWTP process outputs significantly depends on the influent flow and settling conditions. The magnitude of the impact is found to vary, depending on which type of 1-D SST model is used. Therefore, we identify and recommend potential parameter subsets...

  5. Femtosecond Laser Filamentation

    CERN Document Server

    Chin, See Leang

    2010-01-01

    Femtosecond Laser Filamentation gives a comprehensive review of the physics of propagation of intense femtosecond laser pulses in optical media (principally air) and the applications and challenges of this new technique. This book presents the modern understanding of the physics of femtosecond laser pulse propagation, including unusual new effects such as the self-transformation of the pulse into a white light laser pulse, intensity clamping, the physics of multiple filamentation and competition, and how filaments’ ability to melt glass leads to wave guide writing. The potential applications of laser filamentation in atmospheric sensing and the generation of other electromagnetic pulses from the UV to the radio frequency are treated, together with possible future challenges in the excitation of super-excited states of molecules. Exciting new phenomena such as filament induced ultrafast birefringence and the excitation of molecular rotational wave packets and their multiple revivals in air (gases) will also ...

  6. Bacterial intermediate filaments

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Cabeen, M.; Jacobs-Wagner, C.

    2009-01-01

    Crescentin, which is the founding member of a rapidly growing family of bacterial cytoskeletal proteins, was previously proposed to resemble eukaryotic intermediate filament (IF) proteins based on structural prediction and in vitro polymerization properties. Here, we demonstrate that crescentin...

  7. Blistering of viscoelastic filaments

    CERN Document Server

    Sattler, R; Wagner, C

    2007-01-01

    When a dilute polymer solution experiences capillary thinning, it forms an almost uniformly cylindrical thread, which we study experimentally. In the last stages of thinning, when polymers have become fully stretched, the filament becomes prone to instabilities, of which we describe two: A novel "breathing" instability, originating from the edge of the filament, and a sinusoidal instability in the interior, which ultimately gives rise to a "blistering" pattern of beads on the filament. We describe the linear instability with a spatial resolution of 80 nm in the disturbance amplitude. For sufficiently high polymer concentrations, the filament eventually separates out into a "solid" phase of entangled polymers, connected by fluid beads. A solid polymer fiber of about 100 nanometer thickness remains, which is essentially permanent.

  8. Organizing Filament of Small Amplitude Scroll Waves

    Institute of Scientific and Technical Information of China (English)

    ZHOU TianShou; ZHANG SuoChun

    2001-01-01

    We theoretically analyze the organizing filament of small amplitude scroll waves in general excitable media by perturbation method and explicitly give the expressions of coefficients in Keener theory. In particular for the excitable media with equal diffusion, we obtain a close system for the motion of the filament. With an example of the Oregonator model, our results are in good agreement with those simulated by Winfree.``

  9. ExB flow-induced shearing-merging of filaments: a Ginzburg-Landau model of Edge-Localized Mode cycles

    CERN Document Server

    Leconte, M; Jeon, Y M

    2016-01-01

    We derive and study a simple 1D nonlinear model for Edge Localized Mode (ELM) cycles. The nonlinear dynamics of a resistive ballooning mode is modeled via a single nonlinear equation of the Ginzburg-Landau type with a radial frequency gradient due to a prescribed ExB shear layer of finite extent. The nonlinearity is due to the feedback of the mode on the profile. We identify a novel mechanism, whereby the ELM only crosses the linear stability boundary once, and subsequently stays in the nonlinear regime for the full duration of the cycles. This is made possible by the shearing and merging of filaments by the ExB flow, which forces the system to oscillate between a radially-uniform solution and a non-uniform solitary - wave like solution. The model predicts a 'phase-jump' correlated with the ELM bursts.

  10. Picosecond laser filamentation in air

    Science.gov (United States)

    Schmitt-Sody, Andreas; Kurz, Heiko G.; Bergé, Luc; Skupin, Stefan; Polynkin, Pavel

    2016-09-01

    The propagation of intense picosecond laser pulses in air in the presence of strong nonlinear self-action effects and air ionization is investigated experimentally and numerically. The model used for numerical analysis is based on the nonlinear propagator for the optical field coupled to the rate equations for the production of various ionic species and plasma temperature. Our results show that the phenomenon of plasma-driven intensity clamping, which has been paramount in femtosecond laser filamentation, holds for picosecond pulses. Furthermore, the temporal pulse distortions in the picosecond regime are limited and the pulse fluence is also clamped. In focused propagation geometry, a unique feature of picosecond filamentation is the production of a broad, fully ionized air channel, continuous both longitudinally and transversely, which may be instrumental for many applications including laser-guided electrical breakdown of air, channeling microwave beams and air lasing.

  11. Picosecond laser filamentation in air

    CERN Document Server

    Schmitt-Sody, Andreas; Bergé, L; Skupin, S; Polynkin, Pavel

    2016-01-01

    The propagation of intense picosecond laser pulses in air in the presence of strong nonlinear self-action effects and air ionization is investigated experimentally and numerically. The model used for numerical analysis is based on the nonlinear propagator for the optical field coupled with the rate equations for the production of various ionic species and plasma temperature. Our results show that the phenomenon of plasma-driven intensity clamping, which is paramount in femtosecond laser filamentation, holds for picosecond pulses. Furthermore, the temporal pulse distortions are limited and the pulse fluence is also clamped. The resulting unique feature of the picosecond filamentation regime is the production of a broad, fully ionized air channel, continuous both longitudinally and transversely, which may be instrumental for numerous applications.

  12. In situ ellipsometric study of surface immobilization of flagellar filaments

    Energy Technology Data Exchange (ETDEWEB)

    Kurunczi, S., E-mail: kurunczi@mfa.kfki.hu [Department of Photonics, Research Institute for Technical Physics and Materials Science, H-1121, Konkoly Thege Miklos ut 29-33, Budapest (Hungary); Nemeth, A.; Huelber, T. [Department of Photonics, Research Institute for Technical Physics and Materials Science, H-1121, Konkoly Thege Miklos ut 29-33, Budapest (Hungary); Kozma, P. [Department of Photonics, Research Institute for Technical Physics and Materials Science, H-1121, Konkoly Thege Miklos ut 29-33, Budapest (Hungary); Department of Nanotechnology, Research Institute of Chemical and Process Engineering, Faculty of Information Technology, University of Pannonia, Egyetem u. 10, Veszprem, H-8200 (Hungary); Petrik, P. [Department of Photonics, Research Institute for Technical Physics and Materials Science, H-1121, Konkoly Thege Miklos ut 29-33, Budapest (Hungary); Jankovics, H. [Department of Nanotechnology, Research Institute of Chemical and Process Engineering, Faculty of Information Technology, University of Pannonia, Egyetem u. 10, Veszprem, H-8200 (Hungary); Sebestyen, A. [Department of Photonics, Research Institute for Technical Physics and Materials Science, H-1121, Konkoly Thege Miklos ut 29-33, Budapest (Hungary); Department of Nanotechnology, Research Institute of Chemical and Process Engineering, Faculty of Information Technology, University of Pannonia, Egyetem u. 10, Veszprem, H-8200 (Hungary); Vonderviszt, F. [Department of Photonics, Research Institute for Technical Physics and Materials Science, H-1121, Konkoly Thege Miklos ut 29-33, Budapest (Hungary); Department of Nanotechnology, Research Institute of Chemical and Process Engineering, Faculty of Information Technology, University of Pannonia, Egyetem u. 10, Veszprem, H-8200 (Hungary); Institute of Enzymology, Karolina ut 29-33, Budapest, H-1113 (Hungary); and others

    2010-10-15

    Protein filaments composed of thousands of subunits are promising candidates as sensing elements in biosensors. In this work in situ spectroscopic ellipsometry is applied to monitor the surface immobilization of flagellar filaments. This study is the first step towards the development of layers of filamentous receptors for sensor applications. Surface activation is performed using silanization and a subsequent glutaraldehyde crosslinking. Structure of the flagellar filament layers immobilized on activated and non-activated Si wafer substrates is determined using a two-layer effective medium model that accounted for the vertical density distribution of flagellar filaments with lengths of 300-1500 nm bound to the surface. The formation of the first interface layer can be explained by the multipoint covalent attachment of the filaments, while the second layer is mainly composed of tail pinned filaments floating upwards with the free parts. As confirmed by atomic force microscopy, covalent immobilization resulted in an increased surface density compared to absorption.

  13. A multiscale and multiphysics model of strain development in a 1.5 T MRI magnet designed with 36 filament composite MgB2 superconducting wire

    Science.gov (United States)

    Amin, Abdullah Al; Baig, Tanvir; Deissler, Robert J.; Yao, Zhen; Tomsic, Michael; Doll, David; Akkus, Ozan; Martens, Michael

    2016-05-01

    High temperature superconductors such as MgB2 focus on conduction cooling of electromagnets that eliminates the use of liquid helium. With the recent advances in the strain sustainability of MgB2, a full body 1.5 T conduction cooled magnetic resonance imaging (MRI) magnet shows promise. In this article, a 36 filament MgB2 superconducting wire is considered for a 1.5 T full-body MRI system and is analyzed in terms of strain development. In order to facilitate analysis, this composite wire is homogenized and the orthotropic wire material properties are employed to solve for strain development using a 2D-axisymmetric finite element analysis (FEA) model of the entire set of MRI magnet. The entire multiscale multiphysics analysis is considered from the wire to the magnet bundles addressing winding, cooling and electromagnetic excitation. The FEA solution is verified with proven analytical equations and acceptable agreement is reported. The results show a maximum mechanical strain development of 0.06% that is within the failure criteria of -0.6% to 0.4% (-0.3% to 0.2% for design) for the 36 filament MgB2 wire. Therefore, the study indicates the safe operation of the conduction cooled MgB2 based MRI magnet as far as strain development is concerned.

  14. Semiflexible Polymers in Spherical Confinement: Bipolar Orientational Order Versus Tennis Ball States

    Science.gov (United States)

    Nikoubashman, Arash; Vega, Daniel A.; Binder, Kurt; Milchev, Andrey

    2017-05-01

    Densely packed semiflexible polymers with contour length L confined in spheres with radius R of the same order as L cannot exhibit uniform nematic order. Depending on the chain stiffness (which we vary over a wide range), highly distorted structures form with topological defects on the sphere surface. These structures are completely different from previously observed ones of very long chains winding around the inner surface of spheres and from nematic droplets. At high densities, a thin shell of polymers close to the sphere surface exhibits a tennis ball texture due to the confinement-induced gradual bending of polymer bonds. In contrast, when the contour length of the chains is significantly smaller than the radius of the confining sphere, a few bent smectic layers form in the sphere. Molecular dynamics simulations demonstrate these complex structures, and suitable order parameters characterizing them are proposed.

  15. Condensation of semiflexible polyelectrolytes in mixed solutions of mono- and multivalent salts

    Science.gov (United States)

    Plunk, Amelia A.; Luijten, Erik

    2013-03-01

    The salt-dependent condensation of highly charged polyelectrolytes in aqueous solution is a topic of great biological and industrial importance that has been widely studied over the past decades. It is well established that interaction with multivalent counterions leads to the formation of bundle-like aggregates for rigid polyelectrolytes and to collapsed structures or disordered aggregates for flexible polyelectrolytes. Here, we investigate the behavior of semiflexible chain molecules, where the electrostatically induced aggregation is impeded by the intrinsic bending stiffness of the polymer. Moreover, we study the competition between monovalent and multivalent counterions in mixed solutions and establish the threshold salt concentration required for condensation. Our findings are relevant for a range of biomedical problems, including the fabrication of nanoparticles for gene delivery and the packaging of DNA by histones. This work is supported by the National Science Foundation.

  16. Semiflexible Polymers in Spherical Confinement: Bipolar Orientational Order Versus Tennis Ball States.

    Science.gov (United States)

    Nikoubashman, Arash; Vega, Daniel A; Binder, Kurt; Milchev, Andrey

    2017-05-26

    Densely packed semiflexible polymers with contour length L confined in spheres with radius R of the same order as L cannot exhibit uniform nematic order. Depending on the chain stiffness (which we vary over a wide range), highly distorted structures form with topological defects on the sphere surface. These structures are completely different from previously observed ones of very long chains winding around the inner surface of spheres and from nematic droplets. At high densities, a thin shell of polymers close to the sphere surface exhibits a tennis ball texture due to the confinement-induced gradual bending of polymer bonds. In contrast, when the contour length of the chains is significantly smaller than the radius of the confining sphere, a few bent smectic layers form in the sphere. Molecular dynamics simulations demonstrate these complex structures, and suitable order parameters characterizing them are proposed.

  17. Interaction and merging of vortex filaments

    Science.gov (United States)

    Liu, C. H.; Weston, R. P.; Ishii, K.; Ting, L.; Visintainer, J. A.

    1988-01-01

    The asymptotic solutions of Navier-Stokes equations for vortex filaments of finite strength with small effective vortical cores are summarized with special emphasis placed on the physical meaning and the practical limit to the applicability of the asymptotic solution. Finite-difference solutions of Navier-Stokes equations for the marging of the filament(s) are described with a focus on the development of the approximate boundary conditions for the computational domain. An efficiency study employing a model problem is used to assess the advantages of the present approximate boundary condition method over previously used techniques. Applications of the present method are presented for the motion and decay of a 3:1 elliptic vortex ring, and for the merging process of a pair of coaxial vortex rings. A numerical procedure for the problem of local merging of vortex filaments, which requires the asymptotic analysis as well as the numerical Navier-Stokes solver, is also presented.

  18. Nonlinear dynamics of the ion Weibel-filamentation instability: An analytical model for the evolution of the plasma and spectral properties

    Energy Technology Data Exchange (ETDEWEB)

    Ruyer, C., E-mail: charles.ruyer@polytechnique.edu; Gremillet, L., E-mail: laurent.gremillet@cea.fr; Debayle, A. [CEA, DAM, DIF, F-91297 Arpajon (France); Bonnaud, G. [CEA, Saclay, INSTN, F-91191 Gif-sur-Yvette (France)

    2015-03-15

    We present a predictive model of the nonlinear phase of the Weibel instability induced by two symmetric, counter-streaming ion beams in the non-relativistic regime. This self-consistent model combines the quasilinear kinetic theory of Davidson et al. [Phys. Fluids 15, 317 (1972)] with a simple description of current filament coalescence. It allows us to follow the evolution of the ion parameters up to a stage close to complete isotropization, and is thus of prime interest to understand the dynamics of collisionless shock formation. Its predictions are supported by 2-D and 3-D particle-in-cell simulations of the ion Weibel instability. The derived approximate analytical solutions reveal the various dependencies of the ion relaxation to isotropy. In particular, it is found that the influence of the electron screening can affect the results of simulations using an unphysical electron mass.

  19. Nonlinear dynamics of the ion Weibel-filamentation instability: an analytical model for the evolution of the plasma and spectral properties

    CERN Document Server

    Ruyer, C; Debayle, A; Bonnaud, G

    2015-01-01

    We present a predictive model of the nonlinear phase of the Weibel instability induced by two symmetric, counter-streaming ion beams in the non-relativistic regime. This self-consistent model combines the quasilinear kinetic theory of Davidson et al. [Phys. Fluids 15, 317 (1972)] with a simple description of current filament coalescence. It allows us to follow the evolution of the ion parameters up to a stage close to complete isotropization, and is thus of prime interest to understand the dynamics of collisionless shock formation. Its predictions are supported by 2-D and 3-D particle-in-cell simulations of the ion Weibel instability. The derived approximate analytical solutions reveal the various dependencies of the ion relaxation to isotropy. In particular, it is found that the influence of the electron screening can affect the results of simulations using an unphysical electron mass.

  20. Characterization of HI Filaments

    Science.gov (United States)

    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.

  1. Flux Cancellation Leading to CME Filament Eruptions

    Science.gov (United States)

    Popescu, Roxana M.; Panesar, Navdeep K.; Sterling, Alphonse C.; Moore, Ronald L.

    2016-01-01

    Solar filaments are strands of relatively cool, dense plasma magnetically suspended in the lower density hotter solar corona. They trace magnetic polarity inversion lines (PILs) in the photosphere below, and are supported against gravity at heights of up to approx.100 Mm above the chromosphere by the magnetic field in and around them. This field erupts when it is rendered unstable, often by magnetic flux cancellation or emergence at or near the PIL. We have studied the evolution of photospheric magnetic flux leading to ten observed filament eruptions. Specifically, we look for gradual magnetic changes in the neighborhood of the PIL prior to and during eruption. We use Extreme Ultraviolet (EUV) images from the Atmospheric Imaging Assembly (AIA), and magnetograms from the Helioseismic and Magnetic Imager (HMI), both on board the Solar Dynamics Observatory (SDO), to study filament eruptions and their photospheric magnetic fields. We examine whether flux cancellation or/and emergence leads to filament eruptions. We find that continuous flux cancellation was present at the PIL for many hours prior to each eruption. We present two CME-producing eruptions in detail and find the following: (a) the pre-eruption filament-holding core field is highly sheared and appears in the shape of a sigmoid above the PIL; (b) at the start of the eruption the opposite arms of the sigmoid reconnect in the middle above the site of (tether-cutting) flux cancellation at the PIL; (c) the filaments first show a slow-rise, followed by a fast-rise as they erupt. We conclude that these two filament eruptions result from flux cancellation in the middle of the sheared field, and thereafter evolve in agreement with the standard model for a CME/flare filament eruption from a closed bipolar magnetic field [flux cancellation (van Ballegooijen and Martens 1989 and Moore and Roumelrotis 1992) and runaway tether-cutting (Moore et. al 2001)].

  2. Analytical Core Mass Function (CMF) from Filaments: Under Which Circumstances Can Filament Fragmentation Reproduce the CMF?

    Science.gov (United States)

    Lee, Yueh-Ning; Hennebelle, Patrick; Chabrier, Gilles

    2017-10-01

    Observations suggest that star formation in filamentary molecular clouds occurs in a two-step process, with the formation of filaments preceding that of prestellar cores and stars. Here, we apply the gravoturbulent fragmentation theory of Hennebelle & Chabrier to a filamentary environment, taking into account magnetic support. We discuss the induced geometrical effect on the cores, with a transition from 3D geometry at small scales to 1D at large ones. The model predicts the fragmentation behavior of a filament for a given mass per unit length (MpL) and level of magnetization. This core mass function (CMF) for individual filaments is then convolved with the distribution of filaments to obtain the final system CMF. The model yields two major results. (i) The filamentary geometry naturally induces a hierarchical fragmentation process, first into groups of cores, separated by a length equal to a few filament Jeans lengths, i.e., a few times the filament width. These groups then fragment into individual cores. (ii) Non-magnetized filaments with high MpL are found to fragment excessively, at odds with observations. This is resolved by taking into account the magnetic field (treated simply as additional pressure support). The present theory suggests two complementary modes of star formation: although small (spherical or filamentary) structures will collapse directly into prestellar cores, according to the standard Hennebelle–Chabrier theory, the large (filamentary) ones, the dominant population according to observations, will follow the aforedescribed two-step process.

  3. Filaments in Lupus I

    Science.gov (United States)

    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.

  4. Aerogel-supported filament

    Science.gov (United States)

    Wuest, Craig R.; Tillotson, Thomas M.; Johnson, III, Coleman V.

    1995-01-01

    The present invention is a thin filament embedded in a low density aerogel for use in radiation detection instruments and incandescent lamps. The aerogel provides a supportive matrix that is thermally and electrically nonconductive, mechanically strong, highly porous, gas-permeable, and transparent to ionizing radiation over short distances. A low density, open-cell aerogel is cast around a fine filament or wire, which allows the wire to be positioned with little or no tension and keeps the wire in place in the event of breakage. The aerogel support reduces the stresses on the wire caused by vibrational, gravitational, electrical, and mechanical forces.

  5. Heterocyst placement strategies to maximize growth of cyanobacterial filaments

    CERN Document Server

    Brown, Aidan I

    2012-01-01

    Under conditions of limited fixed-nitrogen, some filamentous cyanobacteria develop a regular pattern of heterocyst cells that fix nitrogen for the remaining vegetative cells. We examine three different heterocyst placement strategies by quantitatively modelling filament growth while varying both external fixed-nitrogen and leakage from the filament. We find that there is an optimum heterocyst frequency which maximizes the growth rate of the filament; the optimum frequency decreases as the external fixed-nitrogen concentration increases but increases as the leakage increases. In the presence of leakage, filaments implementing a local heterocyst placement strategy grow significantly faster than filaments implementing random heterocyst placement strategies. With no extracellular fixed-nitrogen, consistent with recent experimental studies of Anabaena sp. PCC 7120, the modelled heterocyst spacing distribution using our local heterocyst placement strategy is qualitatively similar to experimentally observed patterns...

  6. Branching of keratin intermediate filaments.

    Science.gov (United States)

    Nafeey, Soufi; Martin, Ines; Felder, Tatiana; Walther, Paul; Felder, Edward

    2016-06-01

    Keratin intermediate filaments (IFs) are crucial to maintain mechanical stability in epithelial cells. Since little is known about the network architecture that provides this stiffness and especially about branching properties of filaments, we addressed this question with different electron microscopic (EM) methods. Using EM tomography of high pressure frozen keratinocytes, we investigated the course of several filaments in a branching of a filament bundle. Moreover we found several putative bifurcations in individual filaments. To verify our observation we also visualized the keratin network in detergent extracted keratinocytes with scanning EM. Here bifurcations of individual filaments could unambiguously be identified additionally to bundle branchings. Interestingly, identical filament bifurcations were also found in purified keratin 8/18 filaments expressed in Escherichia coli which were reassembled in vitro. This excludes that an accessory protein contributes to the branch formation. Measurements of the filament cross sectional areas showed various ratios between the three bifurcation arms. This demonstrates that intermediate filament furcation is very different from actin furcation where an entire new filament is attached to an existing filament. Instead, the architecture of intermediate filament bifurcations is less predetermined and hence consistent with the general concept of IF formation.

  7. Degradation of thin tungsten filaments at high temperature in HWCVD

    Energy Technology Data Exchange (ETDEWEB)

    Frigeri, P.A., E-mail: pfrigeri@phys.ethz.ch; Nos, O.; Bertomeu, J.

    2015-01-30

    The degradation of the filaments is usually studied by checking the silicidation or carbonization status of the refractory metal used as catalysts, and their effects on the structural stability of the filaments. In this paper, it will be shown that the catalytic stability of a filament heated at high temperature is much shorter than its structural lifetime. The electrical resistance of a thin tungsten filament and the deposition rate of the deposited thin film have been monitored during the filament aging. It has been found that the deposition rate drops drastically once the quantity of dissolved silicon in the tungsten reaches the solubility limit and the silicides start precipitating. This manuscript concludes that the catalytic stability is only guaranteed for a short time and that for sufficiently thick filaments it does not depend on the filament radius. - Highlights: • A model for the electrical resistance of a tungsten filament during aging is presented. • Catalytic activity of the filament drops when W5Si3 precipitation takes place at its surface. • The catalytic stability of the filament does not depend on its radius in most practical situations.

  8. Motion of a Vortex Filament in the Half Space

    CERN Document Server

    Aiki, Masashi

    2010-01-01

    A model equation for the motion of a vortex filament immersed in three dimensional, incompressible and inviscid fluid is investigated as a humble attempt to model the motion of a tornado. We solve an initial-boundary value problem in the half space where we impose a boundary condition in which the vortex filament is allowed to move on the boundary.

  9. Kilometer range filamentation

    OpenAIRE

    Durand, Magali; Houard, Aurélien; Prade, Bernard; Mysyrowicz, André; Durécu, Anne; Moreau, Bernard; Fleury, Didier; Vasseur, Olivier; Borchert, Hartmut; Diener, Karsten; Schmitt, Rudiger; Théberge, Francis; Chateauneuf, Marc; Daigle, Jean-François; Dubois, Jacques

    2013-01-01

    International audience; We demonstrate for the first time the possibility to generate long plasma channels up to a distance of 1 km, using the terawatt femtosecond T&T laser facility. The plasma density was optimized by adjusting the chirp, the focusing and beam diameter. The interaction of filaments with transparent and opaque targets was studied.

  10. The mating-type chromosome in the filamentous ascomycete Neurospora tetrasperma represents a model for early evolution of sex chromosomes.

    Directory of Open Access Journals (Sweden)

    Audrius Menkis

    2008-03-01

    Full Text Available We combined gene divergence data, classical genetics, and phylogenetics to study the evolution of the mating-type chromosome in the filamentous ascomycete Neurospora tetrasperma. In this species, a large non-recombining region of the mating-type chromosome is associated with a unique fungal life cycle where self-fertility is enforced by maintenance of a constant state of heterokaryosis. Sequence divergence between alleles of 35 genes from the two single mating-type component strains (i.e. the homokaryotic mat A or mat a-strains, derived from one N. tetrasperma heterokaryon (mat A+mat a, was analyzed. By this approach we were able to identify the boundaries and size of the non-recombining region, and reveal insight into the history of recombination cessation. The non-recombining region covers almost 7 Mbp, over 75% of the chromosome, and we hypothesize that the evolution of the mating-type chromosome in this lineage involved two successive events. The first event was contemporaneous with the split of N. tetrasperma from a common ancestor with its outcrossing relative N. crassa and suppressed recombination over at least 6.6 Mbp, and the second was confined to a smaller region in which recombination ceased more recently. In spite of the early origin of the first "evolutionary stratum", genealogies of five genes from strains belonging to an additional N. tetrasperma lineage indicate independent initiations of suppressed recombination in different phylogenetic lineages. This study highlights the shared features between the sex chromosomes found in the animal and plant kingdoms and the fungal mating-type chromosome, despite fungi having no separate sexes. As is often found in sex chromosomes of plants and animals, recombination suppression of the mating-type chromosome of N. tetrasperma involved more than one evolutionary event, covers the majority of the mating-type chromosome and is flanked by distal regions with obligate crossovers.

  11. Solar Features - Prominences and Filaments

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Prominences and filaments are two manifestations of the same phenomenon. Both prominences and filaments are features formed above the chromosphere by cool dense...

  12. Positrusion Filament Recycling System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — TUI proposes a novel process to produce 3d printer feedstock filament out of scrap ABS on the ISS. Currently the plastic filament materials that most 3d printers use...

  13. Properties of twisted ferromagnetic filaments

    Energy Technology Data Exchange (ETDEWEB)

    Belovs, Mihails; Cebers, Andrejs [University of Latvia, Zellu 8, LV-1002 (Latvia)], E-mail: aceb@tesla.sal.lv

    2009-02-01

    The full set of equations for twisted ferromagnetic filaments is derived. The linear stability analysis of twisted ferromagnetic filament is carried out. Two different types of the buckling instability are found - monotonous and oscillatory. The first in the limit of large twist leads to the shape of filament reminding pearls on the string, the second to spontaneous rotation of the filament, which may constitute the working of chiral microengine.

  14. Integration of colloids into a semi-flexible network of fibrin.

    Science.gov (United States)

    Bharadwaj, N Ashwin K; Kang, Jin Gu; Hatzell, Marta C; Schweizer, Kenneth S; Braun, Paul V; Ewoldt, Randy H

    2017-02-15

    Typical colloid-polymer composites have particle diameters much larger than the polymer mesh size, but successful integration of smaller colloids into a large-mesh network could allow for the realization of new colloidal states of spatial organization and faster colloid motion which can allow the possibility of switchable re-configuration of colloids or more dramatic stimuli-responsive property changes. Experimental realization of such composites requires solving non-trivial materials selection and fabrication challenges; key questions include composition regime maps of successful composites, the resulting structure and colloidal contact network, and the mechanical properties, in particular the ability to form a network and retain strain stiffening in the presence of colloids. Here, we study these fundamental questions by formulating composites with fluorescent (though not stimuli-responsive) carboxylate modified polystyrene/latex (CML) colloidal particles (diameters 200 nm and 1000 nm) in bovine fibrin networks (a semi-flexible biopolymer network with mesh size 1-5 μm). We describe and characterize two methods of composite preparation: adding colloids before fibrinogen polymerization (Method I), and electrophoretically driving colloids into a network already formed by fibrinogen polymerization (Method II). We directly image the morphology of colloidal and fibrous components with two-color fluorescent confocal microscopy under wet conditions and SEM of fixed dry samples. Mechanical properties are studied with shear and extensional rheology. Both fabrication methods are successful, though with trade-offs. Method I retains the nonlinear strain-stiffening and extensibility of the native fibrin network, but some colloid clustering is observed and fibrin network integrity is lost above a critical colloid concentration that depends on fibrinogen and thrombin concentration. Larger colloids can be included at higher volume fractions before massive aggregation occurs

  15. Formation and evolution of an active region filament

    CERN Document Server

    Kuckein, C; Pillet, V Martínez

    2013-01-01

    Several scenarios explaining how filaments are formed can be found in literature. In this paper, we analyzed the observations of an active region filament and critically evaluated the observed properties in the context of current filament formation models. This study is based on multi-height spectropolarimetric observations. The inferred vector magnetic field has been extrapolated starting either from the photosphere or from the chromosphere. The line-of-sight motions of the filament, which was located near disk center, have been analyzed inferring the Doppler velocities. We conclude that a part of the magnetic structure emerged from below the photosphere.

  16. An explicitly solvated full atomistic model of the cardiac thin filament and application on the calcium binding affinity effects from familial hypertrophic cardiomyopathy linked mutations

    Science.gov (United States)

    Williams, Michael; Schwartz, Steven

    2015-03-01

    The previous version of our cardiac thin filament (CTF) model consisted of the troponin complex (cTn), two coiled-coil dimers of tropomyosin (Tm), and 29 actin units. We now present the newest revision of the model to include explicit solvation. The model was developed to continue our study of genetic mutations in the CTF proteins which are linked to familial hypertrophic cardiomyopathies. Binding of calcium to the cTnC subunit causes subtle conformational changes to propagate through the cTnC to the cTnI subunit which then detaches from actin. Conformational changes propagate through to the cTnT subunit, which allows Tm to move into the open position along actin, leading to muscle contraction. Calcium disassociation allows for the reverse to occur, which results in muscle relaxation. The inclusion of explicit TIP3 water solvation allows for the model to get better individual local solvent to protein interactions; which are important when observing the N-lobe calcium binding pocket of the cTnC. We are able to compare in silica and in vitro experimental results to better understand the physiological effects from mutants, such as the R92L/W and F110V/I of the cTnT, on the calcium binding affinity compared to the wild type.

  17. Filament velocity scaling laws for warm ions

    Energy Technology Data Exchange (ETDEWEB)

    Manz, P. [Physik-Department E28, Technische Universität München, James-Franck-Str. 1, 85748 Garching (Germany); Max-Planck-Institut für Plasmaphysik, EURATOM Assoziation, Boltzmannstr. 2, 85748 Garching (Germany); Carralero, D.; Birkenmeier, G.; Müller, H. W.; Scott, B. D. [Max-Planck-Institut für Plasmaphysik, EURATOM Assoziation, Boltzmannstr. 2, 85748 Garching (Germany); Müller, S. H. [Center for Momentum Transport and Flow Organization, University of California at San Diego, San Diego 92093 (United States); Fuchert, G. [Insitut für Grenzflächenverfahrenstechnik und Plasmatechnologie, Universität Stuttgart, 70569 Stuttgart (Germany); Stroth, U. [Max-Planck-Institut für Plasmaphysik, EURATOM Assoziation, Boltzmannstr. 2, 85748 Garching (Germany); Physik-Department E28, Technische Universität München, James-Franck-Str. 1, 85748 Garching (Germany)

    2013-10-15

    The dynamics of filaments or blobs in the scrape-off layer of magnetic fusion devices are studied by magnitude estimates of a comprehensive drift-interchange-Alfvén fluid model. The standard blob models are reproduced in the cold ion case. Even though usually neglected, in the scrape-off layer, the ion temperature can exceed the electron temperature by an order of magnitude. The ion pressure affects the dynamics of filaments amongst others by adding up to the interchange drive and the polarisation current. It is shown how both effects modify the scaling laws for filament velocity in dependence of its size. Simplifications for experimentally relevant limit regimes are given. These are the sheath dissipation, collisional, and electromagnetic regime.

  18. Filament velocity scaling laws for warm ions

    Science.gov (United States)

    Manz, P.; Carralero, D.; Birkenmeier, G.; Müller, H. W.; Müller, S. H.; Fuchert, G.; Scott, B. D.; Stroth, U.

    2013-10-01

    The dynamics of filaments or blobs in the scrape-off layer of magnetic fusion devices are studied by magnitude estimates of a comprehensive drift-interchange-Alfvén fluid model. The standard blob models are reproduced in the cold ion case. Even though usually neglected, in the scrape-off layer, the ion temperature can exceed the electron temperature by an order of magnitude. The ion pressure affects the dynamics of filaments amongst others by adding up to the interchange drive and the polarisation current. It is shown how both effects modify the scaling laws for filament velocity in dependence of its size. Simplifications for experimentally relevant limit regimes are given. These are the sheath dissipation, collisional, and electromagnetic regime.

  19. Effect of low shear modeled microgravity on phenotypic and central chitin metabolism in the filamentous fungi Aspergillus niger and Penicillium chrysogenum.

    Science.gov (United States)

    Sathishkumar, Yesupatham; Velmurugan, Natarajan; Lee, Hyun Mi; Rajagopal, Kalyanaraman; Im, Chan Ki; Lee, Yang Soo

    2014-08-01

    Phenotypic and genotypic changes in Aspergillus niger and Penicillium chrysogenum, spore forming filamentous fungi, with respect to central chitin metabolism were studied under low shear modeled microgravity, normal gravity and static conditions. Low shear modeled microgravity (LSMMG) response showed a similar spore germination rate with normal gravity and static conditions. Interestingly, high ratio of multiple germ tube formation of A. niger in LSMMG condition was observed. Confocal laser scanning microscopy images of calcofluor flurophore stained A. niger and P. chrysogenum showed no significant variations between different conditions tested. Transmission electron microscopy images revealed number of mitochondria increased in P. chrysogenum in low shear modeled microgravity condition but no stress related-woronin bodies in fungal hyphae were observed. To gain additional insight into the cell wall integrity under different conditions, transcription level of a key gene involved in cell wall integrity gfaA, encoding the glutamine: fructose-6-phosphate amidotransferase enzyme, was evaluated using qRT-PCR. The transcription level showed no variation among different conditions. Overall, the results collectively indicate that the LSMMG has shown no significant stress on spore germination, mycelial growth, cell wall integrity of potentially pathogenic fungi, A. niger and P. chrysogenum.

  20. Filamentous Fungi Fermentation

    DEFF Research Database (Denmark)

    Nørregaard, Anders; Stocks, Stuart; Woodley, John

    2014-01-01

    Filamentous fungi (including microorganisms such as Aspergillus niger and Rhizopus oryzae) represent an enormously important platform for industrial fermentation. Two particularly valuable features are the high yield coefficients and the ability to secrete products. However, the filamentous...... morphology, together with non-Newtonian rheological properties (shear thinning), result in poor oxygen transfer unless sufficient energy is provided to the fermentation. While genomic research may improve the organisms, there is no doubt that to enable further application in future it will be necessary...... to match such research with studies of oxygen transfer and energy supply to high viscosity fluids. Hence, the implementation of innovative solutions (some of which in principle are already possible) will be essential to ensure the further development of such fermentations....

  1. Solid friction between soft filaments

    CERN Document Server

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

    2015-01-01

    Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent 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' 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 prop...

  2. The Semiflexible Polymer Translocation into Laterally Unbounded Region between Two Parallel Flat Membranes

    Directory of Open Access Journals (Sweden)

    Zhi-Yong Yang

    2016-09-01

    Full Text Available Using the dynamic Monte Carlo method, we investigate dynamics of semiflexible polymer translocation through a nanopore into laterally unbounded region between two parallel flat membranes with separation R in presence of an electric field inside the pore. The average translocation time τ initially decreases rapidly with increase of R in the range of R < 10 and then almost keeps constant for R ≥ 10, and the decline range increases with increase of dimensionless bending stiffness κ. We mainly study the effect of chain length N, κ and electric field strength E on the translocation process for R = 5. The translocation dynamics is significantly altered in comparison to an unconfined environment. We find τ ~ Nα, where the exponent α increases with increase of E for small κ. α initially increases slowly with increase of E and then keeps constant for moderate κ. α decreases with increase of E for large κ. However, α decreases with increase of κ under various E. In addition, we find τ ~ κβ. β decreases with increase of N under various E. These behaviors are interpreted in terms of the probability distribution of translocation time and the waiting time of an individual monomer segment passing through the pore during translocation.

  3. SANS measurements of semiflexible xyloglucan polysaccharide chains in water reveal their self-avoiding statistics.

    Science.gov (United States)

    Muller, François; Manet, Sabine; Jean, Bruno; Chambat, Gérard; Boué, François; Heux, Laurent; Cousin, Fabrice

    2011-09-12

    We explored the behavior and the characteristics of xyloglucan polysaccharide chains extracted from tamarind seeds in aqueous media. The initial solubilization is achieved by using a 0.01 M NaOH solution. The absence of compact aggregates in the solution and the average molecular mass of the individual chains were unambiguously demonstrated by size exclusion chromatography with multi-angle light scattering detection. The composition and the stability of the solution were quantitatively checked over weeks by using liquid state nuclear magnetic resonance with DMSO as internal standard. The conformational characteristics of the chains were measured using nondestructive small-angle neutron scattering (SANS). The unambiguous determination of the Flory exponent (ν = 0.588) by SANS enabled us to directly prove that xyloglucan chains in water behave like semiflexible worm-like chains with excluded volume statistics (good solvent), contrary to most of the neutral water-soluble polymer chains that rather exhibit Gaussian statistics (θ-solvent). In addition to the Flory exponent, the persistence length l(p) and the cross section of the chains were also determined by SANS with utmost precision, with values of 80 and of 7 Å, respectively, which provides a complete description of the conformational characteristics of XG chains at all relevant length scales.

  4. Fundamentals of Filament Interaction

    Science.gov (United States)

    2017-05-19

    provide a 1:1 image of the filament profile onto a CCD camera (The Imaging Source DMK72BUC02). Neutral density filters were used to prevent the...thermal velocity, until their momentum was arrested by collisions with neutral air molecules. This results in a short distance, transient current which...Martin Richardson, 3rd ELI-ALPS User Workshop, Szeged, Hungary November 2015 126 “Photonics and the Changing Energy Scene ”, Martin Richardson

  5. Drops moving along and across a filament

    Science.gov (United States)

    Sahu, Rakesh P.; Sinha-Ray, Suman; Yarin, Alexander; Pourdeyhimi, Behnam

    2013-11-01

    The present work is devoted to the experimental study of oil drop motion both along and across a filament due to the air jet blowing. In case of drop moving along the filament, phenomena such as drop stick-slip motion, shape oscillations, shedding of a tail along the filament, the tail capillary instability and drop recoil motion were observed which were rationalized in the framework of simplified models. Experiments with cross-flow of the surrounding gas relative to the filament with an oil drop on it were conducted, with air velocity in the range of 7.23 to 22.7 m s-1. The Weber number varied from 2 to 40 and the Ohnesorge number varied from 0.07 to 0.8. The lower and upper critical Weber numbers were introduced to distinguish between the beginning of the drop blowing off the filament and the onset of the bag-stamen breakup. The range of the Weber number between these two critical values is filled with three types of vibrational breakup: V1 (a balloon-like drop being blown off), V2 (a drop on a single stamen being blown off), and V3 (a drop on a double stamen being blown off). The Weber number/Ohnesorge number plane was delineated into domains of different breakup regimes. The work is supported by the Nonwovens Cooperative Research Center (NCRC).

  6. The hydrodynamic stability of gaseous cosmic filaments

    CERN Document Server

    Birnboim, Yuval; Zinger, Elad

    2016-01-01

    Virial shocks at edges of cosmic-web structures are a clear prediction of standard structure formation theories. We derive a criterion for the stability of the post-shock gas and of the virial shock itself in spherical, filamentary and planar infall geometries. When gas cooling is important, we find that shocks become unstable, and gas flows uninterrupted towards the center of the respective halo, filament or sheet. For filaments, we impose this criterion on self-similar infall solutions. We find that instability is expected for filament masses between $10^{11}-10^{13}M_\\odot Mpc^{-1}.$ Using a simplified toy model, we then show that these filaments will likely feed halos with $10^{10}M_{\\odot}\\lesssim M_{halo}\\lesssim 10^{13}M_{\\odot}$ at redshift $z=3$, as well as $10^{12}M_{\\odot}\\lesssim M_{halo}\\lesssim 10^{15}M_{\\odot}$ at $z=0$. The instability will affect the survivability of the filaments as they penetrate gaseous halos in a non-trivial way. Additionally, smaller halos accreting onto non-stable filam...

  7. Using Drosophila for Studies of Intermediate Filaments.

    Science.gov (United States)

    Bohnekamp, Jens; Cryderman, Diane E; Thiemann, Dylan A; Magin, Thomas M; Wallrath, Lori L

    2016-01-01

    Drosophila melanogaster is a useful organism for determining protein function and modeling human disease. Drosophila offers a rapid generation time and an abundance of genomic resources and genetic tools. Conservation in protein structure, signaling pathways, and developmental processes make studies performed in Drosophila relevant to other species, including humans. Drosophila models have been generated for neurodegenerative diseases, muscular dystrophy, cancer, and many other disorders. Recently, intermediate filament protein diseases have been modeled in Drosophila. These models have revealed novel mechanisms of pathology, illuminated potential new routes of therapy, and make whole organism compound screens feasible. The goal of this chapter is to outline steps to study intermediate filament function and model intermediate filament-associated diseases in Drosophila. The steps are general and can be applied to study the function of almost any protein. The protocols outlined here are for both the novice and experienced Drosophila researcher, allowing the rich developmental and cell biology that Drosophila offers to be applied to studies of intermediate filaments.

  8. Flexible magnetic filaments in a shear flow

    Energy Technology Data Exchange (ETDEWEB)

    Cebers, Andrejs [Institute of Physics, University of Latvia, Salaspils-1 LV-2169 (Latvia)]. E-mail: aceb@tesla.sal.lv

    2006-05-15

    By flexible magnetic filament model its behavior under the simultaneous action of the shear flow and the magnetic field is investigated. It is found that for magnetoelastic numbers larger as the critical value, which depends on the shear rate, the periodic regime is established. For the values of the magnetoelastic number close to the critical the periodical regime is characterized by a rather slow development of the buckling instability due to the action of magnetic torques with the subsequent stage of the fast straightening of the filament. For the magnetoelastic numbers below the critical slightly bent shape of the filament orientated along the flow is established. The application of the results for the description of the viscoelasticity of the magnetorheological suspensions is discussed.

  9. Generation of stable overlaps between antiparallel filaments

    CERN Document Server

    Johann, D; Kruse, K

    2015-01-01

    During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. Establishing a stable overlap region is essential for maintenance of bipolarity, but the underlying mechanisms are poorly understood. Using a particle-based stochastic model, we find that the interplay of motors and passive cross linkers can robustly generate partial overlaps between antiparallel filaments. Our analysis shows that motors reduce the overlap in a length-dependent manner, whereas passive cross linkers increase it independently of the length. In addition to maintaining structural integrity, passive cross linkers can thus also have a dynamic role for size regulation.

  10. Nuclear flow in a filamentous fungus

    CERN Document Server

    Hickey, Patrick C; Read, Nick; Glass, N Louise; Roper, Marcus

    2012-01-01

    The syncytial cells of a filamentous fungus consist of a mass of growing, tube-like hyphae. Each extending tip is fed by a continuous flow of nuclei from the colony interior, pushed by a gradient in turgor pressure. The myco-fluidic flows of nuclei are complex and multidirectional, like traffic in a city. We map out the flows in a strain of the model filamentous fungus {\\it N. crassa} that has been transformed so that nuclei express either hH1-dsRed (a red fluorescent nuclear protein) or hH1-GFP (a green-fluorescent protein) and report our results in a fluid dynamics video.

  11. Patient specific quality assurance of RapidArc pre treatment plans using semiflex 0.125 cc ionization chamber

    Science.gov (United States)

    Kumar, S. A. Syam; Vivekanandan, Nagarajan

    2017-01-01

    Patient specific pre-treatment quality assurance for RapidArc plans were analyzed for hundred patients for different sites. Verification plan was created for each treatment plan in Eclipse 8.6 treatment planning system with the semiflex ionization chamber and the octavius phantom. Absolute point dose were measured for head and neck, thorax and abdomen cases using semiflex (0.125 cc) ionization chamber. Positive absolute mean dose variation of 0.56% was observed with thorax cases with a standard deviation (SD) of ±1.13 between the plans with a range of -1.78% to 2.70%. Negative percentage dose errors were found with head and neck and abdomen cases, with a mean variation of -0.43% (SD±1.50), (range -3.25% to 2.85%) and -0.35% (SD±1.48), (range -3.10% to 2.65%) for head and neck and abdomen cases respectively. Evaluation has been done using PTW verisoft software by keeping the passing criteria as 3 mm DTA, 3% DD, for 95% of the evaluated dose points. The maximum percentage value failed in gamma analysis was found to be 4.95, 4.75, and 4.88 for head and neck, thorax, and abdomen cases respectively. In all the cases analyzed the percentage dose points failed the gamma criteria is less than 5%. On the basis of the studies performed it can be concluded that the semiflex ionization chamber having a volume of 0.125 cc can be used efficiently for measuring the pre-treatment quality assurance of RapidArc plans for all the sites.

  12. Filament Identification through Mathematical Morphology

    CERN Document Server

    Koch, Eric W

    2015-01-01

    We present a new algorithm for detecting filamentary structure FilFinder. The algorithm uses the techniques of mathematical morphology for filament identification, presenting a complementary approach to current algorithms which use matched filtering or critical manifolds. Unlike other methods, FilFinder identifies filaments over a wide dynamic range in brightness. We apply the new algorithm to far infrared imaging data of dust emission released by the Herschel Gould Belt Survey team. Our preliminary analysis characterizes both filaments and fainter striations. We find a typical filament width of 0.09 pc across the sample, but the brightness varies from cloud to cloud. Several regions show a bimodal filament brightness distribution, with the bright mode (filaments) being an order of magnitude brighter than the faint mode (striations). Using the Rolling Hough Transform, we characterize the orientations of the striations in the data, finding preferred directions that agree with magnetic field direction where dat...

  13. Conformational phases of membrane bound cytoskeletal filaments

    Science.gov (United States)

    Quint, David A.; Grason, Gregory; Gopinathan, Ajay

    2013-03-01

    Membrane bound cytoskeletal filaments found in living cells are employed to carry out many types of activities including cellular division, rigidity and transport. When these biopolymers are bound to a membrane surface they may take on highly non-trivial conformations as compared to when they are not bound. This leads to the natural question; What are the important interactions which drive these polymers to particular conformations when they are bound to a surface? Assuming that there are binding domains along the polymer which follow a periodic helical structure set by the natural monomeric handedness, these bound conformations must arise from the interplay of the intrinsic monomeric helicity and membrane binding. To probe this question, we study a continuous model of an elastic filament with intrinsic helicity and map out the conformational phases of this filament for various mechanical and structural parameters in our model, such as elastic stiffness and intrinsic twist of the filament. Our model allows us to gain insight into the possible mechanisms which drive real biopolymers such as actin and tubulin in eukaryotes and their prokaryotic cousins MreB and FtsZ to take on their functional conformations within living cells.

  14. Heterologous gene expression in filamentous fungi.

    Science.gov (United States)

    Su, Xiaoyun; Schmitz, George; Zhang, Meiling; Mackie, Roderick I; Cann, Isaac K O

    2012-01-01

    Filamentous fungi are critical to production of many commercial enzymes and organic compounds. Fungal-based systems have several advantages over bacterial-based systems for protein production because high-level secretion of enzymes is a common trait of their decomposer lifestyle. Furthermore, in the large-scale production of recombinant proteins of eukaryotic origin, the filamentous fungi become the vehicle of choice due to critical processes shared in gene expression with other eukaryotic organisms. The complexity and relative dearth of understanding of the physiology of filamentous fungi, compared to bacteria, have hindered rapid development of these organisms as highly efficient factories for the production of heterologous proteins. In this review, we highlight several of the known benefits and challenges in using filamentous fungi (particularly Aspergillus spp., Trichoderma reesei, and Neurospora crassa) for the production of proteins, especially heterologous, nonfungal enzymes. We review various techniques commonly employed in recombinant protein production in the filamentous fungi, including transformation methods, selection of gene regulatory elements such as promoters, protein secretion factors such as the signal peptide, and optimization of coding sequence. We provide insights into current models of host genomic defenses such as repeat-induced point mutation and quelling. Furthermore, we examine the regulatory effects of transcript sequences, including introns and untranslated regions, pre-mRNA (messenger RNA) processing, transcript transport, and mRNA stability. We anticipate that this review will become a resource for researchers who aim at advancing the use of these fascinating organisms as protein production factories, for both academic and industrial purposes, and also for scientists with general interest in the biology of the filamentous fungi. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. Size, flexibility, and scattering functions of semiflexible polyelectrolytes with excluded volume effects: Monte Carlo simulations and neutron scattering experiments

    DEFF Research Database (Denmark)

    Cannavacciuolo, L.; Sommer, C.; Pedersen, J.S.;

    2000-01-01

    We present a systematic Monte Carlo study of the scattering function S(q) of semiflexible polyelectrolytes at infinite dilution, in solutions with different concentrations of added salt. In the spirit of a theoretical description of polyelectrolytes in terms of the equivalent parameters, namely...... outlined in the Odijk-Skolnick-Fixman theory, in which the behavior of charged polymers is described only in terms of increasing local rigidity and excluded volume effects. Moreover, the Monte Carlo data are found to be in very good agreement with experimental scattering measurements with equilibrium...

  16. Multi-dimensional Vlasov simulations and modeling of trapped-electron-driven filamentation of electron plasma waves

    Energy Technology Data Exchange (ETDEWEB)

    Berger, R. L., E-mail: berger5@llnl.gov; Cohen, B. I. [Lawrence Livermore National Laboratory, University of California, P.O. Box 808, Livermore, California 94551 (United States); Brunner, S., E-mail: stephan.brunner@epfl.ch [Centre de Recherches en Physique des Plasmas, Association Euratom-Confédération Suisse, Ecole Polytechnique Fédérale de Lausanne, CRPP-PPB, CH-1015 Lausanne (Switzerland); Banks, J. W. [Department of Mathematical Sciences, Rensselaer Polytechnic Institute, AE 301, 110 8th Street, Troy, New York 12180 (United States); Winjum, B. J. [Department of Electrical Engineering, University of California, Los Angeles, California 90095 (United States)

    2015-05-15

    Kinetic simulations of two-dimensional finite-amplitude electron plasma waves are performed in a one-wavelength long system. A systematic study of the most unstable linear sideband mode, in particular its growth rate γ and wavenumber k{sub y}, is carried out by scanning the amplitude and wavenumber of the initial wave. Simulation results are compared with numerical and analytical solutions to a two-dimensional nonlinear Schrödinger model [H. A. Rose and L. Yin, Phys. Plasmas 15, 042311 (2008)] and to the reduced model by Kruer et al. [Phys. Rev. Lett. 23, 838 (1969)] generalized to two dimensions.

  17. Chaperonin filaments: The archael cytoskeleton

    Energy Technology Data Exchange (ETDEWEB)

    Trent, J.D.; Kagawa, H.K.; Yaoi, Takuro; Olle, E.; Zaluzec, N.J.

    1997-08-01

    Chaperonins are multi-subunit double-ring complexed composed of 60-kDa proteins that are believed to mediate protein folding in vivo. The chaperonins in the hyperthermophilic archaeon Sulfolobus shibatae are composed of the organism`s two most abundant proteins, which represent 4% of its total protein and have an intracellular concentration of {ge} 3.0 mg/ml. At concentrations of 1.0 mg/ml, purified chaperonin proteins aggregate to form ordered filaments. Filament formation, which requires Mg{sup ++} and nucleotide binding (not hydrolysis), occurs at physiological temperatures under conditions suggesting filaments may exist in vivo. If the estimated 4,600 chaperonins per cell, formed filaments in vivo, they could create a matrix of filaments that would span the diameter of an average S. shibatae cell 100 times. Direct observations of unfixed, minimally treated cells by intermediate voltage electron microscopy (300 kV) revealed an intracellular network of filaments that resembles chaperonin filaments produced in vitro. The hypothesis that the intracellular network contains chaperonins is supported by immunogold analyses. The authors propose that chaperonin activity may be regulated in vivo by filament formation and that chaperonin filaments may serve a cytoskeleton-like function in archaea and perhaps in other prokaryotes.

  18. Filamentation of arbitrary polarized femtosecond laser pulses in case of high-order Kerr effect.

    Science.gov (United States)

    Panov, Nikolay A; Makarov, Vladimir A; Fedorov, Vladimir Y; Kosareva, Olga G

    2013-02-15

    We developed a model of femtosecond filamentation which includes high-order Kerr effect and an arbitrary polarization of a laser pulse. We show that a circularly polarized pulse has maximum filament intensity. Also, we show that, independently of the initial pulse polarization, the value of a maximum filament intensity tends to the maximum intensity of either linearly or circularly polarized pulse.

  19. Biophysics of filament length regulation by molecular motors

    CERN Document Server

    Kuan, Hui-Shun

    2013-01-01

    Regulating physical size is an essential problem that biological organisms must solve from the subcellular to the organismal scales, but it is not well understood what physical principles and mechanisms organisms use to sense and regulate their size. Any biophysical size-regulation scheme operates in a noisy environment and must be robust to other cellular dynamics and fluctuations. This work develops theory of filament length regulation inspired by recent experiments on kinesin-8 motor proteins, which move with directional bias on microtubule filaments and alter microtubule dynamics. Purified kinesin-8 motors can depolymerize chemically-stabilized microtubules. In the length-dependent depolymerization model, the rate of depolymerization tends to increase with filament length, because long filaments accumulate more motors at their tips and therefore shorten more quickly. When balanced with a constant filament growth rate, this mechanism can lead to a fixed polymer length. However, the mechanism by which kines...

  20. Particles trajectories in magnetic filaments

    CERN Document Server

    Bret, Antoine

    2015-01-01

    The motion of a particle in a spatially harmonic magnetic field is a basic problem involved, for example, in the mechanism of formation of a collisionless shock. In such settings, it is generally reasoned that particles entering a Weibel generated turbulence are trapped inside it, provided their Larmor radius in the peak field is smaller than the field coherence length. The goal of this work is to put this heuristic conclusion on firm ground by studying, both analytically and numerically, such motion. A toy model is analyzed, consisting of a relativistic particle entering a region of space occupied by a spatially harmonic field. The particle penetrates the magnetic structure in a direction aligned with the magnetic filaments. Although the conclusions are not trivial, the main result is confirmed.

  1. Filamentous Growth in Eremothecium Fungi

    DEFF Research Database (Denmark)

    Oskarsson, Therese

    , this thesis deals with some of the aspects of hyphal growth, which is an important virulence factor for pathogenic fungi infecting both humans and plants. Hyphal establishment through continuous polar growth is a complex process, requiring the careful coordination of a large subset of proteins involved......-regulatory activity of AgGts1, the protein could have additional actin organizing properties. In the second and third part, this thesis addresses the use of A. gossypii and its relative E. cymbalariae as model organisms for filamentous growth. A series of assays analyzed the capability of Eremothecium genus fungi...... of molecular tools for E. cymbalariae to enable a faster and more efficient approach for genetic comparisons between Eremothecium genus fungi....

  2. Filamentous Growth in Eremothecium Fungi

    DEFF Research Database (Denmark)

    Oskarsson, Therese

    , this thesis deals with some of the aspects of hyphal growth, which is an important virulence factor for pathogenic fungi infecting both humans and plants. Hyphal establishment through continuous polar growth is a complex process, requiring the careful coordination of a large subset of proteins involved......-regulatory activity of AgGts1, the protein could have additional actin organizing properties. In the second and third part, this thesis addresses the use of A. gossypii and its relative E. cymbalariae as model organisms for filamentous growth. A series of assays analyzed the capability of Eremothecium genus fungi...... of molecular tools for E. cymbalariae to enable a faster and more efficient approach for genetic comparisons between Eremothecium genus fungi....

  3. Particles trajectories in magnetic filaments

    Energy Technology Data Exchange (ETDEWEB)

    Bret, A. [ETSI Industriales, Universidad de Castilla-La Mancha, 13071 Ciudad Real (Spain); Instituto de Investigaciones Energéticas y Aplicaciones Industriales, Campus Universitario de Ciudad Real, 13071 Ciudad Real (Spain)

    2015-07-15

    The motion of a particle in a spatially harmonic magnetic field is a basic problem involved, for example, in the mechanism of formation of a collisionless shock. In such settings, it is generally reasoned that particles entering a Weibel generated turbulence are trapped inside it, provided their Larmor radius in the peak field is smaller than the field coherence length. The goal of this work is to put this heuristic conclusion on firm ground by studying, both analytically and numerically, such motion. A toy model is analyzed, consisting of a relativistic particle entering a region of space occupied by a spatially harmonic field. The particle penetrates the magnetic structure in a direction aligned with the magnetic filaments. Although the conclusions are not trivial, the main result is confirmed.

  4. Physical principles of filamentous protein self-assembly kinetics

    Science.gov (United States)

    Michaels, Thomas C. T.; Liu, Lucie X.; Meisl, Georg; Knowles, Tuomas P. J.

    2017-04-01

    The polymerization of proteins and peptides into filamentous supramolecular structures is an elementary form of self-organization of key importance to the functioning biological systems, as in the case of actin biofilaments that compose the cellular cytoskeleton. Aberrant filamentous protein self-assembly, however, is associated with undesired effects and severe clinical disorders, such as Alzheimer’s and Parkinson’s diseases, which, at the molecular level, are associated with the formation of certain forms of filamentous protein aggregates known as amyloids. Moreover, due to their unique physicochemical properties, protein filaments are finding extensive applications as biomaterials for nanotechnology. With all these different factors at play, the field of filamentous protein self-assembly has experienced tremendous activity in recent years. A key question in this area has been to elucidate the microscopic mechanisms through which filamentous aggregates emerge from dispersed proteins with the goal of uncovering the underlying physical principles. With the latest developments in the mathematical modeling of protein aggregation kinetics as well as the improvement of the available experimental techniques it is now possible to tackle many of these complex systems and carry out detailed analyses of the underlying microscopic steps involved in protein filament formation. In this paper, we review some classical and modern kinetic theories of protein filament formation, highlighting their use as a general strategy for quantifying the molecular-level mechanisms and transition states involved in these processes.

  5. Filament Shape Versus Coronal Potential Magnetic Field Structure

    CERN Document Server

    Filippov, Boris

    2015-01-01

    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 H$\\alpha$ chromospheric images. We found that the most of the filament material is enclosed between two polarity inversion lines (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 {\\it STEREO} 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-disk observations. Filament barbs are housed within protruding sections of the low-level PIL. On the base of simple model, we show that th...

  6. Metabolomics protocols for filamentous fungi.

    Science.gov (United States)

    Gummer, Joel P A; Krill, Christian; Du Fall, Lauren; Waters, Ormonde D C; Trengove, Robert D; Oliver, Richard P; Solomon, Peter S

    2012-01-01

    Proteomics and transcriptomics are established functional genomics tools commonly used to study filamentous fungi. Metabolomics has recently emerged as another option to complement existing techniques and provide detailed information on metabolic regulation and secondary metabolism. Here, we describe broad generic protocols that can be used to undertake metabolomics studies in filamentous fungi.

  7. Filaments in the Galactic Center -- with special reference to the Snake

    CERN Document Server

    Bicknell, G V

    2001-01-01

    The nonthermal filaments in the Galactic Center constitute one of the great mysteries of this region of the Galaxy. We summarise the observational data on these filaments and critically review the various theories which currently outnumber the observed filaments. We summarise out theory for the longest of these filaments, the Snake, and discuss the relevance of this model for the other filaments in the Galactic Center region. The physics involved in our model for the Snake involves much of the physics that has dominated the career of Professor Don Melrose. In particular, the diffusion of relativistic electrons in the Snake is determined from the theory of resonant scattering by Alfv\\'en waves.

  8. Morphology and rheology in filamentous cultivations.

    Science.gov (United States)

    Wucherpfennig, T; Kiep, K A; Driouch, H; Wittmann, C; Krull, R

    2010-01-01

    Because of their metabolic diversity, high production capacity, secretion efficiency, and capability of carrying out posttranslational modifications, filamentous fungi are widely exploited as efficient cell factories in the production of metabolites, bioactive substances, and native or heterologous proteins, respectively. There is, however, a complex relationship between the morphology of these microorganisms, transport phenomena, the viscosity of the cultivation broth, and related productivity. The morphological characteristics vary between freely dispersed mycelia and distinct pellets of aggregated biomass, every growth form having a distinct influence on broth rheology. Hence, the advantages and disadvantages for mycelial or pellet cultivation have to be balanced out carefully. Because of the still inadequate understanding of the morphogenesis of filamentous microorganisms, fungal morphology is often a bottleneck of productivity in industrial production. To obtain an optimized production process, it is of great importance to gain a better understanding of the molecular and cell biology of these microorganisms as well as the relevant approaches in biochemical engineering. In this chapter, morphology and growth of filamentous fungi are described, with special attention given to specific problems as they arise from fungal growth forms; growth and mass transfer in fungal biopellets are discussed as an example. To emphasize the importance of the flow behavior of filamentous cultivation broths, an introduction to rheology is also given, reviewing important rheological models and recent studies concerning rheological parameters. Furthermore, current knowledge on morphology and productivity in relation to the environom is outlined in the last section of this review. Copyright 2010 Elsevier Inc. All rights reserved.

  9. Self-assembly of Artificial Actin Filaments

    Science.gov (United States)

    Grosenick, Christopher; Cheng, Shengfeng

    Actin Filaments are long, double-helical biopolymers that make up the cytoskeleton along with microtubules and intermediate filaments. In order to further understand the self-assembly process of these biopolymers, a model to recreate actin filament geometry was developed. A monomer in the shape of a bent rod with vertical and lateral binding sites was designed to assemble into single or double helices. With Molecular Dynamics simulations, a variety of phases were observed to form by varying the strength of the binding sites. Ignoring lateral binding sites, we have found a narrow range of binding strengths that lead to long single helices via various growth pathways. When lateral binding strength is introduced, double helices begin to form. These double helices self-assemble into substantially more stable structures than their single helix counterparts. We have found double helices to form long filaments at about half the vertical binding strength of single helices. Surprisingly, we have found that triple helices occasionally form, indicating the importance of structural regulation in the self-assembly of biopolymers.

  10. Filament Channel Formation, Eruption, and Jet Generation

    Science.gov (United States)

    DeVore, C. Richard; Antiochos, Spiro K.; Karpen, Judith T.

    2017-08-01

    The mechanism behind filament-channel formation is a longstanding mystery, while that underlying the initiation of coronal mass ejections and jets has been studied intensively but is not yet firmly established. In previous work, we and collaborators have investigated separately the consequences of magnetic-helicity condensation (Antiochos 2013) for forming filament channels (Zhao et al. 2015; Knizhnik et al. 2015, 2017a,b) and of the embedded-bipole model (Antiochos 1996) for generating reconnection-driven jets (Pariat et al. 2009, 2010, 2015, 2016; Wyper et al. 2016, 2017). Now we have taken a first step toward synthesizing these two lines of investigation. Our recent study (Karpen et al. 2017) of coronal-hole jets with gravity and wind employed an ad hoc, large-scale shear flow at the surface to introduce magnetic free energy and form the filament channel. In this effort, we replace the shear flow with an ensemble of local rotation cells, to emulate the Sun’s ever-changing granules and supergranules. As in our previous studies, we find that reconnection between twisted flux tubes within the closed-field region concentrates magnetic shear and free energy near the polarity inversion line, forming the filament channel. Onset of reconnection between this field and the external, unsheared, open field releases stored energy to drive the impulsive jet. We discuss the results of our new simulations with implications for understanding solar activity and space weather.

  11. Perturbation growth in accreting filaments

    CERN Document Server

    Clarke, Seamus D; Hubber, David A

    2016-01-01

    We use smoothed particle hydrodynamic simulations to investigate the growth of perturbations in infinitely long, initially sub-critical but accreting filaments. The growth of these perturbations leads to filament fragmentation and the formation of cores. Most previous work on this subject has been confined to the growth and fragmentation of equilibrium filaments and has found that there exists a preferential fragmentation length scale which is roughly 4 times the filament's diameter. Our results show a more complicated dispersion relation with a series of peaks linking perturbation wavelength and growth rate. These are due to gravo-acoustic oscillations along the longitudinal axis during the sub-critical phase of growth. The positions of the peaks in growth rate have a strong dependence on both the mass accretion rate onto the filament and the temperature of the gas. When seeded with a multi-wavelength density power spectrum there exists a clear preferred core separation equal to the largest peak in the dispe...

  12. Resonantly enhanced filamentation in gases

    CERN Document Server

    Doussot, J; Billard, F; Béjot, P; Faucher, O

    2016-01-01

    In this Letter, a low-loss Kerr-driven optical filament in Krypton gas is experimentally reported in the ultraviolet. The experimental findings are supported by ab initio quantum calculations describing the atomic optical response. Higher-order Kerr effect induced by three-photon resonant transitions is identified as the underlying physical mechanism responsible for the intensity stabilization during the filamentation process, while ionization plays only a minor role. This result goes beyond the commonly-admitted paradigm of filamentation, in which ionization is a necessary condition of the filament intensity clamping. At resonance, it is also experimentally demonstrated that the filament length is greatly extended because of a strong decrease of the optical losses.

  13. Motility patterns of filamentous sulfur bacteria, Beggiatoa spp

    DEFF Research Database (Denmark)

    Dunker, Rita; Røy, Hans; Kamp, Anja;

    2011-01-01

    was constructed based on our observations. The model was applied to virtual filaments in the oxygen- and sulfide-free zone of the sediment, which is a main habitat of Beggiatoa in the natural environment. The model predicts a long residence time of the virtual filament in the suboxic zone and explains why...... Beggiatoa accumulate high nitrate concentrations in internal vacuoles as an alternative electron acceptor to oxygen....

  14. Origin of the dense core mass function in contracting filaments

    CERN Document Server

    Myers, Philip C

    2013-01-01

    Mass functions of starless dense cores (CMFs) may arise from contraction and dispersal of core-forming filaments. In an illustrative model, a filament contracts radially by self-gravity, increasing the mass of its cores. During this contraction, FUV photoevaporation and ablation by shocks and winds disperse filament gas and limit core growth. The stopping times of core growth are described by a waiting-time distribution. The initial filament column density profile and the resulting CMF each match recent Herschel observations in detail. Then low-mass cores have short growth ages and arise from the innermost filament gas, while massive cores have long growth ages and draw from more extended filament gas. The model fits the initial density profile and CMF best for mean core density 2 10^4 cm^-3 and filament dispersal time scale 0.5 Myr. Then the typical core mass, radius, mean column density, and contraction speed are respectively 0.8 solar masses, 0.06 pc, 6 10^21 cm^-2, and 0.07 km s^-1, also in accord with ob...

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

    Science.gov (United States)

    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.

  16. Successive filament eruptions within one solar breakout event

    CERN Document Server

    Shen, Yuandeng

    2014-01-01

    The magnetic breakout model has been widely used to explain solar eruptive activities. Here, we apply it to explain successive filament eruptions occurred in a quadrupolar magnetic source region. Based on the high temporal and spatial resolution, multi-wavelengths observations taken by the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamic Observatory (SDO), we find some signatures that support the occurrence of breakout-like external reconnection just before the start of the successive filament eruptions. Furthermore, the extrapolated three-dimensional coronal field also reveals that the magnetic topology above the quadrupolar source region resembles that of the breakout model. We propose a possible mechanism within the framework of the breakout model to interpret the successive filament eruptions, in which the so-called magnetic implosion mechanism is firstly introduced to be the physical linkage of successive filament eruptions. We conclude that the structural properties of coronal fields are im...

  17. Activity Cycle of Solar Filaments

    Indian Academy of Sciences (India)

    K. J. Li; Q. X. Li; P. X. Gao; J. Mu; H. D. Chen; T. W. Su

    2007-06-01

    Long-term variation in the distribution of the solar filaments observed at the Observatorie de Paris, Section de Meudon from March 1919 to December 1989 is presented to compare with sunspot cycle and to study the periodicity in the filament activity, namely the periods of the coronal activity with the Morlet wavelet used. It is inferred that the activity cycle of solar filaments should have the same cycle length as sunspot cycle, but the cycle behavior of solar filaments is globally similar in profile with, but different in detail from, that of sunspot cycles. The amplitude of solar magnetic activity should not keep in phase with the complexity of solar magnetic activity. The possible periods in the filament activity are about 10.44 and 19.20 years. The wavelet local power spectrum of the period 10.44 years is statistically significant during the whole consideration time. The wavelet local power spectrum of the period 19.20 years is under the 95% confidence spectrum during the whole consideration time, but over the mean red-noise spectrum of = 0.72 before approximate Carrington rotation number 1500, and after that the filament activity does not statistically show the period. Wavelet reconstruction indicates that the early data of the filament archive (in and before cycle 16) are more noiseful than the later (in and after cycle 17).

  18. A Comparison Study of a Solar Active-Region Eruptive Filament and a Neighboring Non-Eruptive Filament

    CERN Document Server

    Jiang, Chaowei; Feng, Xueshang; Hu, Qiang

    2015-01-01

    Solar active region (AR) 11283 is a very magnetically complex region and it has produced many eruptions. However, there exists a non-eruptive filament in the plage region just next to an eruptive one in the AR, which gives us an opportunity to perform a comparison analysis of these two filaments. The coronal magnetic field extrapolated using a CESE-MHD-NLFFF code (Jiang & Feng 2013) reveals that two magnetic flux ropes (MFRs) exist in the same extrapolation box supporting these two filaments, respectively. Analysis of the magnetic field shows that the eruptive MFR contains a bald-patch separatrix surface (BPSS) co-spatial very well with a pre-eruptive EUV sigmoid, which is consistent with the BPSS model for coronal sigmoids. The magnetic dips of the non-eruptive MFRs match H{\\alpha} observation of the non-eruptive filament strikingly well, which strongly supports the MFR-dip model for filaments. Compared with the non-eruptive MFR/filament (with a length of about 200 Mm), the eruptive MFR/filament is much ...

  19. Dynamics of the current filament formation and its steady-state characteristics in chalcogenide based PCM

    Science.gov (United States)

    Bogoslovskiy, Nikita; Tsendin, Konstantin

    2017-03-01

    In the phase-change memory (PCM) crystallization occurs in the high-current filament which forms during switching to the conductive state. In the present paper we conduct a numerical modeling of the current filament formation dynamics in thin chalcogenide films using an electronic-thermal model based on negative-U centers tunnel ionization and Joule heating. The key role of inhomogeneities in the filament formation process is shown. Steady-state filament parameters were obtained from the analysis of the stationary heat conduction equation. The filament formation dynamics and the steady-state filament radius and temperature could be controlled by material parameters and contact resistance. Consequently it is possible to control the size of the region wherein crystallization occurs. A good agreement with numerous experimental data leads to the conclusion that thermal effects play a significant role in CGS conduction and high-current filament formation while switching.

  20. Comparative Biomechanics of Thick Filaments and Thin Filaments with Functional Consequences for Muscle Contraction

    Directory of Open Access Journals (Sweden)

    Mark S. Miller

    2010-01-01

    Full Text Available The scaffold of striated muscle is predominantly comprised of myosin and actin polymers known as thick filaments and thin filaments, respectively. The roles these filaments play in muscle contraction are well known, but the extent to which variations in filament mechanical properties influence muscle function is not fully understood. Here we review information on the material properties of thick filaments, thin filaments, and their primary constituents; we also discuss ways in which mechanical properties of filaments impact muscle performance.

  1. Is Gravitational Lensing by Intercluster Filaments Always Negligible?

    CERN Document Server

    Xu, Dong; Shan, HuanYuan; Famaey, Benoit; Limousin, Marceau; Zhao, HongSheng

    2007-01-01

    Intercluster filaments negligibly contribute to the weak lensing signal in General Relativity (GR), $\\gamma_{N}\\sim 10^{-4}-10^{-3}$. In the context of relativistic Modified Newtonian Dynamics (MOND) (Bekenstein 2004), however, a single filament inclined by $\\approx 45^\\circ$ from the line of sight can cause substantial distortion of background sources pointing towards the filament's axis ($\\kappa=\\gamma=(1-A^{-1})/2\\sim 0.01$); this is rigourous for infinitely long uniform filaments, but also qualitatively true for short filaments ($\\sim 30$Mpc), and even in regions where the projected matter density of the filament equals to zero. Since galaxies and galaxy clusters are generally embedded in filaments or are projected on such structures, this contribution complicates the interpretation of the weak lensing shear map in the context of MOND. While our analysis is of mainly theoretical interest providing order-of-magnitude estimates only, it seems safe to conclude that when modeling systems with anomalous weak l...

  2. Centromeres of filamentous fungi

    Science.gov (United States)

    Smith, Kristina M.; Galazka, Jonathan M.; Phatale, Pallavi A.; Connolly, Lanelle R.; Freitag, Michael

    2012-01-01

    How centromeres are assembled and maintained remains one of the fundamental questions in cell biology. Over the past 20 years the idea of centromeres as precise genetic loci has been replaced by the realization that it is predominantly the protein complement that defines centromere localization and function. Thus, placement and maintenance of centromeres are excellent examples of epigenetic phenomena in the strict sense. In contrast, the highly derived “point centromeres” of the budding yeast Saccharomyces cerevisiae and its close relatives are counterexamples for this general principle of centromere maintenance. While we have learned much in the past decade, it remains unclear if mechanisms for epigenetic centromere placement and maintenance are shared amongst various groups of organisms. For that reason it seems prudent to examine species from many different phylogenetic groups with the aim to extract comparative information that will yield a more complete picture of cell division in all eukaryotes. This review addresses what has been learned by studying the centromeres of filamentous fungi, a large, heterogeneous group of organisms that includes important plant, animal and human pathogens, saprobes and symbionts that fulfill essential roles in the biosphere, as well as a growing number of taxa that have become indispensable for industrial use. PMID:22752455

  3. 基于离散单元法的丝状颗粒传热数学模型%Model of heat transfer in filamentous granular materials based on discrete element method

    Institute of Scientific and Technical Information of China (English)

    朱立平; 袁竹林; 闫亚明; 罗登山; 王宏生; 李斌

    2012-01-01

    丝状颗粒作为一类长径比较大的非球形颗粒,其传热特性及相关技术广泛应用于工农业生产的诸多领域.但目前颗粒在运动过程中传热问题的研究还很不充分,特别是对于丝状颗粒,更是缺乏有效的数学模型进行描述.从颗粒传热机理出发,提出了一种基于离散单元法的丝状颗粒传热模型,模型中综合考虑了颗粒碰撞(接触)传热、颗粒的内部导热以及颗粒与气体间的对流换热.利用该模型,对固定床中堆积丝状颗粒的热量迁移过程进行了数值模拟,着重比较了各种传热方式对传热过程的影响.研究表明,对流换热对整体传热量的贡献较大.此外,还获得了不同工况下颗粒温度随时间的变化规律.%Filamentous particle is a kind of non-spherical particles with large aspect ratio. It has been widely applied in industrial and agricultural processes. However, the heat transfer phenomenon about particles is not well understood, especially the filamentous particle. In this study, in order to describe the heat transfer process of filamentous particle, a new mathematical model based on the discrete element method was proposed through the analysis of heat transfer mechanisms. The impact heat transfer between particles, the internal heat conduction and the convection heat exchange between gas and particles were considered in this model, and then it was used to numerically study the heat transfer process of filamentous particles in a fixed bed. Comparing the mechanisms with each other, it showed that the convection heat exchange had greater contribution to the total heat transfer. In addition, the simulation results revealed some internal temperature rules in filamentous particles under different operating conditions.

  4. Elastic response of filamentous networks with compliant crosslinks.

    Science.gov (United States)

    Sharma, A; Sheinman, M; Heidemann, K M; MacKintosh, F C

    2013-11-01

    Experiments have shown that elasticity of disordered filamentous networks with compliant crosslinks is very different from networks with rigid crosslinks. Here, we model and analyze filamentous networks as a collection of randomly oriented rigid filaments connected to each other by flexible crosslinks that are modeled as wormlike chains. For relatively large extensions we allow for enthalpic stretching of crosslink backbones. We show that for sufficiently high crosslink density, the network linear elastic response is affine on the scale of the filaments' length. The nonlinear regime can become highly nonaffine and is characterized by a divergence of the elastic modulus at finite strain. In contrast to the prior predictions, we do not find an asymptotic regime in which the differential elastic modulus scales linearly with the stress, although an approximate linear dependence can be seen in a transition from entropic to enthalpic regimes. We discuss our results in light of recent experiments.

  5. Elastic response of filamentous networks with compliant crosslinks

    CERN Document Server

    Sharma, A; Heidemann, K M; MacKintosh, F C

    2013-01-01

    Experiments have shown that elasticity of disordered filamentous networks with compliant crosslinks is very different from networks with rigid crosslinks. Here, we model and analyze filamentous networks as a collection of randomly oriented rigid filaments connected to each other by flexible crosslinks that are modeled as worm-like chains. For relatively large extensions we allow for enthalpic stretching of crosslinks' backbones. We show that for sufficiently high crosslink density, the network linear elastic response is affine on the scale of the filaments' length. The nonlinear regime can become highly nonaffine and is characterized by a divergence of the elastic modulus at finite strain. In contrast to the prior predictions, we do not find an asymptotic regime in which the differential elastic modulus scales linearly with the stress, although an approximate linear dependence can be seen in a transition from entropic to enthalpic regimes. We discuss our results in light of the recent experiments.

  6. A first approach to filament dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Silva, P E S; De Abreu, F Vistulo; Dias, R G [Department of Physics, University of Aveiro (Portugal); Simoes, R, E-mail: fva@ua.p [I3N-Institute for Nanostructures, Nanomodelling and Nanofabrication (Portugal)

    2010-11-15

    Modelling elastic filament dynamics is a topic of high interest due to the wide range of applications. However, it has reached a high level of complexity in the literature, making it unaccessible to a beginner. In this paper we explain the main steps involved in the computational modelling of the dynamics of an elastic filament. We first derive equations governing the dynamics of an elastic lament suitable for a computer simulation implementation. The derivation starts from the relation between forces and potential energy in conservative systems in order to derive the equation of motion of any bead in the filament. Only two-dimensional movements are considered, but extensions to three dimensions can follow similar lines. Suggestions for computer implementations are provided in Matlab as well as an example of application related to the generation of musical sounds. This example allows a critical analysis of the numerical results obtained using a cross-disciplinary perspective. Since derivations start from basic physics equations, use simple calculus and computational implementations are straightforward, this paper proposes a different approach to introduce simple molecular dynamics simulations or animations of real systems in undergraduate elasticity or computer modelling courses.

  7. Filament Identification through Mathematical Morphology

    OpenAIRE

    Koch, Eric W.; Rosolowsky, Erik W.

    2015-01-01

    We present a new algorithm for detecting filamentary structure FilFinder. The algorithm uses the techniques of mathematical morphology for filament identification, presenting a complementary approach to current algorithms which use matched filtering or critical manifolds. Unlike other methods, FilFinder identifies filaments over a wide dynamic range in brightness. We apply the new algorithm to far infrared imaging data of dust emission released by the Herschel Gould Belt Survey team. Our prel...

  8. Stretching instability of intrinsically curved semiflexible biopolymers:A lattice model approach

    Institute of Scientific and Technical Information of China (English)

    周子聪; 林方庭; 陈柏翰

    2015-01-01

    We apply Monte Carlo simulation method to lattice systems to study the effect of an intrinsic curvature on the me-chanical property of a semifl exible biopolymer. We find that when the intrinsic curvature is sufficient large, the extension of a semifl exible biopolymer can undergo a first-order transition at finite temperature. The critical force increases with in-creasing intrinsic curvature. But the relationship between the critical force and the bending rigidity is structure-dependent. In triangle lattice system, when the intrinsic curvature is smaller than a critical value, the critical force increases with the increasing bending rigidity first, and then decreases with the increasing bending rigidity. But in square lattice system, the critical force always decreases with the increasing bending rigidity. In contrast, when the intrinsic curvature is greater than the critical value, the larger bending rigidity always results in a larger critical force in both lattice systems.

  9. Shape selection of surface-bound helical filaments: biopolymers on curved membranes

    CERN Document Server

    Quint, D A; Grason, G M

    2016-01-01

    Motivated to understand the behavior of biological filaments interacting with membranes of various types, we study a theoretical model for the shape and thermodynamics of intrinsically-helical filaments bound to curved membranes. We show filament-surface interactions lead to a host of non-uniform shape equilibria, in which filaments progressively unwind from their native twist with increasing surface interaction and surface curvature, ultimately adopting uniform-contact curved shapes. The latter effect is due to non-linear coupling between elastic twist and bending of filaments on anisotropically-curved surfaces, such as the cylindrical surfaces considered here. Via a combination of numerical solutions and asymptotic analysis of shape equilibria we show that filament conformations are critically sensitive to the surface curvature in both the strong- and weak-binding limits. These results suggest that local structure of membrane-bound chiral filaments is generically sensitive to the curvature-radius of the sur...

  10. Collective alignment of polar filaments by molecular motors.

    Science.gov (United States)

    Ziebert, F; Vershinin, M; Gross, S P; Aranson, I S

    2009-04-01

    We study the alignment of polar biofilaments, such as microtubules and actin, subject to the action of multiple molecular motors attached simultaneously to more than one filament. Focusing on a paradigm model of only two filaments interacting with multiple motors, we were able to investigate in detail the alignment dynamics. While almost no alignment occurs in the case of a single motor, the filaments become rapidly aligned due to the collective action of the motors. Our analysis shows that the alignment time is governed by the number of bound motors and the magnitude of the motors' stepping fluctuations. We predict that the time scale of alignment is in the order of seconds, much faster than that reported for passive crosslink-induced bundling. In vitro experiments on the alignment of microtubules by multiple-motor covered beads are in qualitative agreement. We also discuss another mode of fast alignment of filaments, namely the cooperation between motors and passive crosslinks.

  11. Calibration and temperature profile of a tungsten filament lamp

    Energy Technology Data Exchange (ETDEWEB)

    De Izarra, Charles [Groupe de Recherche sur l' Energetique des Milieux Ionises, UMR6606 Universite d' Orleans, CNRS, Faculte des Sciences, Site de Bourges, rue Gaston Berger, BP 4043, 18028 Bourges Cedex (France); Gitton, Jean-Michel, E-mail: Charles.De_Izarra@univ-orleans.f [College Littre, 10 rue Littre, Bourges (France)

    2010-07-15

    The goal of this work proposed for undergraduate students and teachers is the calibration of a tungsten filament lamp from electric measurements that are both simple and precise, allowing to determine the temperature of tungsten filament as a function of the current intensity. This calibration procedure was first applied to a conventional filament lamp (lamp used in automotive lighting) and then tested on a standard tungsten ribbon lamp. The calibration procedure developed was checked by determining the calibration point of the tungsten ribbon lamp with an accuracy of 2%. In addition, for low current intensity, it was observed that the temperature of the filament was not uniform; an explanation is proposed by considering a simple heat transfer model.

  12. Appearance of Dusty Filaments at Different Viewing Angles

    CERN Document Server

    Chira, R -A; Henning, Th; Kainulainen, J

    2016-01-01

    Context: In the last years, there have been many studies on the omnipresence and structures of filaments in star-forming regions, as well as their role in the process of star formation. Those filaments are normally identified as elongated fibres across the plane of the sky. But how would we detect filaments that are inclined? Aims: We aim to learn more about whether, and how, total column density or dust temperature change with respect to the line of sight. Such variations would enable observers to use dust observations to identify and study filaments at any inclination and gain more insight on the distribution and orientations of filaments within the Galactic plane. Methods: As a first step, we perform numerical calculations on simple cylindrical models to evaluate the influence of filament geometry on the average flux density. After that, we apply our three-dimensional Monte Carlo dust radiative transfer code on two models of star-forming regions and derive maps of effective total column density and dust te...

  13. Formation of magnetic filaments: A kinetic study

    Science.gov (United States)

    Martínez-Pedrero, F.; Tirado-Miranda, M.; Schmitt, A.; Callejas-Fernández, J.

    2007-07-01

    In order to form magnetic filaments or chains, aqueous suspensions of superparamagnetic colloidal particles were aggregated under the action of an external magnetic field in the presence of different amounts of an indifferent 1:1 electrolyte (KBr). This allowed the influence of the anisotropic magnetic and isotropic electrostatic interactions on the aggregation behavior of these electric double-layered magnetic particles to be studied. Dynamic light scattering was used for monitoring the average diffusion coefficient of the magnetic filaments formed. Hydrodynamic equations were employed for obtaining the average chain lengths from the experimental mean diffusion coefficients. The results show that, for the same exposure time to the magnetic field, the average filament size is monotonously related to the amount of electrolyte added. The chain growth behavior was found to follow a power law with a similar exponent for all electrolyte concentrations used in this work. The time evolution of the average filament size can be rescaled such that all the curves collapse on a single master curve. Since the electrolyte added does not have any effect on the scaling behavior, the mechanism of aggregation seems to be completely controlled by the dipolar interaction. However, electrolyte addition not only controls the range of the total interaction between the particles, but also enhances the growth rate of the aggregation process. Taking into account the anisotropic character of these aggregation processes we propose a kernel that depends explicitly on the range of the dipolar interaction. The corresponding solutions of the Smoluchowski equation combined with theoretical models for the diffusion and light scattering by rigid rods reproduce the measured time evolution of the average perpendicular aggregate diffusion coefficient quite satisfactorily.

  14. A combined stretching-tilting mechanism produces negative, zero and positive linear thermal expansion in a semi-flexible Cd(II)-MOF.

    Science.gov (United States)

    Lama, Prem; Das, Raj Kumar; Smith, Vincent J; Barbour, Leonard J

    2014-06-21

    A novel semi-flexible Cd(II)-MOF has been synthesized and characterized by variable temperature powder and single-crystal X-ray diffraction. The material displays an unusual combination of thermal expansion (TE) i.e. negative, zero and positive, which is an extremely rare finding, especially for metal-organic frameworks as a result of a combined stretching-tilting mechanism.

  15. Force-velocity measurements of a few growing actin filaments.

    Directory of Open Access Journals (Sweden)

    Coraline Brangbour

    2011-04-01

    Full Text Available The polymerization of actin in filaments generates forces that play a pivotal role in many cellular processes. We introduce a novel technique to determine the force-velocity relation when a few independent anchored filaments grow between magnetic colloidal particles. When a magnetic field is applied, the colloidal particles assemble into chains under controlled loading or spacing. As the filaments elongate, the beads separate, allowing the force-velocity curve to be precisely measured. In the widely accepted Brownian ratchet model, the transduced force is associated with the slowing down of the on-rate polymerization. Unexpectedly, in our experiments, filaments are shown to grow at the same rate as when they are free in solution. However, as they elongate, filaments are more confined in the interspace between beads. Higher repulsive forces result from this higher confinement, which is associated with a lower entropy. In this mechanism, the production of force is not controlled by the polymerization rate, but is a consequence of the restriction of filaments' orientational fluctuations at their attachment point.

  16. Force-Velocity Measurements of a Few Growing Actin Filaments

    Science.gov (United States)

    Brangbour, Coraline; du Roure, Olivia; Helfer, Emmanuèle; Démoulin, Damien; Mazurier, Alexis; Fermigier, Marc; Carlier, Marie-France; Bibette, Jérôme; Baudry, Jean

    2011-01-01

    The polymerization of actin in filaments generates forces that play a pivotal role in many cellular processes. We introduce a novel technique to determine the force-velocity relation when a few independent anchored filaments grow between magnetic colloidal particles. When a magnetic field is applied, the colloidal particles assemble into chains under controlled loading or spacing. As the filaments elongate, the beads separate, allowing the force-velocity curve to be precisely measured. In the widely accepted Brownian ratchet model, the transduced force is associated with the slowing down of the on-rate polymerization. Unexpectedly, in our experiments, filaments are shown to grow at the same rate as when they are free in solution. However, as they elongate, filaments are more confined in the interspace between beads. Higher repulsive forces result from this higher confinement, which is associated with a lower entropy. In this mechanism, the production of force is not controlled by the polymerization rate, but is a consequence of the restriction of filaments' orientational fluctuations at their attachment point. PMID:21541364

  17. SDC13 infrared dark clouds: Longitudinally collapsing filaments?

    CERN Document Server

    Peretto, N; André, Ph; Arzoumanian, D; Rivilla, V M; Bardeau, S; Puertas, S Duarte; Fernandez, J P Guzman; Lenfestey, C; Li, G -X; Olguin, F A; Röck, B R; de Villiers, H; Williams, J

    2013-01-01

    Formation of stars is now believed to be tightly linked to the dynamical evolution of interstellar filaments in which they form. In this paper we analyze the density structure and kinematics of a small network of infrared dark filaments, SDC13, observed in both dust continuum and molecular line emission with the IRAM 30m telescope. These observations reveal the presence of 18 compact sources amongst which the two most massive, MM1 and MM2, are located at the intersection point of the parsec-long filaments. The dense gas velocity and velocity dispersion observed along these filaments show smooth, strongly correlated, gradients. We discuss the origin of the SDC13 velocity field in the context of filament longitudinal collapse. We show that the collapse timescale of the SDC13 filaments (from 1 Myr to 4 Myr depending on the model parameters) is consistent with the presence of Class I sources in them, and argue that, on top of bringing more material to the centre of the system, collapse could generate additional k...

  18. Geometrical and mechanical properties control actin filament organization.

    Directory of Open Access Journals (Sweden)

    Gaëlle Letort

    2015-05-01

    Full Text Available The different actin structures governing eukaryotic cell shape and movement are not only determined by the properties of the actin filaments and associated proteins, but also by geometrical constraints. We recently demonstrated that limiting nucleation to specific regions was sufficient to obtain actin networks with different organization. To further investigate how spatially constrained actin nucleation determines the emergent actin organization, we performed detailed simulations of the actin filament system using Cytosim. We first calibrated the steric interaction between filaments, by matching, in simulations and experiments, the bundled actin organization observed with a rectangular bar of nucleating factor. We then studied the overall organization of actin filaments generated by more complex pattern geometries used experimentally. We found that the fraction of parallel versus antiparallel bundles is determined by the mechanical properties of actin filament or bundles and the efficiency of nucleation. Thus nucleation geometry, actin filaments local interactions, bundle rigidity, and nucleation efficiency are the key parameters controlling the emergent actin architecture. We finally simulated more complex nucleation patterns and performed the corresponding experiments to confirm the predictive capabilities of the model.

  19. Temperature Controlled Filamentation in Argon Gas

    Institute of Scientific and Technical Information of China (English)

    CAO Shi-Ying; KONG Wei-Peng; SONG Zhen-Ming; QIN Yu; LI Ru-Xin; WANG Qing-Yue; ZHANG Zhi-Gang

    2008-01-01

    Temperature controlled filamentation is experimentally demonstrated in a temperature gradient gas-filled tube.The proper position of the tube is heated by a furnace and two ends of the tube are cooled by air. The experimental results show that multiple filaments are shrunken into a single fila.ment or no filament only by increasing the temperature at the beginning of the filament. This technique offers another degree of freedom of controlling the filamentation and opens a new way for intense monocycle pulse generation through gradient temperature in a noble gas.

  20. Intermediate Filaments in Caenorhabditis elegans.

    Science.gov (United States)

    Zuela, Noam; Gruenbaum, Yosef

    2016-01-01

    More than 70 different genes in humans and 12 different genes in Caenorhabditis elegans encode the superfamily of intermediate filament (IF) proteins. In C. elegans, similar to humans, these proteins are expressed in a cell- and tissue-specific manner, can assemble into heteropolymers and into 5-10nm wide filaments that account for the principal structural elements at the nuclear periphery, nucleoplasm, and cytoplasm. At least 5 of the 11 cytoplasmic IFs, as well as the nuclear IF, lamin, are essential. In this chapter, we will include a short review of our current knowledge of both cytoplasmic and nuclear IFs in C. elegans and will describe techniques used for their analyses.

  1. Quantification of Processing Effects on Filament Wound Pressure Vessels

    Science.gov (United States)

    Aiello, Robert A.; Chamis, Christos C.

    1999-01-01

    A computational simulation procedure is described which is designed specifically for the modeling and analysis of filament wound pressure vessels. Cylindrical vessels with spherical or elliptical end caps can be generated automatically. End caps other than spherical or elliptical may be modeled by varying circular sections along the x-axis according to the C C! end cap shape. The finite element model generated is composed of plate type quadrilateral shell elements on the entire vessel surface. This computational procedure can also be sued to generate grid, connectivity and material cards (bulk data) for component parts of a larger model. These bulk data are assigned to a user designated file for finite element structural/stress analysis of composite pressure vessels. The procedure accommodates filament would pressure vessels of all types of shells-of-revolution. It has provisions to readily evaluate initial stresses due to pretension in the winding filaments and residual stresses due to cure temperature.

  2. Quantification of Processing Effects on Filament Wound Pressure Vessels. Revision

    Science.gov (United States)

    Aiello, Robert A.; Chamis, Christos C.

    2002-01-01

    A computational simulation procedure is described which is designed specifically for the modeling and analysis of filament wound pressure vessels. Cylindrical vessels with spherical or elliptical end caps can be generated automatically. End caps other than spherical or elliptical may be modeled by varying circular sections along the x-axis according to the end cap shape. The finite element model generated is composed of plate type quadrilateral shell elements on the entire vessel surface. This computational procedure can also be used to generate grid, connectivity and material cards (bulk data) for component parts of a larger model. These bulk data are assigned to a user designated file for finite element structural/stress analysis of composite pressure vessels. The procedure accommodates filament wound pressure vessels of all types of shells-of -revolution. It has provisions to readily evaluate initial stresses due to pretension in the winding filaments and residual stresses due to cure temperature.

  3. Stellar filaments in self-interacting Brans-Dicke gravity

    Energy Technology Data Exchange (ETDEWEB)

    Sharif, M. [University of the Punjab, Department of Mathematics, Lahore (Pakistan); Manzoor, Rubab [University of the Punjab, Department of Mathematics, Lahore (Pakistan); University of Management and Technology, Department of Mathematics, Lahore (Pakistan)

    2016-05-15

    This paper is devoted to the study of the cylindrically symmetric stellar filaments in self-interacting Brans-Dicke gravity. For this purpose, we construct polytropic filamentary models through a generalized Lane-Emden equation in the Newtonian regime. The resulting models depend upon the values of the cosmological constant (due to the scalar field) along with the polytropic index and represent a generalization of the corresponding models in general relativity. We also investigate the fragmentation of the filaments by exploring the radial oscillations through a stability analysis. This stability criterion depends only upon the adiabatic index. (orig.)

  4. Stellar Filaments in Self-Interacting Brans-Dicke Gravity

    CERN Document Server

    Sharif, M

    2016-01-01

    This paper is devoted to study cylindrically symmetric stellar filaments in self-interacting Brans-Dicke gravity. For this purpose, we construct polytropic filamentary models through generalized Lane-Emden equation in Newtonian regime. The resulting models depend upon the values of cosmological constant (due to scalar field) along with polytropic index and represent a generalization of the corresponding models in general relativity. We also investigate fragmentation of filaments by exploring the radial oscillations through stability analysis. This stability criteria depends only upon the adiabatic index.

  5. Evolutionarily divergent, unstable filamentous actin is essential for gliding motility in apicomplexan parasites.

    Science.gov (United States)

    Skillman, Kristen M; Diraviyam, Karthikeyan; Khan, Asis; Tang, Keliang; Sept, David; Sibley, L David

    2011-10-01

    Apicomplexan parasites rely on a novel form of actin-based motility called gliding, which depends on parasite actin polymerization, to migrate through their hosts and invade cells. However, parasite actins are divergent both in sequence and function and only form short, unstable filaments in contrast to the stability of conventional actin filaments. The molecular basis for parasite actin filament instability and its relationship to gliding motility remain unresolved. We demonstrate that recombinant Toxoplasma (TgACTI) and Plasmodium (PfACTI and PfACTII) actins polymerized into very short filaments in vitro but were induced to form long, stable filaments by addition of equimolar levels of phalloidin. Parasite actins contain a conserved phalloidin-binding site as determined by molecular modeling and computational docking, yet vary in several residues that are predicted to impact filament stability. In particular, two residues were identified that form intermolecular contacts between different protomers in conventional actin filaments and these residues showed non-conservative differences in apicomplexan parasites. Substitution of divergent residues found in TgACTI with those from mammalian actin resulted in formation of longer, more stable filaments in vitro. Expression of these stabilized actins in T. gondii increased sensitivity to the actin-stabilizing compound jasplakinolide and disrupted normal gliding motility in the absence of treatment. These results identify the molecular basis for short, dynamic filaments in apicomplexan parasites and demonstrate that inherent instability of parasite actin filaments is a critical adaptation for gliding motility.

  6. Evolutionarily divergent, unstable filamentous actin is essential for gliding motility in apicomplexan parasites.

    Directory of Open Access Journals (Sweden)

    Kristen M Skillman

    2011-10-01

    Full Text Available Apicomplexan parasites rely on a novel form of actin-based motility called gliding, which depends on parasite actin polymerization, to migrate through their hosts and invade cells. However, parasite actins are divergent both in sequence and function and only form short, unstable filaments in contrast to the stability of conventional actin filaments. The molecular basis for parasite actin filament instability and its relationship to gliding motility remain unresolved. We demonstrate that recombinant Toxoplasma (TgACTI and Plasmodium (PfACTI and PfACTII actins polymerized into very short filaments in vitro but were induced to form long, stable filaments by addition of equimolar levels of phalloidin. Parasite actins contain a conserved phalloidin-binding site as determined by molecular modeling and computational docking, yet vary in several residues that are predicted to impact filament stability. In particular, two residues were identified that form intermolecular contacts between different protomers in conventional actin filaments and these residues showed non-conservative differences in apicomplexan parasites. Substitution of divergent residues found in TgACTI with those from mammalian actin resulted in formation of longer, more stable filaments in vitro. Expression of these stabilized actins in T. gondii increased sensitivity to the actin-stabilizing compound jasplakinolide and disrupted normal gliding motility in the absence of treatment. These results identify the molecular basis for short, dynamic filaments in apicomplexan parasites and demonstrate that inherent instability of parasite actin filaments is a critical adaptation for gliding motility.

  7. Magnetic signature of current carrying edge localized modes filaments on the Joint European Torus tokamak

    DEFF Research Database (Denmark)

    Migliucci, P.; Naulin, Volker

    2010-01-01

    Fast magnetic pickup coils are used in forward modeling to match parameters in a simple edge localized mode (ELM) filament model. This novel method allows us to determine key parameters for the evolution of the ELM filaments, as effective mode number, radial and toroidal velocities, and average...

  8. Capillary thinning of polymeric filaments

    DEFF Research Database (Denmark)

    Kolte, Mette Irene; Szabo, Peter

    1999-01-01

    The capillary thinning of filaments of a Newtonian polybutene fluid and a viscoelastic polyisobutylene solution are analyzed experimentally and by means of numerical simulation. The experimental procedure is as follows. Initially, a liquid sample is placed between two cylindrical plates. Then, th...... and quantified. (C) 1999 The Society of Rheology. [S0148-6055(99)00103-0]....

  9. Merger of Long Vortex Filaments

    CERN Document Server

    Khandekar, Akshay

    2012-01-01

    This fluid dynamics video demonstrates the merger of long vortex filaments is shown experimentally. Two counter-rotating vortices are generated using in a tank with very high aspect ratio. PIV demonstrates the merger of the vortices within a single orbit.

  10. Picosecond laser filamentation in air

    Science.gov (United States)

    2016-09-02

    LeibnizUniversityHannover,Welfengarten 1, D-30167Hannover, Germany 3 CEA-DAM,DIF, F-91297Arpajon, France 4 Univ.Bordeaux—CNRS—CEA,Centre Lasers ...optics.arizona.edu Keywords: laser filamentation, picosecond laser pulses, nonlinear propagation, optical ionization Abstract The propagation of intense

  11. Filament Winding. A Unified Approach

    NARCIS (Netherlands)

    Koussios, S.

    2004-01-01

    In this dissertation we have presented an overview and comprehensive treatment of several facets of the filament winding process. With the concepts of differential geometry and the theory of thin anisotropic shells of revolution, a parametric shape generator has been formulated for the design proced

  12. Role of Intermediate Filaments in Vesicular Traffic

    Directory of Open Access Journals (Sweden)

    Azzurra Margiotta

    2016-04-01

    Full Text Available 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.

  13. Sufficient conditions for the additivity of stall forces generated by multiple filaments or motors

    Science.gov (United States)

    Bameta, Tripti; Das, Dipjyoti; Das, Dibyendu; Padinhateeri, Ranjith; Inamdar, Mandar M.

    2017-02-01

    Molecular motors and cytoskeletal filaments work collectively most of the time under opposing forces. This opposing force may be due to cargo carried by motors or resistance coming from the cell membrane pressing against the cytoskeletal filaments. Some recent studies have shown that the collective maximum force (stall force) generated by multiple cytoskeletal filaments or molecular motors may not always be just a simple sum of the stall forces of the individual filaments or motors. To understand this excess or deficit in the collective force, we study a broad class of models of both cytoskeletal filaments and molecular motors. We argue that the stall force generated by a group of filaments or motors is additive, that is, the stall force of N number of filaments (motors) is N times the stall force of one filament (motor), when the system is reversible at stall. Conversely, we show that this additive property typically does not hold true when the system is irreversible at stall. We thus present a novel and unified understanding of the existing models exhibiting such non-addivity, and generalise our arguments by developing new models that demonstrate this phenomena. We also propose a quantity similar to thermodynamic efficiency to easily predict this deviation from stall-force additivity for filament and motor collectives.

  14. Large-scale Motion of Solar Filaments

    Indian Academy of Sciences (India)

    Pavel Ambrož; Alfred Schroll

    2000-09-01

    Precise measurements of heliographic position of solar filaments were used for determination of the proper motion of solar filaments on the time-scale of days. The filaments have a tendency to make a shaking or waving of the external structure and to make a general movement of whole filament body, coinciding with the transport of the magnetic flux in the photosphere. The velocity scatter of individual measured points is about one order higher than the accuracy of measurements.

  15. Preparation and Characterization of Carbon Filaments

    Science.gov (United States)

    1991-04-01

    catalysts gave straight filaments, while the use of nickel and other catalysts resulted in a variety of vermicular forms of filaments. Ferrocene, (C5H5)2Fe...vapor deposition of carbon filaments is presented along with a theory for the vermicular growth of filaments on quartz substrates. I U I I I I I I...one hour. The experimental details of the matrix and results are discussed, also theories for the role of hydrogen and the vermicular growth of

  16. Analysis of a filament stretching rheometer

    DEFF Research Database (Denmark)

    Kolte, Mette Irene; Rasmussen, Henrik K.; Hassager, Ole

    1996-01-01

    A finite element analysis of the stretching filament rheometer of Tirtaadmadja and Sridhar (1993) is presenetd. Simulations of the stretching of a filament of the polymet test solution, fluid A, between two plates are shown.......A finite element analysis of the stretching filament rheometer of Tirtaadmadja and Sridhar (1993) is presenetd. Simulations of the stretching of a filament of the polymet test solution, fluid A, between two plates are shown....

  17. Development and Application of Wood Flour-Filled Polylactic Acid Composite Filament for 3D Printing.

    Science.gov (United States)

    Tao, Yubo; Wang, Honglei; Li, Zelong; Li, Peng; Shi, Sheldon Q

    2017-03-24

    This paper presents the development of wood flour (WF)-filled polylactic acid (PLA) composite filaments for a fused deposition modeling (FDM) process with the aim of application to 3D printing. The composite filament consists of wood flour (5 wt %) in a PLA matrix. The detailed formulation and characterization of the composite filament were investigated experimentally, including tensile properties, microstructure, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and X-ray diffraction (XRD). The feedstock filaments of this composite were produced and used successfully in an assembled FDM 3D printer. The research concludes that compared with pure PLA filament, adding WF changed the microstructure of material fracture surface, the initial deformation resistance of the composite was enhanced, the starting thermal degradation temperature of the composite decreased slightly, and there were no effects on the melting temperature. The WF/PLA composite filament is suitable to be printed by the FDM process.

  18. The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube Formation.

    Directory of Open Access Journals (Sweden)

    Julian Weichsel

    2016-07-01

    Full Text Available Tubular protrusions are a common feature of living cells, arising from polymerization of stiff protein filaments against a comparably soft membrane. Although this process involves many accessory proteins in cells, in vitro experiments indicate that similar tube-like structures can emerge without them, through spontaneous bundling of filaments mediated by the membrane. Using theory and simulation of physical models, we have elaborated how nonequilibrium fluctuations in growth kinetics and membrane shape can yield such protrusions. Enabled by a new grand canonical Monte Carlo method for membrane simulation, our work reveals a cascade of dynamical transitions from individually polymerizing filaments to highly cooperatively growing bundles as a dynamical bottleneck to tube formation. Filament network organization as well as adhesion points to the membrane, which bias filament bending and constrain membrane height fluctuations, screen the effective attractive interactions between filaments, significantly delaying bundling and tube formation.

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

    Science.gov (United States)

    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.

  20. Remote electrical arc suppression by laser filamentation

    CERN Document Server

    Schubert, Elise; Kasparian, Jérôme; Wolf, Jean-Pierre

    2015-01-01

    We investigate the interaction of narrow plasma channels formed in the filamentation of ultrashort laser pulses, with a DC high voltage. The laser filaments prevent electrical arcs by triggering corona that neutralize the high-voltage electrodes. This phenomenon, due to the electric field modulation and free electron release around the filament, opens new prospects to lightning and over-voltage mitigation.

  1. Giant quiescent solar filament observed with high-resolution spectroscopy

    Science.gov (United States)

    Kuckein, C.; Verma, M.; Denker, C.

    2016-05-01

    Aims: An extremely large filament was studied in various layers of the solar atmosphere. The inferred physical parameters and the morphological aspects are compared with smaller quiescent filaments. Methods: A giant quiet-Sun filament was observed with the high-resolution Echelle spectrograph at the Vacuum Tower Telescope at Observatorio del Teide, Tenerife, Spain, on 2011 November 15. A mosaic of spectra (ten maps of 100″ × 182″) was recorded simultaneously in the chromospheric absorption lines Hα and Na i D2. Physical parameters of the filament plasma were derived using cloud model (CM) inversions and line core fits. The spectra were complemented with full-disk filtergrams (He i λ10830 Å, Hα, and Ca ii K) of the Chromospheric Telescope (ChroTel) and full-disk magnetograms of the Helioseismic and Magnetic Imager (HMI). Results: The filament had extremely large linear dimensions (~817 arcsec), which corresponds to about 658 Mm along a great circle on the solar surface. A total amount of 175119 Hα contrast profiles were inverted using the CM approach. The inferred mean line-of-sight (LOS) velocity, Doppler width, and source function were similar to previous works of smaller quiescent filaments. However, the derived optical thickness was higher. LOS velocity trends inferred from the Hα line core fits were in accord but weaker than those obtained with CM inversions. Signatures of counter-streaming flows were detected in the filament. The largest brightening conglomerates in the line core of Na i D2 coincided well with small-scale magnetic fields as seen by HMI. Mixed magnetic polarities were detected close to the ends of barbs. The computation of photospheric horizontal flows based on HMI magnetograms revealed flow kernels with a size of 5-8 Mm and velocities of 0.30-0.45 km s-1 at the ends of the filament. Conclusions: The physical properties of extremely large filaments are similar to their smaller counterparts, except for the optical thickness, which in

  2. Cell envelope components influencing filament length in the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120.

    Science.gov (United States)

    Burnat, Mireia; Schleiff, Enrico; Flores, Enrique

    2014-12-01

    Heterocyst-forming cyanobacteria grow as chains of cells (known as trichomes or filaments) that can be hundreds of cells long. The filament consists of individual cells surrounded by a cytoplasmic membrane and peptidoglycan layers. The cells, however, share a continuous outer membrane, and septal proteins, such as SepJ, are important for cell-cell contact and filament formation. Here, we addressed a possible role of cell envelope components in filamentation, the process of producing and maintaining filaments, in the model cyanobacterium Anabaena sp. strain PCC 7120. We studied filament length and the response of the filaments to mechanical fragmentation in a number of strains with mutations in genes encoding cell envelope components. Previously published peptidoglycan- and outer membrane-related gene mutants and strains with mutations in two genes (all5045 and alr0718) encoding class B penicillin-binding proteins isolated in this work were used. Our results show that filament length is affected in most cell envelope mutants, but the filaments of alr5045 and alr2270 gene mutants were particularly fragmented. All5045 is a dd-transpeptidase involved in peptidoglycan elongation during cell growth, and Alr2270 is an enzyme involved in the biosynthesis of lipid A, a key component of lipopolysaccharide. These results indicate that both components of the cell envelope, the murein sacculus and the outer membrane, influence filamentation. As deduced from the filament fragmentation phenotypes of their mutants, however, none of these elements is as important for filamentation as the septal protein SepJ.

  3. A filament of dark matter between two clusters of galaxies.

    Science.gov (United States)

    Dietrich, Jörg P; Werner, Norbert; Clowe, Douglas; Finoguenov, Alexis; Kitching, Tom; Miller, Lance; Simionescu, Aurora

    2012-07-12

    It is a firm prediction of the concordance cold-dark-matter cosmological model that galaxy clusters occur at the intersection of large-scale structure filaments. The thread-like structure of this 'cosmic web' has been traced by galaxy redshift surveys for decades. More recently, the warm–hot intergalactic medium (a sparse plasma with temperatures of 10(5) kelvin to 10(7) kelvin) residing in low-redshift filaments has been observed in emission and absorption. However, a reliable direct detection of the underlying dark-matter skeleton, which should contain more than half of all matter, has remained elusive, because earlier candidates for such detections were either falsified or suffered from low signal-to-noise ratios and unphysical misalignments of dark and luminous matter. Here we report the detection of a dark-matter filament connecting the two main components of the Abell 222/223 supercluster system from its weak gravitational lensing signal, both in a non-parametric mass reconstruction and in parametric model fits. This filament is coincident with an overdensity of galaxies and diffuse, soft-X-ray emission, and contributes a mass comparable to that of an additional galaxy cluster to the total mass of the supercluster. By combining this result with X-ray observations, we can place an upper limit of 0.09 on the hot gas fraction (the mass of X-ray-emitting gas divided by the total mass) in the filament.

  4. Undulatory locomotion of finite filaments: lessons from C. elegans

    CERN Document Server

    Berman, R; Sznitman, J; Leshansky, A

    2013-01-01

    Undulatory swimming is a widespread propulsion strategy adopted by many small-scale organisms including various single-cell eukaryotes and nematodes. In this work, we report a comprehensive study of undulatory locomotion of a finite filament using (i) approximate resistive force theory (RFT) assuming a local nature of hydrodynamic interaction between the filament and the surrounding viscous liquid, and (ii) particle-based numerical computations taking into account the intra-filament hydrodynamic interaction. Using the ubiquitous model of a propagating sinusoidal waveform, we identify the limit of applicability of the RFT and determine the optimal propulsion gait in terms of (i) swimming distance per period of undulation and (ii) hydrodynamic propulsion efficiency. The occurrence of the optimal swimming gait maximizing hydrodynamic efficiency at finite wavelength in particle-based computations diverges from the prediction of the RFT. To compare the model swimmer powered by sine wave undulations to biological u...

  5. Persistence of activity in noisy motor-filament assemblies

    CERN Document Server

    Chelakkot, Raghunath; Mahadevan, L

    2015-01-01

    Long, elastic filaments cross-linked and deformed by active molecular motors occur in various natural settings. The overall macroscopic mechanical response of such a composite network depends on the coupling between the active and the passive properties of the underlying constituents and nonlocal interactions between different parts of the composite. In a simple one dimensional system, using a mean field model, it has been shown that the combination of motor activity and finite filament extensibility yields a persistence length scale over which strain decays. Here we study a similar system, in the complementary limit of strong noise and moderate extensibility, using Brownian multi-particle collision dynamics-based numerical simulations that includes the coupling between motor kinetics and local filament extensibility. While the numerical model shows deviations from the mean field predictions due to the presence of strong active noise caused by the variations in individual motor activity, several qualitative f...

  6. Elastic filament velocimetry (EFV)

    Science.gov (United States)

    Fu, M. K.; Fan, Y.; Byers, C. P.; Chen, T.-H.; Arnold, C. B.; Hultmark, M.

    2017-02-01

    A novel method for velocity measurements in both gaseous and liquid flows is presented. The sensing element is comprised of a free-standing electrically conductive nanoscale ribbon suspended between silicon supports. Due to its minuscule size, the nanoribbon deflects in flow due to viscously dominated fluid forcing inducing an axial strain of the sensing element. The strain leads to a resistance change, which is measurable through a simple Wheatstone bridge circuit and can be related to the flow velocity through semi-analytic analysis. Two methods of characterization are employed to validate the sensor functionality. First, confocal microscopy was used to validate physical models and assumptions through imaging of the nanoribbon deformation under different fluid loads. Second, the resistance measurements of various nanoribbons under different flow conditions exhibited sensitivity to fluid flow consistent with lower order model predictions.

  7. How tension propagates for a driven semi-flexible chain while translocating through a nano-pore

    Science.gov (United States)

    Adhikari, Ramesh; Bhattacharya, Aniket

    2013-03-01

    Driven translocation of a stiff chain through a nano-pore is studied using Langevin dynamics in two dimension (2D). We observe that for a given chain length N the mean first passage time (MFPT) increases for a stiffer chain and the translocation exponent α ( ~Nα) satisfies the inequality 2 ν exponent for a given chain stiffness. We calculate the residence time of the individual monomers and observe that the peak position of the residence time W (m) as a function of the monomer index m shifts at a lower m-value with increasing chain stiffness κb. Finally, we provide qualitative physical explanation for dependence of various quantities on chain stiffness κb by using ideas from Sakaue's tension propagation(TP) theory [Phys. Rev. E 76, 021803 (2007)] and its recent implementation into a Brownian dynamics tension propagation (BDTP) scheme for a finite chain by Ikonen et al. [J. Chem. Phys. 137, 085101 (2012); Phys. Rev. E 85, 051803 (2012)]for a semi-flexible chain. Partially supported by UCF Office of Research and Commercialization & College of Science SEED grant.

  8. Microwave processing of ceramic oxide filaments

    Energy Technology Data Exchange (ETDEWEB)

    Vogt, G.J.; Katz, J.D. [Los Alamos National Laboratory, NM (United States)

    1995-05-01

    The objective of the microwave filament processing project is to develop microwave techniques at 2.45 GHZ to manufacture continuous ceramic oxide filaments. Microwave processing uses the volumetric absorption of microwave power in oxide filament tows to drive off process solvents, to burn out organic binders, and to sinter the dried fibers to produce flexible, high-strength ceramic filaments. The technical goal is to advance filament processing technology by microwave heating more rapidly with less energy and at a lower cost than conventional processing, but with the same quality as conventional processing. The manufacturing goal is to collaborate with the 3M Company, a US manufacturer of ceramic oxide filaments, to evaluate the technology using a prototype filament system and to transfer the microwave technology to the 3M Company.

  9. Dynamics of 3D isolated thermal filaments

    CERN Document Server

    Walkden, N R; Militello, F; Omotani, J T

    2016-01-01

    Simulations have been carried out to establish how electron thermal physics, introduced in the form of a dynamic electron temperature, affects isolated filament motion and dynamics in 3D. It is found that thermal effects impact filament motion in two major ways when the filament has a significant temperature perturbation compared to its density perturbation: They lead to a strong increase in filament propagation in the bi-normal direction and a significant decrease in net radial propagation. Both effects arise from the temperature dependence of the sheath current which leads to a non-uniform floating potential, with the latter effect supplemented by faster pressure loss. The reduction in radial velocity can only occur when the filament cross-section loses angular symmetry. The behaviour is observed across different filament sizes and suggests that filaments with much larger temperature perturbations than density perturbations are more strongly confined to the near SOL region.

  10. Dynamics of 3D isolated thermal filaments

    Science.gov (United States)

    Walkden, N. R.; Easy, L.; Militello, F.; Omotani, J. T.

    2016-11-01

    Simulations have been carried out to establish how electron thermal physics, introduced in the form of a dynamic electron temperature, affects isolated filament motion and dynamics in 3D. It is found that thermal effects impact filament motion in two major ways when the pressure perturbation within the filament is supported primarily through a temperature increase as opposed to density: they lead to a strong increase in filament propagation in the bi-normal direction and a significant decrease in net radial propagation. Both effects arise from the temperature dependence of the sheath current which leads to a non-uniform floating potential, with the latter effect supplemented by faster pressure loss. The reduction in radial velocity can only occur when the filament cross-section loses angular symmetry. The behaviour is observed across different filament sizes and suggests that filaments with much larger temperature perturbations than density perturbations are more strongly confined to the near SOL region.

  11. The interaction between plasma filaments in dielectric barrier discharges and liquid covered wounds: electric fields delivered to model platelets and cells

    Science.gov (United States)

    Babaeva, Natalia Yu; Tian, Wei; Kushner, Mark J.

    2014-06-01

    The treatment of wounds by atmospheric pressure plasmas in the context of plasma medicine typically proceeds through a liquid layer covering exposed cells. The wounds and their liquid covering often have irregular shapes with electrical properties (i.e. conductivity and permittivities) that may differ not only from wound-to-wound but also for a single wound as healing proceeds. The differing shapes and electrical properties extend into the liquid within the wound that typically contains cellular materials such as blood platelets. The plasma, wound, liquid and intra-liquid cellular components represent an interacting system of mutual dependence. In this paper, we discuss the results from a computational investigation of the treatment of small, liquid-covered wounds by filamentary dielectric barrier discharges. The sizes of the wounds are of the order of the plasma filaments and the liquid within the wound, an approximation of blood serum, contains idealized blood platelets. We find that the electrical properties of a wound can have significant effects on the spreading of the plasma on its surface by virtue of the deformation of the vacuum electric fields due to the shape, the effective capacitance of the wound and the discontinuities in electrical permittivity. This in turn effects the penetration of the electric field to cells under the liquid. The orientation and permittivity of the platelets relative to the liquid determines the electric fields that may stimulate the platelets.

  12. Filament Eruptions, Jets, and Space Weather

    Science.gov (United States)

    Moore, Ronald; Sterling, Alphonse; Robe, Nick; Falconer, David; Cirtain, Jonathan

    2013-01-01

    Previously, from chromospheric H alpha and coronal X-ray movies of the Sun's polar coronal holes, it was found that nearly all coronal jets (greater than 90%) are one or the other of two roughly equally common different kinds, different in how they erupt: standard jets and blowout jets (Yamauchi et al 2004, Apl, 605, 5ll: Moore et all 2010, Apj, 720, 757). Here, from inspection of SDO/AIA He II 304 A movies of 54 polar x-ray jets observed in Hinode/XRT movies, we report, as Moore et al (2010) anticipated, that (1) most standard x-ray jets (greater than 80%) show no ejected plasma that is cool enough (T is less than or approximately 10(exp 5K) to be seen in the He II 304 A movies; (2) nearly all blownout X-ray jets (greater than 90%) show obvious ejection of such cool plasma; (3) whereas when cool plasma is ejected in standard X-ray jets, it shows no lateral expansion, the cool plasma ejected in blowout X-ray jets shows strong lateral expansion; and (4) in many blowout X-ray jets, the cool plasma ejection displays the erupting-magnetic-rope form of clasic filament eruptions and is thereby seen to be a miniature filament eruption. The XRT movies also showed most blowout X-ray jets to be larger and brighter, and hence to apparently have more energy, than most standard X-ray jets. These observations (1) confirm the dichotomy of coronal jets, (2) agree with the Shibata model for standard jets, and (3) support the conclusion of Moore et al (2010) that in blowout jets the magnetic-arch base of the jet erupts in the manner of the much larger magnetic arcades in which the core field, the field rooted along the arcade's polarity inversion line, is sheared and twisted (sigmoid), often carries a cool-plasma filament, and erupts to blowout the arcade, producing a CME. From Hinode/SOT Ca II movies of the polar limb, Sterling et al (2010, ApJ, 714, L1) found that chromospheric Type-II spicules show a dichotomy of eruption dynamics similar to that found here for the cool

  13. Simultaneous longitudinal and transverse oscillation in an active filament

    CERN Document Server

    Pant, V; Yuan, D; Banerjee, D; Srivastava, A K; Shen, Y

    2016-01-01

    We report on the co-existence of longitudinal and transverse oscillations in an active filament. On March 15$^{th}$ 2013, a M1.1 class flare was observed in the active region AR 11692. A CME was found to be associated with the flare. {The CME generated a shock wave that triggered the oscillations in a nearby filament}, situated at the south-west of the active region as observed from National Solar Observatory (NSO)\\textit{Global Oscillation Network Group}(GONG) H$\\alpha$ images. In this work we report the longitudinal oscillations in the two ends of the filament, co-existing with the transverse oscillations. We propose a scenario in which {an} incoming shock wave hits the filament obliquely and triggers both longitudinal and transverse oscillations. Using the observed parameters, we estimate the lower limit of the magnetic field strength. We use simple pendulum model with gravity as the restoring force to estimate the radius of curvature. We also calculate the mass accretion rate which causes the filament mot...

  14. The role of filament-packing dynamics in powering amoeboid cell motility

    NARCIS (Netherlands)

    Miao, L.; Vanderlinde, O.; Liu, J.; Grant, R.P.; Wouterse, A.; Shimabukuro, K.; Philipse, A.; Stewart, M.; Roberts, T.M.

    2008-01-01

    Although several models have been proposed to account for how cytoskeleton polymerization drives protrusion in cell motility, the precise mechanism remains controversial. Here, we show that, in addition to force exerted directly against the membrane by growing filaments, the way elongating filaments

  15. Magnetic diagnostic of SOL-filaments generated by type I ELMs on JET and ASDEX Upgrade

    DEFF Research Database (Denmark)

    Naulin, Volker; Vianello, N.; Schrittwieser, R.

    2011-01-01

    This contribution is focused on the magnetic signatures of type I ELM filaments. On JET a limited number of high time resolution magnetic coils were used to derive essential ELM filament parameters. The method uses forward modelling and simultaneous fitting of magnetic pickup coil signals to a si...

  16. Shape Selection of Surface-Bound Helical Filaments: Biopolymers on Curved Membranes.

    Science.gov (United States)

    Quint, David A; Gopinathan, Ajay; Grason, Gregory M

    2016-10-04

    Motivated to understand the behavior of biological filaments interacting with membranes of various types, we employ a theoretical model for the shape and thermodynamics of intrinsically helical filaments bound to curved membranes. We show that filament-surface interactions lead to a host of nonuniform shape equilibria, in which filaments progressively unwind from their native twist with increasing surface interaction and surface curvature, ultimately adopting uniform-contact curved shapes. The latter effect is due to nonlinear coupling between elastic twist and bending of filaments on anisotropically curved surfaces such as the cylindrical surfaces considered here. Via a combination of numerical solutions and asymptotic analysis of shape equilibria, we show that filament conformations are critically sensitive to the surface curvature in both the strong- and weak-binding limits. These results suggest that local structure of membrane-bound chiral filaments is generically sensitive to the curvature radius of the surface to which it is bound, even when that radius is much larger than the filament's intrinsic pitch. Typical values of elastic parameters and interaction energies for several prokaryotic and eukaryotic filaments indicate that biopolymers are inherently very sensitive to the coupling between twist, interactions, and geometry and that this could be exploited for regulation of a variety of processes such as the targeted exertion of forces, signaling, and self-assembly in response to geometric cues including the local mean and Gaussian curvatures. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. Formation and Transport of Atomic Hydrogen in Hot-Filament Chemical Vapor Deposition Reactors

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    In this paper we focus on diamond film hot-filament chemical vapor deposition reactors where the only reactant ishydrogen so as to study the formation and transport of hydrogen atoms. Analysis of dimensionless numbers forheat and mass transfer reveals that thermal conduction and diffusion are the dominant mechanisms for gas-phaseheat and mass transfer, respectively. A simplified model has been established to simulate gas-phase temperature andH concentration distributions between the filament and the substrate. Examination of the relative importance ofhomogeneous and heterogeneous production of H atoms indicates that filament-surface decomposition of molecularhydrogen is the dominant source of H and gas-phase reaction plays a negligible role. The filament-surface dissociationrates of H2 for various filament temperatures were calculated to match H-atom concentrations observed in the liter-ature or derived from power consumption by filaments. Arrhenius plots of the filament-surface hydrogen dissociationrates suggest that dissociation of H2 at refractory filament surface is a catalytic process, which has a rather lowereffective activation energy than homogeneous thermal dissociation. Atomic hydrogen, acting as an important heattransfer medium to heat the substrate, can freely diffuse from the filament to the substrate without recombination.

  18. Force-induced dynamical properties of multiple cytoskeletal filaments are distinct from that of single filaments

    CERN Document Server

    Das, Dipjyoti; Padinhateeri, Ranjith

    2014-01-01

    How cytoskeletal filaments collectively undergo growth and shrinkage is an intriguing question. Collective properties of multiple bio-filaments (actin or microtubules) undergoing hydrolysis, have not been studied extensively earlier, within simple theoretical frameworks. In this paper, we show that collective properties of multiple filaments under force are very distinct from the properties of a single filament under similar conditions -- these distinctions manifest as follows: (i) the collapse time during collective catastrophe for a multifilament system is much larger than that of a single filament with the same average length, (ii) force-dependence of the cap-size distribution of multiple filaments are quantitatively different from that of single filament, (iii) the diffusion constant associated with the system length fluctuations is distinct for multiple filaments, (iv) switching dynamics of multiple filaments between capped and uncapped states and the fluctuations therein are also distinct. We build a un...

  19. Filament Discharge Phenomena in Fingerprint Acquisition by Dielectric Barrier Discharge

    Institute of Scientific and Technical Information of China (English)

    WENG Ming; XU Weijun; LIU Qiang

    2007-01-01

    In this paper, the dielectric barrier discharge fingerprint acquisition technique is introduced. The filament discharge phenomena were observed in the process of fingerprint acquisition. The filament discharge reduced the quality of fingerprint images. Obviously, it was necessary to eliminate streamer discharges in order to get good fingerprint images. The streamer discharge was considered to be the cause of the filament discharge in the experiment. The relationship between the critical electric field and the discharge gap was calculated with the Raether's model of streamer discharge. The calculated results and our experiment proved that it would be difficult for the streamer discharge to occur when the discharge gap was narrow. With a narrow discharge gap, the discharge was homogeneous, and the fingerprint images were clear and large in area. The images obtained in the experiment are very suitable for fingerprint identification as they contain more information.

  20. Intermediate filament transcription in astrocytes is repressed by proteasome inhibition

    Science.gov (United States)

    Middeldorp, Jinte; Kamphuis, Willem; Sluijs, Jacqueline A.; Achoui, Dalila; Leenaars, Cathalijn H. C.; Feenstra, Matthijs G. P.; van Tijn, Paula; Fischer, David F.; Berkers, Celia; Ovaa, Huib; Quinlan, Roy A.; Hol, Elly M.

    2009-01-01

    Increased expression of the astrocytic intermediate filament protein glial fibrillary acidic protein (GFAP) is a characteristic of astrogliosis. This process occurs in the brain during aging and neurodegeneration and coincides with impairment of the ubiquitin proteasome system. Inhibition of the proteasome impairs protein degradation; therefore, we hypothesized that the increase in GFAP may be the result of impaired proteasomal activity in astrocytes. We investigated the effect of proteasome inhibitors on GFAP expression and other intermediate filament proteins in human astrocytoma cells and in a rat brain model for astrogliosis. Extensive quantitative RT-PCR, immunocytochemistry, and Western blot analysis resulted unexpectedly in a strong decrease of GFAP mRNA to Hol, E. M. Intermediate filament transcription in astrocytes is repressed by proteasome inhibition. PMID:19332645

  1. Science-based bioprocess design for filamentous fungi.

    Science.gov (United States)

    Posch, Andreas E; Herwig, Christoph; Spadiut, Oliver

    2013-01-01

    Industrial bioprocesses are commonly based on empiricism rather than scientific process understanding. In this review, we summarize current strategies for science-based bioprocess design and control for filamentous fungi aiming at reducing development times and increasing process economics. We discuss recent developments and trends regarding three crucial aspects throughout the bioprocess life cycle of filamentous fungi, namely (i) strain and inoculum characterization, (ii) morphology, and (iii) rheology, as well as their effects on process performance. Complex interconnections between strain, inoculum, morphology, rheology, and process design are outlined and discussed. Only combining different hard type sensors with soft sensor technology and the development of simplified mechanistic models can enable science-based bioprocess design for filamentous fungi. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Edge localized mode rotation and the nonlinear dynamics of filaments

    Energy Technology Data Exchange (ETDEWEB)

    Morales, J. A.; Bécoulet, M.; Garbet, X.; Dif-Pradalier, G.; Huijsmans, G. T. A.; Fil, A.; Nardon, E.; Passeron, C.; Latu, G. [CEA, IRFM, 13108 St. Paul-Lez-Durance (France); Orain, F.; Hoelzl, M. [Max Planck Institute for Plasma Physics, Boltzmannstr. 2, 85748 Garching (Germany); Pamela, S. [CCFE, Culham Science Centre, Abingdon, Oxon OX14 3DB (United Kingdom); Cahyna, P. [Institute of Plasma Physics ASCR, Za Slovankou 1782/3, 182 00 Prague 8 (Czech Republic)

    2016-04-15

    Edge Localized Modes (ELMs) rotating precursors were reported few milliseconds before an ELM crash in several tokamak experiments. Also, the reversal of the filaments rotation at the ELM crash is commonly observed. In this article, we present a mathematical model that reproduces the rotation of the ELM precursors as well as the reversal of the filaments rotation at the ELM crash. Linear ballooning theory is used to establish a formula estimating the rotation velocity of ELM precursors. The linear study together with nonlinear magnetohydrodynamic simulations give an explanation to the rotations observed experimentally. Unstable ballooning modes, localized at the pedestal, grow and rotate in the electron diamagnetic direction in the laboratory reference frame. Approaching the ELM crash, this rotation decreases corresponding to the moment when the magnetic reconnection occurs. During the highly nonlinear ELM crash, the ELM filaments are cut from the main plasma due to the strong sheared mean flow that is nonlinearly generated via the Maxwell stress tensor.

  3. Edge localized mode rotation and the nonlinear dynamics of filaments

    Science.gov (United States)

    Morales, J. A.; Bécoulet, M.; Garbet, X.; Orain, F.; Dif-Pradalier, G.; Hoelzl, M.; Pamela, S.; Huijsmans, G. T. A.; Cahyna, P.; Fil, A.; Nardon, E.; Passeron, C.; Latu, G.

    2016-04-01

    Edge Localized Modes (ELMs) rotating precursors were reported few milliseconds before an ELM crash in several tokamak experiments. Also, the reversal of the filaments rotation at the ELM crash is commonly observed. In this article, we present a mathematical model that reproduces the rotation of the ELM precursors as well as the reversal of the filaments rotation at the ELM crash. Linear ballooning theory is used to establish a formula estimating the rotation velocity of ELM precursors. The linear study together with nonlinear magnetohydrodynamic simulations give an explanation to the rotations observed experimentally. Unstable ballooning modes, localized at the pedestal, grow and rotate in the electron diamagnetic direction in the laboratory reference frame. Approaching the ELM crash, this rotation decreases corresponding to the moment when the magnetic reconnection occurs. During the highly nonlinear ELM crash, the ELM filaments are cut from the main plasma due to the strong sheared mean flow that is nonlinearly generated via the Maxwell stress tensor.

  4. Dynamic Star Formation in the Massive DR21 Filament

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, N.; /Saclay; Csengeri, T.; /Saclay; Bontemps, S.; /OASU, Floirac; Motte, F.; /Saclay; Simon, R.; /Cologne U.; Hennebelle, P.; /Paris Observ.; Federrath, C.; /ZAH, Heidelberg; Klessen, R.; /ZAH, Heidelberg /KIPAC, Menlo Park

    2010-08-25

    The formation of massive stars is a highly complex process in which it is unclear whether the star-forming gas is in global gravitational collapse or an equilibrium state supported by turbulence and/or magnetic fields. By studying one of the most massive and dense star-forming regions in the Galaxy at a distance of less than 3 kpc, i.e. the filament containing the well-known sources DR21 and DR21(OH), we attempt to obtain observational evidence to help us to discriminate between these two views. We use molecular line data from our {sup 13}CO 1 {yields} 0, CS 2 {yields} 1, and N{sub 2}H{sup +} 1 {yields} 0 survey of the Cygnus X region obtained with the FCRAO and CO, CS, HCO{sup +}, N{sub 2}H{sup +}, and H{sub 2}CO data obtained with the IRAM 30m telescope. We observe a complex velocity field and velocity dispersion in the DR21 filament in which regions of the highest column-density, i.e., dense cores, have a lower velocity dispersion than the surrounding gas and velocity gradients that are not (only) due to rotation. Infall signatures in optically thick line profiles of HCO{sup +} and {sup 12}CO are observed along and across the whole DR21 filament. By modelling the observed spectra, we obtain a typical infall speed of {approx}0.6 km s{sup -1} and mass accretion rates of the order of a few 10{sup -3} M{sub {circle_dot}} yr{sup -1} for the two main clumps constituting the filament. These massive clumps (4900 and 3300 M{sub {circle_dot}} at densities of around 10{sup 5} cm{sup -3} within 1 pc diameter) are both gravitationally contracting. The more massive of the clumps, DR21(OH), is connected to a sub-filament, apparently 'falling' onto the clump. This filament runs parallel to the magnetic field. Conclusions. All observed kinematic features in the DR21 filament (velocity field, velocity dispersion, and infall), its filamentary morphology, and the existence of (a) sub-filament(s) can be explained if the DR21 filament was formed by the convergence of flows

  5. Characterising Radio Emissions in Cosmic Filaments

    Science.gov (United States)

    Miller, R. O.

    2014-02-01

    A growing number of radio studies probe galaxy clusters into the low-power regime in which star formation is the dominant source of radio emission. However, at the time of writing no comparably deep observations have focused exclusively on the radio populations of cosmic filaments. This thesis describes the ATCA 2.1 GHz observations and subsequent analysis of two such regions - labelled Zone 1 (between clusters A3158 and A3125/A3128) and Zone 2 (between A3135 and A3145) - in the Horologium-Reticulum Supercluster (HRS). Source count profiles of both populations are discussed and a radio luminosity function for Zone 1 is generated. While the source counts of Zone 2 appear to be consistent with expected values, Zone 1 exhibits an excess of counts across a wide flux range (1 mJy< S_1.4 < 200 mJy). An excess in radio activity at the lower extent of this range (log P_1.4 < 22.5; within the SF-dominated regime) is also suggested by the radio luminosity function for that region, and brief colour analysis suggests that such an excess is indeed predominantly associated with a starforming population. The differences between the two filamentary zones is attributed to cosmic variation. The regions are both small (~ 1 degree square), and are significantly separated in the HRS. Further radio observations of filaments are required and the results combined into a larger sample size in order to arrive at a generalised model filamentary population.

  6. The Golgi apparatus: insights from filamentous fungi.

    Science.gov (United States)

    Pantazopoulou, Areti

    2016-01-01

    Cargo passage through the Golgi, albeit an undoubtedly essential cellular function, is a mechanistically unresolved and much debated process. Although the main molecular players are conserved, diversification of the Golgi among different eukaryotic lineages is providing us with tools to resolve standing controversies. During the past decade the Golgi apparatus of model filamentous fungi, mainly Aspergillus nidulans, has been intensively studied. Here an overview of the most important findings in the field is provided. Golgi architecture and dynamics, as well as the novel cell biology tools that were developed in filamentous fungi in these studies, are addressed. An emphasis is placed on the central role the Golgi has as a crossroads in the endocytic and secretory-traffic pathways in hyphae. Finally the major advances that the A. nidulans Golgi biology has yielded so far regarding our understanding of key Golgi regulators, such as the Rab GTPases RabC(Rab6) and RabE(Rab11), the oligomeric transport protein particle, TRAPPII, and the Golgi guanine nucleotide exchange factors of Arf1, GeaA(GBF1/Gea1) and HypB(BIG/Sec7), are highlighted.

  7. Zebrafish cardiac muscle thick filaments: isolation technique and three-dimensional structure.

    Science.gov (United States)

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

    2014-04-15

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

  8. Upwelling filaments are cold, typically narrow features in surface ...

    African Journals Online (AJOL)

    spamer

    strong offshore flows and often terminate in eddy-like structures ... model initiated with observed velocity profiles. Mc-. Creary et al. ... These are a forced equatorward flow at the surface ...... 1991 — Dynamical simulations of filament formation and evolution in ... MOOERS, C. N. K. and A. R. ROBINSON 1984 — Turbulent jets.

  9. Effect of superconductor filament magnetization on the field errors

    CERN Document Server

    Wolf, R

    1999-01-01

    One of the main source of field errors in a superconducting magnet is the magnetization M of the superconducting filaments. Screening currents, of persistent nature, are induced by any. field change during operation of the magnet. This chapter describes the models for the calculation of these effects and the parameters to be defined in ROXIE. (3 refs).

  10. Three-dimensional simulations of viscoelastic instability in polymeric filaments

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Koblitz; Hassager, Ole

    1999-01-01

    The three-dimensional Langrangian integral method is used to simulate the elastic end-plate instability that occurs in the rapid extension of some polymeric filaments between parallel plates. It is demonstrated that the upper convected Maxwell model describes the essential features of the instabi...

  11. Mechanical behaviors of multi-filament twist superconducting strand under tensile and cyclic loading

    Science.gov (United States)

    Wang, Xu; Li, Yingxu; Gao, Yuanwen

    2016-01-01

    The superconducting strand, serving as the basic unit cell of the cable-in-conduit-conductors (CICCs), is a typical multi-filament twist composite which is always subjected to a cyclic loading under the operating condition. Meanwhile, the superconducting material Nb3Sn in the strand is sensitive to strain frequently relating to the performance degradation of the superconductivity. Therefore, a comprehensive study on the mechanical behavior of the strand helps understanding the superconducting performance of the strained Nb3Sn strands. To address this issue, taking the LMI (internal tin) strand as an example, a three-dimensional structural finite element model, named as the Multi-filament twist model, of the strand with the real configuration of the LMI strand is built to study the influences of the plasticity of the component materials, the twist of the filament bundle, the initial thermal residual stress and the breakage and its evolution of the filaments on the mechanical behaviors of the strand. The effective properties of superconducting filament bundle with random filament breakage and its evolution versus strain are obtained based on the damage theory of fiber-reinforced composite materials proposed by Curtin and Zhou. From the calculation results of this model, we find that the occurrence of the hysteresis loop in the cyclic loading curve is determined by the reverse yielding of the elastic-plastic materials in the strand. Both the initial thermal residual stress in the strand and the pitch length of the filaments have significant impacts on the axial and hysteretic behaviors of the strand. The damage of the filaments also affects the axial mechanical behavior of the strand remarkably at large axial strain. The critical current of the strand is calculated by the scaling law with the results of the Multi-filament twist model. The predicted results of the Multi-filament twist model show an acceptable agreement with the experiment.

  12. On the relation between non-exponential Scrape Off Layer profiles and the dynamics of filaments

    CERN Document Server

    Militello, F

    2016-01-01

    A theoretical framework is developed to clarify the relation between the profiles of density and temperature in the Scrape Off Layer (SOL) with the fluctuations (filaments) that generate them. The framework is based on the dynamics of independent filaments and on their statistical behaviour and can be used to rigorously understand the mechanisms that lead to the non-exponential nature of the radial SOL profiles as well as the increase of the relative fluctuation amplitude in the far SOL. Several models for the dynamics of the filaments, which can be applied to the framework, are derived and discussed for the purpose of identifying how different assumptions lead to the emergence of features in the profiles. It is found that multiple alternative models can explain the observations, thus motivating more stringent and focused experimental analysis. In particular, radially accelerating filaments, less efficient parallel exhaust and also a statistical distribution of the velocity of the filaments can all contribute...

  13. SU-E-T-134: Patient Specific Quality Assurance of RapidArc Pre Treatment Plans Using Semiflex 0.125 Cc Ionization Chamber.

    Science.gov (United States)

    Kumar, Sa Syam; Prabakar, S; Sriram, P; Vivekanandan, N

    2012-06-01

    To evaluate the Patient specific pre-treatment quality assurance for hundred RapidArc plans using semiflex (0.125cc) ionization chambers. Absolute point dose were measured for head and neck, thorax and abdomen cases using semiflex (0.125 cc) ionization chamber. Verification plan was created for each treatment plan in eclipse 8.6 treatment planning system with the semiflex ionization chamber and the octavius phantom. Measurements were performed on a Varian Clinac2100C/D linear accelerator equipped with a millennium 120 leaf collimator. All the results were compared with the fluence measurements using 2D Seven29 ion chamber array combined with octavius phantom. Positive absolute mean dose variation of 0.56 % was observed with thorax cases with a standard deviation (SD) of ± 1.13 between the plans with a range of -1.78% to 2.70%. Negative percentage dose errors were found with head and neck and abdomen cases, with a mean variation of -0.43 % (SD ± 1.50), (range -3.25 % to 2.85 %) and -0.35 % (SD ± 1.48), (range -3.10 % to 2.65 %) for head and neck and abdomen cases respectively. Relative dose measurements with 2D array agreed well with the TPS calculate for all the cases. The maximum percentage value failed in gamma analysis was found to be 4.95, 4.75, and 4.88 for head and neck, thorax, and abdomen cases respectively. In all the cases analysed the percentage dose points failed the gamma criteria was less than 5%. On the basis of the studies performed it can be concluded that the semiflex ionization chamber having a volume of 0.125cc can be used efficiently for measuring the pre-treatment quality assurance of RapidArc plans for all the sites. The results provide an overall accuracy when compared to fluence measurement done using 2D array seven29. © 2012 American Association of Physicists in Medicine.

  14. Muscle myosin filaments: cores, crowns and couplings.

    Science.gov (United States)

    Squire, John M

    2009-09-01

    Myosin filaments in muscle, carrying the ATPase myosin heads that interact with actin filaments to produce force and movement, come in multiple varieties depending on species and functional need, but most are based on a common structural theme. The now successful journeys to solve the ultrastructures of many of these myosin filaments, at least at modest resolution, have not been without their false starts and erroneous sidetracks, but the picture now emerging is of both diversity in the rotational symmetries of different filaments and a degree of commonality in the way the myosin heads are organised in resting muscle. Some of the remaining differences may be associated with how the muscle is regulated. Several proteins in cardiac muscle myosin filaments can carry mutations associated with heart disease, so the elucidation of myosin filament structure to understand the effects of these mutations has a clear and topical clinical relevance.

  15. Stereoscopic Analysis of 19 May and 31 Aug 2007 Filament Eruptions

    Science.gov (United States)

    Liewer, Paulett; DeJong, E. M.; Hall, J. R.

    2008-01-01

    The presentation outline includes results from stereoscopic analysis of SECCHI/EUVI data for 19 May 2007 filament eruption, including the determined 3D trajectory of erupting filament, strong evidence for reconnection below erupting filament as consistent with standard model, and comparison of EUVI and H-alpha images during eruption; and results from stereoscopic analytic of 21 August 2007 filament eruption. Slide topics include standard model of filament eruption; 2007 May 19 STEREO A/SECCHI/EUVI 195 and 304 A: CME signatures and filament eruption, 3D reconstruction of erupting prominence; filament's relation to coronal magnetic fields; 3d reconstructions of filament eruption; height-time plot of eruption from 3D reconstructions; detailed pre-eruptions comparison of H-alpha and EUVI 304 at 12:42 UT; comparisons during the eruption; STEREO prominence and CME August 31, 2007; reconstructions of prominence and leading edges of both dark cavity and CME; and 3D reconstructions of prominence and leading edges.

  16. Titin Isoform Size is Not Correlated with Thin Filament Length in Rat Skeletal Muscle

    Directory of Open Access Journals (Sweden)

    Marion Lewis Greaser

    2014-02-01

    Full Text Available The mechanisms controlling thin filament length in muscle remain controversial. It was recently reported that thin filament length was related to titin size, and that the latter might be involved in thin filament length determination. Titin plays several crucial roles in the sarcomere, but its function as it pertains to the thin filament has not been explored. We tested this relationship using several muscles from wild type rats and from a mutant rat model which results in increased titin size. Myofibrils were isolated from skeletal muscles (extensor digitorum longus, external oblique, gastrocnemius, longissimus dorsi, psoas major, and tibialis anterior using both adult wild type (WT and homozygous mutant (HM rats. Phalloidin and antibodies against tropomodulin-4 and nebulin’s N-terminus were used to determine thin filament length. The WT rats studied express skeletal muscle titin sizes ranging from 3.2 to 3.7 MDa, while the HM rats express a giant titin isoform sized at 3.7 MDa. No differences in phalloidin-based thin filament length, nebulin N terminus distances from the Z line, or tropomodulin distances from the Z line were observed across genotypes. The data indicates that, although titin performs many sarcomeric functions, its correlation with thin filament length and structure could not be demonstrated in the rat. Current models of thin filament assembly are inadequate to explain the phalloidin, nebulin N terminus, and tropomodulin staining patterns in the myofibril.

  17. Propulsion by passive filaments and active flagella near boundaries

    CERN Document Server

    Evans, Arthur A; 10.1103/PhysRevE.82.041915

    2010-01-01

    Confinement and wall effects are known to affect the kinematics and propulsive characteristics of swimming microorganisms. When a solid body is dragged through a viscous fluid at constant velocity, the presence of a wall increases fluid drag, and thus the net force required to maintain speed has to increase. In contrast, recent optical trapping experiments have revealed that the propulsive force generated by human spermatozoa is decreased by the presence of boundaries. Here, we use a series of simple models to analytically elucidate the propulsive effects of a solid boundary on passively actuated filaments and model flagella. For passive flexible filaments actuated periodically at one end, the presence of the wall is shown to increase the propulsive forces generated by the filaments in the case of displacement-driven actuation, while it decreases the force in the case of force-driven actuation. In the case of active filaments as models for eukaryotic flagella, we demonstrate that the manner in which a solid w...

  18. Large-scale filaments-newtonian vs. modified dynamics

    CERN Document Server

    Milgrom, M

    1996-01-01

    Eisenstein Loeb and Turner (ELT) have recently proposed a method for estimating the dynamical masses of large-scale filaments, whereby the filament is modeled by an axisymmetric, isothermal cylinder, for which ELT derive a global relation between the (constant) velocity dispersion and the total line density. We first show that the model assumptions of ELT can be relaxed materially: an exact relation between the velocity and line density is derived for any cylinder (not necessarily axisymmetric), with an arbitrary constituent distribution function (so isothermality need not be assumed). We then consider the same problem in the context of the modified dynamics (MOND). After a brief comparison between scaling properties in the two theories, we study idealized MOND model filaments. A preliminary application to the segment of the Perseus-Pisces filament treated by ELT, gives MOND M/L estimates of order 10 s.u., compared with the Newtonian value of about 450, which ELT find. In spite of the large uncertainties stil...

  19. Filamentous Biological Entities Obtained from the Stratosphere

    Science.gov (United States)

    Wainwright, Milton; Rose, Christopher E.; Baker, Alexander J.; Wickramasinghe, N. Chandra

    2013-03-01

    We previously reported the presence of large, non-filamentous, biological entities including a diatom fragment in the stratosphere at heights of between 22-27km. Here we report clear evidence for the presence of filamentous entities associated with a relatively large particle mass collected from the stratosphere. Although viable fungi have previously been isolated from the stratosphere, this is the first report of a filamentous microorganism being observed in situ on a stratospheric particle mass.

  20. Solubilization and fractionation of paired helical filaments.

    Science.gov (United States)

    González, P J; Correas, I; Avila, J

    1992-09-01

    Paired helical filaments isolated from brains of two different patients with Alzheimer's disease were extensively treated with the ionic detergent, sodium dodecyl sulphate. Filaments were solubilized at different extents, depending on the brain examined, thus suggesting the existence of two types of paired helical filaments: sodium dodecyl sulphate-soluble and insoluble filaments. In the first case, the number of structures resembling paired helical filaments greatly decreased after the detergent treatment, as observed by electron microscopy. Simultaneously, a decrease in the amount of sedimentable protein was also observed upon centrifugation of the sodium dodecyl sulfate-treated paired helical filaments. A sodium dodecyl sulphate-soluble fraction was isolated as a supernatant after low-speed centrifugation of the sodium dodecyl sulphate-treated paired helical filaments. The addition of the non-ionic detergent Nonidet-P40 to this fraction resulted in the formation of paired helical filament-like structures. When the sodium dodecyl sulphate-soluble fraction was further fractionated by high-speed centrifugation, three subfractions were observed: a supernatant, a pellet and a thin layer between these two subfractions. No paired helical filaments were observed in any of these subfractions, even after addition of Nonidet P-40. However, when they were mixed back together, the treatment with Nonidet P-40 resulted in the visualization of paired helical filament-like structures. These results suggest that at least two different components are needed for the reconstitution of paired helical filaments as determined by electron microscopy. The method described here may allow the study of the components involved in the formation of paired helical filaments and the identification of possible factors capable of blocking this process.

  1. Equilibrium shapes of twisted magnetic filaments

    Energy Technology Data Exchange (ETDEWEB)

    Belovs, Mihails; Cirulis, Teodors; Cebers, Andrejs [University of Latvia, Zellu 8, LV-1002 (Latvia)], E-mail: aceb@tesla.sal.lv

    2009-06-12

    It is shown that ferromagnetic filaments with free and unclamped ends undergo buckling instabilities under the action of twist. Solutions of nonlinear equations describing the buckled shapes are found, and it is shown that the transition to the buckled shape is subcritical if the magnetization is parallel to the field and supercritical when the magnetization of the straight filament is opposite to the external field. Solutions with the localized curvature distribution are found in the case of long filaments. The class of solutions corresponding to helices is described, and the behavior of coiled ferromagnetic and superparamagnetic filaments is compared.

  2. Probing the Physical Structures of Dense Filaments

    Science.gov (United States)

    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.

  3. Deep coronal hole associated with quiescent filament

    Science.gov (United States)

    Kesumaningrum, Rasdewita; Herdiwidjaya, Dhani

    2014-03-01

    We present a study of the morphology of quiescent filament observed by H-alpha Solar Telescope at Bosscha Observatory in association with coronal hole observed by Atmospheric Imaging Assembly (AIA) instrument in 193 Å from Solar Dynamics Observatory. H-alpha images were processed by imaging softwares, namely Iris 5.59 and ImageJ, to enhance the signal to noise ratio and to identify the filament features associated with coronal hole. For images observed on October 12, 2011, November 14, 2011 and January 2, 2012, we identified distinct features of coronal holes above the quiescent filaments. This associated coronal holes have filament-like morphology with a thick long thread as it's `spine', defined as Deep Coronal Hole. Because of strong magnetic field of sunspot, these filaments and coronal holes emerged far from active region and lasted for several days. It is interesting as for segmented filament, deep coronal holes above the filaments lasted for a quite long period of time and merged. This association between filament and deep coronal hole can be explained by filament magnetic loop.

  4. Electro-mechanical behaviors of composite superconducting strand with filament breakage

    Science.gov (United States)

    Wang, Xu; Gao, Yuanwen; Zhou, Youhe

    2016-10-01

    The bending behaviors of superconducting strand with typical multi-filament twist configuration are investigated based on a three-dimensional finite element method (FEM) model, named as the Multi-filament twist model, of the strand. In this 3D FEM model, the impacts of initial thermal residual stress, filament-breakage and its evaluation are taken into accounts. The mechanical responses of the strand under bending load are studied with the factors taken into consideration one by one. The distribution of the damage of the filaments and its evolution and the movement of the neutral axis caused by it are studied and displayed in detail. Besides, taking the advantages of the Multi-filament twist model, the normalized critical current of the strand under bending load is also calculated based on the invariant temperature and field strain functions. In addition, the non-negligible influences of the pitch length of the filaments on both the mechanical behaviors and the normalized critical current are discussed. The stress-strain characteristics of the strand under tensile load and the normalized critical current of it under axial and bending loads resulting from the Multi-filament twist model show good agreement with the experimental data.

  5. Filamentation with nonlinear Bessel vortices.

    Science.gov (United States)

    Jukna, V; Milián, C; Xie, C; Itina, T; Dudley, J; Courvoisier, F; Couairon, A

    2014-10-20

    We present a new type of ring-shaped filaments featured by stationary nonlinear high-order Bessel solutions to the laser beam propagation equation. Two different regimes are identified by direct numerical simulations of the nonlinear propagation of axicon focused Gaussian beams carrying helicity in a Kerr medium with multiphoton absorption: the stable nonlinear propagation regime corresponds to a slow beam reshaping into one of the stationary nonlinear high-order Bessel solutions, called nonlinear Bessel vortices. The region of existence of nonlinear Bessel vortices is found semi-analytically. The influence of the Kerr nonlinearity and nonlinear losses on the beam shape is presented. Direct numerical simulations highlight the role of attractors played by nonlinear Bessel vortices in the stable propagation regime. Large input powers or small cone angles lead to the unstable propagation regime where nonlinear Bessel vortices break up into an helical multiple filament pattern or a more irregular structure. Nonlinear Bessel vortices are shown to be sufficiently intense to generate a ring-shaped filamentary ionized channel in the medium which is foreseen as opening the way to novel applications in laser material processing of transparent dielectrics.

  6. Filament poisoning at typical carbon nanotube deposition conditions by hot-filament CVD

    CSIR Research Space (South Africa)

    Oliphant, CJ

    2009-05-01

    Full Text Available This paper reports on the poisoning of tungsten filaments during the hot-filament chemical vapour deposition process at typical carbon nanotube (CNT) deposition conditions and filament temperatures ranging from 1400 to 2000 °C. The morphological...

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

    Science.gov (United States)

    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.

  8. Stimulated electromagnetic terahertz emissions (SEE) from laser-induced plasma filaments

    Science.gov (United States)

    Isham, Brett; Kunhardt, Erich

    2016-07-01

    Advances in terawatt laser technology have made it possible to ionize the troposphere in long (centimeters to kilometers), narrow (less than 1 mm), wire-like plasma filaments. These filaments emit high-power stimulated electromagnetic emissions (SEE) at terahertz (submillimeter) frequencies, a frontier in the electromagnetic spectrum lying between the microwave and far infrared bands. Using an accepted model for the plasma oscillations in the filament and a thin-wire approximation, we have calculated the current density and the resulting pattern of terahertz radiation emitted by the filament. The conical shape and opening angle of the calculated radiation pattern match those of recent measurements. Future work could include measurements of both the radiation pattern and of the frequency spectrum, for comparison with detailed calculations of filament plasma processes. Potential applications include high-resolution imaging and remote spectroscopic identification of chemical substances.

  9. Radial interchange motions of plasma filaments

    DEFF Research Database (Denmark)

    Garcia, O.E.; Bian, N.H.; Fundamenski, W.

    2006-01-01

    Radial convection of isolated filamentary structures due to interchange motions in magnetized plasmas is investigated. Following a basic discussion of vorticity generation, ballooning, and the role of sheaths, a two-field interchange model is studied by means of numerical simulations...... on a biperiodic domain perpendicular to the magnetic field. It is demonstrated that a blob-like plasma structure develops dipolar vorticity and electrostatic potential fields, resulting in rapid radial acceleration and formation of a steep front and a trailing wake. While the dynamical evolution strongly depends...... as the acoustic speed times the square root of the structure size relative to the length scale of the magnetic field. The plasma filament eventually decelerates due to mixing and collisional dissipation. Finally, the role of sheath dissipation is investigated. When included in the simulations, it significantly...

  10. Angle-resolved multioctave supercontinua from mid-infrared laser filaments.

    Science.gov (United States)

    Mitrofanov, A V; Voronin, A A; Sidorov-Biryukov, D A; Mitryukovsky, S I; Rozhko, M V; Pugžlys, A; Fedotov, A B; Panchenko, V Ya; Baltuška, A; Zheltikov, A M

    2016-08-01

    Angle-resolved spectral analysis of a multioctave high-energy supercontinuum output of mid-infrared laser filaments is shown to provide a powerful tool for understanding intricate physical scenarios behind laser-induced filamentation in the mid-infrared. The ellipticity of the mid-infrared driver beam breaks the axial symmetry of filamentation dynamics, offering a probe for a truly (3+1)-dimensional spatiotemporal evolution of mid-IR pulses in the filamentation regime. With optical harmonics up to the 15th order contributing to supercontinuum generation in such filaments alongside Kerr-type and ionization-induced nonlinearities, the output supercontinuum spectra span over five octaves from the mid-ultraviolet deep into the mid-infrared. Full (3+1)-dimensional field evolution analysis is needed for an adequate understanding of this regime of laser filamentation. Supercomputer simulations implementing such analysis articulate the critical importance of angle-resolved measurements for both descriptive and predictive power of filamentation modeling. Strong enhancement of ionization-induced blueshift is shown to offer new approaches in filamentation-assisted pulse compression, enabling the generation of high-power few- and single-cycle pulses in the mid-infrared.

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

    Science.gov (United States)

    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.

  12. A Statistical Study of Solar Filament Eruptions

    Science.gov (United States)

    Schanche, Nicole; Aggarwal, Ashna; Reeves, Kathy; Kempton, Dustin James; Angryk, Rafal

    2016-05-01

    Solar filaments are cool, dark channels of partially-ionized plasma that lie above the chromosphere. Their structure follows the neutral line between local regions of opposite magnetic polarity. Previous research (e.g. Schmieder et al. 2013, McCauley et al. 2015) has shown a positive correlation (70-80%) between the occurrence of filament eruptions and coronal mass ejections (CME’s). In this study, we attempt to use properties of the filament in order to predict whether or not a given filament will erupt. This prediction would help to better predict the occurrence of an oncoming CME. To track the evolution of a filament over time, a spatio-temporal algorithm that groups separate filament instances from the Heliophysics Event Knowledgebase (HEK) into filament tracks was developed. Filament features from the HEK metadata, such as length, chirality, and tilt are then combined with other physical features, such as the overlying decay index for two sets of filaments tracks - those that erupt and those that remain bound. Using statistical methods such as the Kolmogrov-Smirnov test and a Random Forest Classifier, we determine the effectiveness of the combined features in prediction. We conclude that there is significant overlap between the properties of filaments that erupt and those that do not, leading to predictions only ~5-10% above chance. However, the changes in features, such as a change in the filament's length over time, were determined to have the highest predictive power. We discuss the possible physical connections with the change in these features."This project has been supported by funding from the Division of Advanced Cyberinfrastructure within the Directorate for Computer and Information Science and Engineering, the Division of Astronomical Sciences within the Directorate for Mathematical and Physical Sciences, and the Division of Atmospheric and Geospace Sciences within the Directorate for Geosciences, under NSF award #1443061.”

  13. Spectral stability of Alfven filament configurations

    NARCIS (Netherlands)

    Bergmans, J.; Kuvshinov, B. N.; Lakhin, V. P.; Schep, T. J.

    2000-01-01

    The two-fluid plasma equations that describe nonlinear Alfven perturbations have singular solutions in the form of current-vortex filaments. These filaments are analogous to point vortices in ideal hydrodynamics and geostrophic fluids. In this work the spectral (linear) stability of current-vortex f

  14. Radial interchange motions of plasma filaments

    DEFF Research Database (Denmark)

    Garcia, O.E.; Bian, N.H.; Fundamenski, W.

    2006-01-01

    reduces the radial velocity of isolated filaments. The results are discussed in the context of convective transport in scrape-off layer plasmas, comprising both blob-like structures in low confinement modes and edge localized mode filaments in unstable high confinement regimes. (c) 2006 American Institute...

  15. Elasticity of flexible and semiflexible polymers with extensible bonds in the Gibbs and Helmholtz ensembles.

    Science.gov (United States)

    Manca, Fabio; Giordano, Stefano; Palla, Pier Luca; Zucca, Rinaldo; Cleri, Fabrizio; Colombo, Luciano

    2012-04-21

    Stretching experiments on single molecules of arbitrary length opened the way for studying the statistical mechanics of small systems. In many cases in which the thermodynamic limit is not satisfied, different macroscopic boundary conditions, corresponding to different statistical mechanics ensembles, yield different force-displacement curves. We formulate analytical expressions and develop Monte Carlo simulations to quantitatively evaluate the difference between the Helmholtz and the Gibbs ensembles for a wide range of polymer models of biological relevance. We consider generalizations of the freely jointed chain and of the worm-like chain models with extensible bonds. In all cases we show that the convergence to the thermodynamic limit upon increasing contour length is described by a suitable power law and a specific scaling exponent, characteristic of each model.

  16. Reconstitution of the muscle thin filament from recombinant troponin components and the native thin filaments.

    Science.gov (United States)

    Matsumoto, Fumiko; Deshimaru, Shungo; Oda, Toshiro; Fujiwara, Satoru

    2010-04-15

    We have developed a technique by which muscle thin filaments are reconstituted from the recombinant troponin components and the native thin filaments. By this technique, the reconstituted troponin complex is exchanged into the native thin filaments in the presence of 20% glycerol and 0.3M KCl at pH 6.2. More than 90% of endogenous troponin complex was replaced with the recombinant troponin complex. Structural integrity and Ca(2+) sensitivity of the reconstituted thin filament prepared by this technique was confirmed by X-ray fiber diffraction measurements and the thin filament-activated myosin subfragment 1 ATPase measurements, respectively.

  17. Characterization of type-I ELM induced filaments in the far scrape-off layer of ASDEX upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Schmid, Andreas

    2008-03-18

    This thesis focuses on the characterization of filaments and their propagation in the ASDEX Upgrade tokamak. The aim is to provide experimental measurements for understanding the filament formation process and their temporal evolution, and to provide a comprehensive database for an extrapolation to future fusion devices. For this purpose, a new magnetically driven probe for filament measurements has been developed and installed in ASDEX Upgrade. The probe carries several Langmuir probes and a magnetic coil in between. The Langmuir probes allow for measurements of the radial and poloidal/toroidal propagation of filaments as well as for measurements of filament size, density, and their radial (or temporal) evolution. The magnetic coil on the filament probe allows for measurements of currents in the filaments. A set of 7 coils, measuring 3 field components at different positions along the filament, has been used to measure the magnetic signature during an ELM. The aim was, on the one hand, to study which role filaments play for the magnetic structure, and on the other hand if the parallel currents predicted by the sheath damped model could be verified. Filament temperatures have been derived and the corresponding heat transport mechanisms have been studied. (orig.)

  18. Characterization of type-I ELM induced filaments in the far scrape-off layer of ASDEX upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Schmid, Andreas

    2008-03-18

    This thesis focuses on the characterization of filaments and their propagation in the ASDEX Upgrade tokamak. The aim is to provide experimental measurements for understanding the filament formation process and their temporal evolution, and to provide a comprehensive database for an extrapolation to future fusion devices. For this purpose, a new magnetically driven probe for filament measurements has been developed and installed in ASDEX Upgrade. The probe carries several Langmuir probes and a magnetic coil in between. The Langmuir probes allow for measurements of the radial and poloidal/toroidal propagation of filaments as well as for measurements of filament size, density, and their radial (or temporal) evolution. The magnetic coil on the filament probe allows for measurements of currents in the filaments. A set of 7 coils, measuring 3 field components at different positions along the filament, has been used to measure the magnetic signature during an ELM. The aim was, on the one hand, to study which role filaments play for the magnetic structure, and on the other hand if the parallel currents predicted by the sheath damped model could be verified. Filament temperatures have been derived and the corresponding heat transport mechanisms have been studied. (orig.)

  19. The role of macroautophagy in development of filamentous fungi.

    Science.gov (United States)

    Bartoszewska, Magdalena; Kiel, Jan A K W

    2011-06-01

    Autophagy (macroautophagy) is a bulk degradative pathway by which cytoplasmic components are delivered to the vacuole for recycling. This process is conserved from yeast to human, where it is implicated in cancer and neurodegenerative diseases. During the last decade, many ATG genes involved in autophagy have been identified, initially in Saccharomyces cerevisiae. This review summarizes the knowledge on the molecular mechanisms of autophagy using yeast as model system. Although many of the core components involved in autophagy are conserved from yeast to human, there are, nevertheless, significant differences between these organisms, for example, during autophagy initiation. Autophagy also plays an essential role in filamentous fungi especially during differentiation. Remarkably, in these species autophagy may reflect features of both yeast and mammals. This is exemplified by the finding that filamentous fungi lack the S. cerevisiae clade-specific Atg31 protein, but contain Atg101, which is absent in this clade. A reappraisal of genome data further suggests that, similar to yeast and mammals, filamentous fungi probably also contain two distinct phosphatidylinositol 3-kinase complexes. This review also summarizes the state of knowledge on the role of autophagy in filamentous fungi during differentiation, such as pathogenic development, programmed cell death during heteroincompatibility, and spore formation.

  20. Multifunction of autophagy-related genes in filamentous fungi.

    Science.gov (United States)

    Khan, Irshad Ali; Lu, Jian-Ping; Liu, Xiao-Hong; Rehman, Abdur; Lin, Fu-Cheng

    2012-06-20

    Autophagy (macroautophagy), a highly conserved eukaryotic mechanism, is a non-selective degradation process, helping to maintain a balance between the synthesis, degradation and subsequent recycling of macromolecules to overcome various stress conditions. The term autophagy denotes any cellular process which involves the delivery of cytoplasmic material to the lysosome for degradation. Autophagy, in filamentous fungi plays a critical role during cellular development and pathogenicity. Autophagy, like the mitogen-activated protein (MAP) kinase cascade and nutrient-sensing cyclic AMP (cAMP) pathway, is also an important process for appressorium turgor accumulation in order to penetrate the leaf surface of host plant and destroy the plant defense. Yeast, an autophagy model, has been used to compare the multi-valued functions of ATG (autophagy-related genes) in different filamentous fungi. The autophagy machinery in both yeast and filamentous fungi is controlled by Tor kinase and both contain two distinct phosphatidylinositol 3-kinase complexes. In this review, we focus on the functions of ATG genes during pathogenic development in filamentous fungi. Copyright © 2012 Elsevier GmbH. All rights reserved.

  1. Solution processed silver sulfide thin films for filament memory applications

    Science.gov (United States)

    Yin, Shong

    Filament Memories based on resistive switching have been attracting attention in recent years as a potential replacement for flash memory in CMOS technology and as a potential candidate memory for low-cost, large-area electronics. These memories operate at low voltages with fast switching speeds. These devices are based on ionic conduction through an electrolyte layer and differ fundamentally in operation from conventional flash memory, which is based on the field effect transistor. To facilitate development of this technology, effects of film structure on ionic and electronic conducting properties and the filament formation processes must be studied. In this work, silver sulfide, a mixed ionic-electronic conductor, is used as a model material for studying the solution processing of filament memories, and to study the impact of film structure on conducting and switching properties. Three different solution processing methods are investigated for depositing silver sulfide: sulfidation of elemental silver films, and sintering of two types of silver sulfide nanoparticles. Effects of nanoparticle sintering conditions on electrolyte structured and mixed conducting properties are investigated by a combination of X-ray diffraction, electrical impedance spectroscopy and thermo-gravimetric analysis. Impact of forming voltage and time on filament morphology is examined to provide an overall view of the impact of electrical and material parameters on device operation.

  2. RecA filament sliding on DNA facilitates homology search

    Science.gov (United States)

    Ragunathan, Kaushik; Liu, Cheng; Ha, Taekjip

    2012-01-01

    During homologous recombination, RecA forms a helical filament on a single stranded (ss) DNA that searches for a homologous double stranded (ds) DNA and catalyzes the exchange of complementary base pairs to form a new heteroduplex. Using single molecule fluorescence imaging tools with high spatiotemporal resolution we characterized the encounter complex between the RecA filament and dsDNA. We present evidence in support of the ‘sliding model’ wherein a RecA filament diffuses along a dsDNA track. We further show that homology can be detected during sliding. Sliding occurs with a diffusion coefficient of approximately 8000 bp2/s allowing the filament to sample several hundred base pairs before dissociation. Modeling suggests that sliding can accelerate homology search by as much as 200 fold. Homology recognition can occur for as few as 6 nt of complementary basepairs with the recognition efficiency increasing for higher complementarity. Our data represents the first example of a DNA bound multi-protein complex which can slide along another DNA to facilitate target search. DOI: http://dx.doi.org/10.7554/eLife.00067.001 PMID:23240082

  3. Solar Filaments as Tracers of Subsurface Processes

    Indian Academy of Sciences (India)

    D. M. Rust

    2000-09-01

    Solar filaments are discussed in terms of two contrasting paradigms. The standard paradigm is that filaments are formed by condensation of coronal plasma into magnetic fields that are twisted or dimpled as a consequence of motions of the fields' sources in the photo-sphere. According to a new paradigm, filaments form in rising, twisted flux ropes and are a necessary intermediate stage in the transfer to interplanetary space of dynamo-generated magnetic flux. It is argued that the accumulation of magnetic helicity in filaments and their coronal surroundings leads to filament eruptions and coronal mass ejections. These ejections relieve the Sun of the flux generated by the dynamo and make way for the flux of the next cycle.

  4. Quantifying protein diffusion and capture on filaments

    CERN Document Server

    Reithmann, Emanuel; Frey, Erwin

    2015-01-01

    The functional relevance of regulating proteins is often limited to specific binding sites such as the ends of microtubules or actin-filaments. A localization of proteins on these functional sites is of great importance. We present a quantitative theory for a diffusion and capture process, where proteins diffuse on a filament and stop diffusing when reaching the filament's end. It is found that end-association after one-dimensional diffusion is the main source for tip-localization of such proteins. As a consequence, diffusion and capture is highly efficient in enhancing the reaction velocity of enzymatic reactions, where proteins and filament ends are to each other as enzyme and substrate. We show that the reaction velocity can effectively be described within a Michaelis-Menten framework. Together one-dimensional diffusion and capture beats the (three-dimensional) Smoluchowski diffusion limit for the rate of protein association to filament ends.

  5. Natural colorants from filamentous fungi.

    Science.gov (United States)

    Torres, Fábio Aurélio Esteves; Zaccarim, Bruna Regina; de Lencastre Novaes, Letícia Celia; Jozala, Angela Faustino; Dos Santos, Carolina Alves; Teixeira, Maria Francisca Simas; Santos-Ebinuma, Valéria Carvalho

    2016-03-01

    In the last years, there is a trend towards the replacement of synthetic colorants by natural ones, mainly due to the increase of consumer demand for natural products. The natural colorants are used to enhance the appearance of pharmaceutical products, food, and different materials, making them preferable or attractive. This review intends to provide and describe a comprehensive overview of the history of colorants, from prehistory to modern time, of their market and their applications, as well as of the most important aspects of the fermentation process to obtain natural colorants. Focus is given to colorants produced by filamentous fungal species, aiming to demonstrate the importance of these microorganisms and biocompounds, highlighting the production performance to get high yields and the aspects of conclusion that should be taken into consideration in future studies about natural colorants.

  6. Application of a Mechanistic Model as a Tool for On-line Monitoring of Pilot Scale Filamentous Fungal Fermentation Processes - The Importance of Evaporation Effects

    DEFF Research Database (Denmark)

    Mears, Lisa; Stocks, Stuart M.; Albæk, Mads Orla

    2017-01-01

    block models the changing rates of formation of product, biomass, and water, and the rate of consumption of feed using standard, available on-line measurements. This parameter estimation block, is coupled to a mechanistic process model, which solves the current states of biomass, product, substrate......, dissolved oxygen and mass, as well as other process parameters including kLa, viscosity and partial pressure of CO2. State estimation at this scale requires a robust mass model including evaporation, which is a factor not often considered at smaller scales of operation.The model is developed using...... sensor at this scale, this allows for improved process monitoring, as well as opening up further possibilities for on-line control algorithms, utilizing these on-line model outputs. This article is protected by copyright. All rights reserved...

  7. A MULTI-SPACECRAFT VIEW OF A GIANT FILAMENT ERUPTION DURING 2009 SEPTEMBER 26/27

    Energy Technology Data Exchange (ETDEWEB)

    Gosain, Sanjay [National Solar Observatory, 950 N. Cherry Avenue, Tucson, AZ 85719 (United States); Schmieder, Brigitte [LESIA, Observatoire de Paris, CNRS, UPMC, Universite Paris Diderot, 5 Place Jules Janssen, F-92190 Meudon (France); Artzner, Guy [CNRS UMR 8617, Institut d' astrophysique Spatiale (IAS), F-91405 Orsay Cedex (France); Bogachev, Sergei [Lebedev Physical Institute of Russian Academy of Science, Leninskij prospekt 53, Moscow 119991 (Russian Federation); Toeroek, Tibor [Predictive Science, Inc., 9990 Mesa Rim Rd., Suite 170, San Diego, CA 92121 (United States)

    2012-12-10

    We analyze multi-spacecraft observations of a giant filament eruption that occurred during 2009 September 26 and 27. The filament eruption was associated with a relatively slow coronal mass ejection. The filament consisted of a large and a small part, and both parts erupted nearly simultaneously. Here we focus on the eruption associated with the larger part of the filament. The STEREO satellites were separated by about 117 Degree-Sign during this event, so we additionally used SoHO/EIT and CORONAS/TESIS observations as a third eye (Earth view) to aid our measurements. We measure the plane-of-sky trajectory of the filament as seen from STEREO-A and TESIS viewpoints. Using a simple trigonometric relation, we then use these measurements to estimate the true direction of propagation of the filament which allows us to derive the true R/R{sub Sun }-time profile of the filament apex. Furthermore, we develop a new tomographic method that can potentially provide a more robust three-dimensional (3D) reconstruction by exploiting multiple simultaneous views. We apply this method also to investigate the 3D evolution of the top part of filament. We expect this method to be useful when SDO and STEREO observations are combined. We then analyze the kinematics of the eruptive filament during its rapid acceleration phase by fitting different functional forms to the height-time data derived from the two methods. We find that for both methods an exponential function fits the rise profile of the filament slightly better than parabolic or cubic functions. Finally, we confront these results with the predictions of theoretical eruption models.

  8. A Multi-spacecraft View of a Giant Filament Eruption during 2009 September 26/27

    Science.gov (United States)

    Gosain, Sanjay; Schmieder, Brigitte; Artzner, Guy; Bogachev, Sergei; Török, Tibor

    2012-12-01

    We analyze multi-spacecraft observations of a giant filament eruption that occurred during 2009 September 26 and 27. The filament eruption was associated with a relatively slow coronal mass ejection. The filament consisted of a large and a small part, and both parts erupted nearly simultaneously. Here we focus on the eruption associated with the larger part of the filament. The STEREO satellites were separated by about 117° during this event, so we additionally used SoHO/EIT and CORONAS/TESIS observations as a third eye (Earth view) to aid our measurements. We measure the plane-of-sky trajectory of the filament as seen from STEREO-A and TESIS viewpoints. Using a simple trigonometric relation, we then use these measurements to estimate the true direction of propagation of the filament which allows us to derive the true R/R ⊙-time profile of the filament apex. Furthermore, we develop a new tomographic method that can potentially provide a more robust three-dimensional (3D) reconstruction by exploiting multiple simultaneous views. We apply this method also to investigate the 3D evolution of the top part of filament. We expect this method to be useful when SDO and STEREO observations are combined. We then analyze the kinematics of the eruptive filament during its rapid acceleration phase by fitting different functional forms to the height-time data derived from the two methods. We find that for both methods an exponential function fits the rise profile of the filament slightly better than parabolic or cubic functions. Finally, we confront these results with the predictions of theoretical eruption models.

  9. Application of a Mechanistic Model as a Tool for On-line Monitoring of Pilot Scale Filamentous Fungal Fermentation Processes - The Importance of Evaporation Effects

    DEFF Research Database (Denmark)

    Mears, Lisa; Stocks, Stuart M.; Albæk, Mads Orla

    2017-01-01

    block models the changing rates of formation of product, biomass, and water, and the rate of consumption of feed using standard, available on-line measurements. This parameter estimation block, is coupled to a mechanistic process model, which solves the current states of biomass, product, substrate...... a historical dataset of eleven batches from the fermentation pilot plant (550L) at Novozymes A/S. The model is then implemented on-line in 550L fermentation processes operated at Novozymes A/S in order to validate the state estimator model on fourteen new batches utilizing a new strain. The product...... of the input data. Parameter estimation uncertainty is also carried out. The application of this on-line state estimator allows for on-line monitoring of pilot scale batches, including real-time estimates of multiple parameters which are not able to be monitored on-line. With successful application of a soft...

  10. Automatic Detect and Trace of Solar Filaments

    Science.gov (United States)

    Fang, Cheng; Chen, P. F.; Tang, Yu-hua; Hao, Qi; Guo, Yang

    We developed a series of methods to automatically detect and trace solar filaments in solar Hα images. The programs are able to not only recognize filaments and determine their properties, such as the position, the area and other relevant parameters, but also to trace the daily evolution of the filaments. For solar full disk Hα images, the method consists of three parts: first, preprocessing is applied to correct the original images; second, the Canny edge-detection method is used to detect the filaments; third, filament properties are recognized through the morphological operators. For each Hα filament and its barb features, we introduced the unweighted undirected graph concept and adopted Dijkstra shortest-path algorithm to recognize the filament spine; then, using polarity inversion line shift method for measuring the polarities in both sides of the filament to determine the filament axis chirality; finally, employing connected components labeling method to identify the barbs and calculating the angle between each barb and spine to indicate the barb chirality. Our algorithms are applied to the observations from varied observatories, including the Optical & Near Infrared Solar Eruption Tracer (ONSET) in Nanjing University, Mauna Loa Solar Observatory (MLSO) and Big Bear Solar Observatory (BBSO). The programs are demonstrated to be effective and efficient. We used our method to automatically process and analyze 3470 images obtained by MLSO from January 1998 to December 2009, and a butterfly diagram of filaments is obtained. It shows that the latitudinal migration of solar filaments has three trends in the Solar Cycle 23: The drift velocity was fast from 1998 to the solar maximum; after the solar maximum, it became relatively slow and after 2006, the migration became divergent, signifying the solar minimum. About 60% filaments with the latitudes larger than 50 degree migrate towards the Polar Regions with relatively high velocities, and the latitudinal migrating

  11. Unwinding motion of a twisted active region filament

    Energy Technology Data Exchange (ETDEWEB)

    Yan, X. L.; Xue, Z. K.; Kong, D. F. [Yunnan Observatories, Chinese Academy of Sciences, Kunming 650011 (China); Liu, J. H. [Department of Physics, Shijiazhuang University, Shijiazhuang 050035 (China); Xu, C. L. [Yunnan Normal University, Kunming 650092 (China)

    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. Unwinding Motion of a Twisted Active Region Filament

    Science.gov (United States)

    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.

  13. Striation and convection in penumbral filaments

    Science.gov (United States)

    Spruit, H. C.; Scharmer, G. B.; Löfdahl, M. G.

    2010-10-01

    Observations with the 1-m Swedish Solar Telescope of the flows seen in penumbral filaments are presented. Time sequences of bright filaments show overturning motions strikingly similar to those seen along the walls of small isolated structures in the active regions. The filaments show outward propagating striations with inclination angles suggesting that they are aligned with the local magnetic field. We interpret it as the equivalent of the striations seen in the walls of small isolated magnetic structures. Their origin is then a corrugation of the boundary between an overturning convective flow inside the filament and the magnetic field wrapping around it. The outward propagation is a combination of a pattern motion due to the downflow observed along the sides of bright filaments, and the Evershed flow. The observed short wavelength of the striation argues against the existence of a dynamically significant horizontal field inside the bright filaments. Its intensity contrast is explained by the same physical effect that causes the dark cores of filaments, light bridges and “canals”. In this way striation represents an important clue to the physics of penumbral structure and its relation with other magnetic structures on the solar surface. We put this in perspective with results from the recent 3-D radiative hydrodynamic simulations. 4 movies are only available in electronic form at http://www.aanda.org

  14. Filamentation of Campylobacter in broth cultures

    Directory of Open Access Journals (Sweden)

    Nacheervan M Ghaffar

    2015-06-01

    Full Text Available The transition from rod to filamentous cell morphology has been identified as a response to stressful conditions in many bacterial species and has been ascribed to confer certain survival advantages. Filamentation of Campylobacter jejuni was demonstrated to occur spontaneously on entry in to stationary phase distinguishing it from many other bacteria where a reduction in size is more common. The aim of this study was to investigate the cues that give rise to filamentation of C. jejuni and C. coli and gain insights into the process. Using minimal medium, augmentation of filamentation occurred and it was observed that this morphological change was wide spread amongst C. jejuni strains tested but was not universal in C. coli strains. Filamentation did not appear to be due to release of diffusible molecules, toxic metabolites, or be in response to oxidative stress in the medium. Separated filaments exhibited greater intracellular ATP contents (2.66 to 17.4 fg than spiral forms (0.99 to 1.7 fg and showed enhanced survival in water at 4oC and 37oC compared to spiral cells. These observations support the conclusion that the filaments are adapted to survive extra-intestinal environments. Differences in cell morphology and physiology need to be considered in the context of the design of experimental studies and the methods adopted for the isolation of campylobacters from food, clinical and environmental sources.

  15. Filamentous Biopolymers on Surfaces: Atomic Force Microscopy Images Compared with Brownian Dynamics Simulation of Filament Deposition

    Science.gov (United States)

    Mücke, Norbert; Klenin, Konstantin; Kirmse, Robert; Bussiek, Malte; Herrmann, Harald; Hafner, Mathias; Langowski, Jörg

    2009-01-01

    Nanomechanical properties of filamentous biopolymers, such as the persistence length, may be determined from two-dimensional images of molecules immobilized on surfaces. For a single filament in solution, two principal adsorption scenarios are possible. Both scenarios depend primarly on the interaction strength between the filament and the support: i) For interactions in the range of the thermal energy, the filament can freely equilibrate on the surface during adsorption; ii) For interactions much stronger than the thermal energy, the filament will be captured by the surface without having equilibrated. Such a ‘trapping’ mechanism leads to more condensed filament images and hence to a smaller value for the apparent persistence length. To understand the capture mechanism in more detail we have performed Brownian dynamics simulations of relatively short filaments by taking the two extreme scenarios into account. We then compared these ‘ideal’ adsorption scenarios with observed images of immobilized vimentin intermediate filaments on different surfaces. We found a good agreement between the contours of the deposited vimentin filaments on mica (‘ideal’ trapping) and on glass (‘ideal’ equilibrated) with our simulations. Based on these data, we have developed a strategy to reliably extract the persistence length of short worm-like chain fragments or network forming filaments with unknown polymer-surface interactions. PMID:19888472

  16. Filamentous biopolymers on surfaces: atomic force microscopy images compared with Brownian dynamics simulation of filament deposition.

    Directory of Open Access Journals (Sweden)

    Norbert Mücke

    Full Text Available Nanomechanical properties of filamentous biopolymers, such as the persistence length, may be determined from two-dimensional images of molecules immobilized on surfaces. For a single filament in solution, two principal adsorption scenarios are possible. Both scenarios depend primarily on the interaction strength between the filament and the support: i For interactions in the range of the thermal energy, the filament can freely equilibrate on the surface during adsorption; ii For interactions much stronger than the thermal energy, the filament will be captured by the surface without having equilibrated. Such a 'trapping' mechanism leads to more condensed filament images and hence to a smaller value for the apparent persistence length. To understand the capture mechanism in more detail we have performed Brownian dynamics simulations of relatively short filaments by taking the two extreme scenarios into account. We then compared these 'ideal' adsorption scenarios with observed images of immobilized vimentin intermediate filaments on different surfaces. We found a good agreement between the contours of the deposited vimentin filaments on mica ('ideal' trapping and on glass ('ideal' equilibrated with our simulations. Based on these data, we have developed a strategy to reliably extract the persistence length of short worm-like chain fragments or network forming filaments with unknown polymer-surface interactions.

  17. Flexible-to-semiflexible chain crossover on the pressure-area isotherm of a lipid bilayer

    Science.gov (United States)

    Krivonos, I. N.; Mukhin, S. I.

    2008-01-01

    We find theoretically that competition between ˜ K f q 4 and ˜ Qq 2 terms in the Fourier-transformed conformational energy of a single-lipid chain, in combination with interchain entropic repulsion in the hydrophobic part of the lipid (bi)layer, may cause a crossover on the bilayer pressure-area isotherm P( A)˜( A- A 0)-α. The crossover manifests itself in the transition from α = 5/3 to α = 3. Our microscopic model represents a single-lipid molecule as a worm-like chain with a finite irreducible cross-section area A 0, a flexural rigidity K f , and a stretching modulus Q in a parabolic potential with the self-consistent curvature B( A) formed by entropic interactions between hydrocarbon chains in the lipid layer. The crossover area A* obeys the relation Q/√ K f B( A*) ≈ 2. We predict a peculiar possibility of deducing the effective elastic moduli K f and Q of an individual hydrocarbon chain from the analysis of the isotherm with such a crossover. Also calculated is the crossover-related behavior of the area compressibility modulus K A , the equilibrium area per lipid A t , and the chain order parameter S(θ).

  18. Expanded experimental parameter space of semiflexible polymer assemblies through programmable nanomaterials

    Science.gov (United States)

    Smith, David; Schuldt, Carsten; Lorenz, Jessica; Tschirner, Teresa; Moebius-Winkler, Maximilian; Kaes, Josef; Glaser, Martin; Haendler, Tina; Schnauss, Joerg

    2015-03-01

    Biologically evolved materials are often used as inspiration in the development of new materials as well as examinations into the underlying physical principles governing their behavior. For instance, the biopolymer constituents of the highly dynamic cellular cytoskeleton such as actin have inspired a deep understanding of soft polymer-based materials. However, the molecular toolbox provided by biological systems has been evolutionarily optimized to carry out the necessary functions of cells, and the inability modify basic properties such as biopolymer stiffness hinders a meticulous examination of parameter space. Using actin as inspiration, we circumvent these limitations using model systems assembled from programmable materials such as DNA. Nanorods with comparable, but controllable dimensions and mechanical properties as actin can be constructed from small sets of specially designed DNA strands. In entangled gels, these allow us to systematically determine the dependence of network mechanical properties on parameters such as persistence length and crosslink strength. At higher concentrations in the presence of local attractive forces, we see a transition to highly-ordered bundled and ``aster'' phases similar to those previously characterized in systems of actin or microtubules.

  19. Thermal and Chemical Evolution of Collapsing Filaments

    Energy Technology Data Exchange (ETDEWEB)

    Gray, William J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Scannapieco, Evan [Arizona State Univ., Mesa, AZ (United States). School of Earth and Space Exploration

    2013-01-15

    Intergalactic filaments form the foundation of the cosmic web that connect galaxies together, and provide an important reservoir of gas for galaxy growth and accretion. Here we present very high resolution two-dimensional simulations of the thermal and chemical evolution of such filaments, making use of a 32 species chemistry network that tracks the evolution of key molecules formed from hydrogen, oxygen, and carbon. We study the evolution of filaments over a wide range of parameters including the initial density, initial temperature, strength of the dissociating UV background, and metallicity. In low-redshift, Z ≈ 0.1Z filaments, the evolution is determined completely by the initial cooling time. If this is sufficiently short, the center of the filament always collapses to form dense, cold core containing a substantial fraction of molecules. In high-redshift, Z = 10-3Z filaments, the collapse proceeds much more slowly. This is due mostly to the lower initial temperatures, which leads to a much more modest increase in density before the atomic cooling limit is reached, making subsequent molecular cooling much less efficient. Finally, we study how the gravitational potential from a nearby dwarf galaxy affects the collapse of the filament and compare this to NGC 5253, a nearby starbusting dwarf galaxy thought to be fueled by the accretion of filament gas. In contrast to our fiducial case, a substantial density peak forms at the center of the potential. This peak evolves faster than the rest of the filament due to the increased rate at which chemical species form and cooling occur. We find that we achieve similar accretion rates as NGC 5253, but our two-dimensional simulations do not recover the formation of the giant molecular clouds that are seen in radio observations.

  20. Thermal and Chemical Evolution of Collapsing Filaments

    Energy Technology Data Exchange (ETDEWEB)

    Gray, William J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Scannapieco, Evan [Arizona State Univ., Mesa, AZ (United States). School of Earth and Space Exploration

    2013-01-15

    Intergalactic filaments form the foundation of the cosmic web that connect galaxies together, and provide an important reservoir of gas for galaxy growth and accretion. Here we present very high resolution two-dimensional simulations of the thermal and chemical evolution of such filaments, making use of a 32 species chemistry network that tracks the evolution of key molecules formed from hydrogen, oxygen, and carbon. We study the evolution of filaments over a wide range of parameters including the initial density, initial temperature, strength of the dissociating UV background, and metallicity. In low-redshift, Z ≈ 0.1Z filaments, the evolution is determined completely by the initial cooling time. If this is sufficiently short, the center of the filament always collapses to form dense, cold core containing a substantial fraction of molecules. In high-redshift, Z = 10-3Z filaments, the collapse proceeds much more slowly. This is due mostly to the lower initial temperatures, which leads to a much more modest increase in density before the atomic cooling limit is reached, making subsequent molecular cooling much less efficient. Finally, we study how the gravitational potential from a nearby dwarf galaxy affects the collapse of the filament and compare this to NGC 5253, a nearby starbusting dwarf galaxy thought to be fueled by the accretion of filament gas. In contrast to our fiducial case, a substantial density peak forms at the center of the potential. This peak evolves faster than the rest of the filament due to the increased rate at which chemical species form and cooling occur. We find that we achieve similar accretion rates as NGC 5253 but our two-dimensional simulations do not recover the formation of the giant molecular clouds that are seen in radio observations.

  1. Electro-mechanical behaviors of composite superconducting strand with filament breakage

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xu [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China); Gao, Yuanwen, E-mail: ywgao@lzu.edu.cn [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China); Zhou, Youhe [Key Laboratory of Mechanics on Environment and Disaster in Western China, The Ministry of Education of China, Lanzhou, Gansu 730000 (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China)

    2016-10-15

    Highlights: • The electromechanical behaviors of the superconducting (SC) strand are investigated. • A 3D FEM model for bending behaviors and electric properties of strand is developed. • The influence of breakage of filaments on the critical current of SC strand is calculated. • The impact of current transfer length on the electric properties of SC strand is discussed. - Abstract: The bending behaviors of superconducting strand with typical multi-filament twist configuration are investigated based on a three-dimensional finite element method (FEM) model, named as the Multi-filament twist model, of the strand. In this 3D FEM model, the impacts of initial thermal residual stress, filament-breakage and its evaluation are taken into accounts. The mechanical responses of the strand under bending load are studied with the factors taken into consideration one by one. The distribution of the damage of the filaments and its evolution and the movement of the neutral axis caused by it are studied and displayed in detail. Besides, taking the advantages of the Multi-filament twist model, the normalized critical current of the strand under bending load is also calculated based on the invariant temperature and field strain functions. In addition, the non-negligible influences of the pitch length of the filaments on both the mechanical behaviors and the normalized critical current are discussed. The stress-strain characteristics of the strand under tensile load and the normalized critical current of it under axial and bending loads resulting from the Multi-filament twist model show good agreement with the experimental data.

  2. Metal ion-dependent, reversible, protein filament formation by designed beta-roll polypeptides

    Directory of Open Access Journals (Sweden)

    Campbell Robert L

    2007-10-01

    Full Text Available Abstract Background A right-handed, calcium-dependent β-roll structure found in secreted proteases and repeat-in-toxin proteins was used as a template for the design of minimal, soluble, monomeric polypeptides that would fold in the presence of Ca2+. Two polypeptides were synthesised to contain two and four metal-binding sites, respectively, and exploit stacked tryptophan pairs to stabilise the fold and report on the conformational state of the polypeptide. Results Initial analysis of the two polypeptides in the presence of calcium suggested the polypeptides were disordered. The addition of lanthanum to these peptides caused aggregation. Upon further study by right angle light scattering and electron microscopy, the aggregates were identified as ordered protein filaments that required lanthanum to polymerize. These filaments could be disassembled by the addition of a chelating agent. A simple head-to-tail model is proposed for filament formation that explains the metal ion-dependency. The model is supported by the capping of one of the polypeptides with biotin, which disrupts filament formation and provides the ability to control the average length of the filaments. Conclusion Metal ion-dependent, reversible protein filament formation is demonstrated for two designed polypeptides. The polypeptides form filaments that are approximately 3 nm in diameter and several hundred nm in length. They are not amyloid-like in nature as demonstrated by their behaviour in the presence of congo red and thioflavin T. A capping strategy allows for the control of filament length and for potential applications including the "decoration" of a protein filament with various functional moieties.

  3. Detecting filamentary pattern in the cosmic web: a catalogue of filaments for the SDSS

    CERN Document Server

    Tempel, E; Saar, E; Martinez, V J; Liivamägi, L J; Castellan, G

    2013-01-01

    The main feature of the spatial large-scale galaxy distribution is its intricate network of galaxy filaments. This network is spanned by the galaxy locations that can be interpreted as a three-dimensional point distribution. The global properties of the point process can be measured by different statistical methods, which, however, do not describe directly the structure elements. The morphology of the large scale structure is an important property of the galaxy distribution. Here we apply an object point process with interactions (the Bisous model) to trace and extract the filamentary network in the presently largest galaxy redshift survey, the Sloan Digital Sky Survey (SDSS). We search for filaments in the galaxy distribution having a radius of about 0.5 Mpc/h. We divide the detected network into single filaments and present a public catalogue of filaments. We study the filament length distribution and show that the longest filaments reach the length of 60 Mpc/h. The filaments contain 35-40% of the total gal...

  4. The availability of filament ends modulates actin stochastic dynamics in live plant cells

    Science.gov (United States)

    Li, Jiejie; Staiger, Benjamin H.; Henty-Ridilla, Jessica L.; Abu-Abied, Mohamad; Sadot, Einat; Blanchoin, Laurent; Staiger, Christopher J.

    2014-01-01

    A network of individual filaments that undergoes incessant remodeling through a process known as stochastic dynamics comprises the cortical actin cytoskeleton in plant epidermal cells. From images at high spatial and temporal resolution, it has been inferred that the regulation of filament barbed ends plays a central role in choreographing actin organization and turnover. How this occurs at a molecular level, whether different populations of ends exist in the array, and how individual filament behavior correlates with the overall architecture of the array are unknown. Here we develop an experimental system to modulate the levels of heterodimeric capping protein (CP) and examine the consequences for actin dynamics, architecture, and cell expansion. Significantly, we find that all phenotypes are the opposite for CP-overexpression (OX) cells compared with a previously characterized cp-knockdown line. Specifically, CP OX lines have fewer filament–filament annealing events, as well as reduced filament lengths and lifetimes. Further, cp-knockdown and OX lines demonstrate the existence of a subpopulation of filament ends sensitive to CP concentration. Finally, CP levels correlate with the biological process of axial cell expansion; for example, epidermal cells from hypocotyls with reduced CP are longer than wild-type cells, whereas CP OX lines have shorter cells. On the basis of these and other genetic studies in this model system, we hypothesize that filament length and lifetime positively correlate with the extent of axial cell expansion in dark-grown hypocotyls. PMID:24523291

  5. Can We Determine the Filament Chirality by the Filament Footpoint Location or the Barb-bearing?

    CERN Document Server

    Hao, Q; Fang, C; Chen, P F; Cao, W

    2015-01-01

    We attempt to propose a method for automatically detecting the solar filament chirality and barb bearing. We first introduce the unweighted undirected graph concept and adopt the Dijkstra shortest-path algorithm to recognize the filament spine. Then, we use the polarity inversion line (PIL) shift method for measuring the polarities on both sides of the filament, and employ the connected components labeling method to identify the barbs and calculate the angle between each barb and the spine to determine the bearing of the barbs, i.e., left or right. We test the automatic detection method with H-alpha filtergrams from the Big Bear Solar Observatory (BBSO) H-alpha archive and magnetograms observed with the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO). Four filaments are automatically detected and illustrated to show the results. The barbs in different parts of a filament may have opposite bearings. The filaments in the southern hemisphere (northern hemisphere) mainly have ...

  6. Self-assembly of a filament by curvature-inducing proteins

    Science.gov (United States)

    Kwiecinski, James; Chapman, S. Jonathan; Goriely, Alain

    2017-04-01

    We explore a simplified macroscopic model of membrane shaping by means of curvature-sensing BAR proteins. Equations describing the interplay between the shape of a freely floating filament in a fluid and the adhesion kinetics of proteins are derived from mechanical principles. The constant curvature solutions that arise from this system are studied using weakly nonlinear analysis. We show that the stability of the filament's shape is completely characterized by the parameters associated with protein recruitment and establish that in the bistable regime, proteins aggregate on the filament forming regions of high and low curvatures. This pattern formation is then followed by phase-coarsening that resolves on a time-scale dependent on protein diffusion and drift across the filament, which contend to smooth and maintain the pattern respectively. The model is generalized for multiple species of BAR proteins and we show that the stability of the assembled shape is determined by a competition between proteins attaching on opposing sides.

  7. Filaments in Galactic Winds Driven by Young Stellar Clusters

    CERN Document Server

    Rodriguez-Gonzalez, Ary; Velazquez, Pablo; Raga, Alejandro; Melo, Veronica

    2008-01-01

    The starburst galaxy M82 shows a system of H$\\alpha$-emitting filaments which extend to each side of the galactic disk. We model these filaments as the result of the interaction between the winds from a distribution of Super Stellar Clusters (SSCs). We first derive the condition necessary for producing a radiative interaction between the cluster winds (a condition which is met by the SSC distribution of M82). We then compute 3D simulations for SSC wind distributions which satisfy the condition for a radiative interaction, and also for distributions which do not satisfy this condition. We find that the highly radiative models, that result from the interaction of high metallicity cluster winds, produce a structure of H$\\alpha$ emitting filaments, which qualitatively agrees with the observations of the M82, while the non-radiative SSC wind interaction models do not produce filamentary structures. Therefore, our criterion for radiative interactions (which depends on the mass loss rate and the terminal velocity of...

  8. Effects of Using Silica Fume and Polycarboxylate-Type Superplasticizer on Physical Properties of Cementitious Grout Mixtures for Semiflexible Pavement Surfacing

    Science.gov (United States)

    Karim, Mohamed Rehan; Mahmud, Hilmi; Mashaan, Nuha S.; Katman, Herdayati; Husain, Nadiah Md

    2014-01-01

    Semi-flexible pavement surfacing is a composite pavement that utilizes the porous pavement structure of the flexible bituminous pavement, which is subsequently grouted with appropriate cementitious materials. This study aims to investigate the compressive strength, flexural strength, and workability performance of cementitious grout. The grout mixtures are designed to achieve high strength and maintain flow properties in order to allow the cement slurries to infiltrate easily through unfilled compacted skeletons. A paired-sample t-test was carried out to find out whether water/cement ratio, SP percentages, and use of silica fume influence the cementitious grout performance. The findings showed that the replacement of 5% silica fume with an adequate amount of superplasticizer and water/cement ratio was beneficial in improving the properties of the cementitious grout. PMID:24526911

  9. Real-time monitoring of the silicidation process of tungsten filaments at high temperature used as catalysers for silane decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Nos, O., E-mail: oriol.nos@gmail.com; Frigeri, P.A.; Bertomeu, J.

    2014-01-15

    The scope of this work is the systematic study of the silicidation process affecting tungsten filaments at high temperature (1900 °C) used for silane decomposition in the hot-wire chemical vapour deposition technique (HWCVD). The correlation between the electrical resistance evolution of the filaments, R{sub fil}(t), and the different stages of the their silicidation process is exposed. Said stages correspond to: the rapid formation of two WSi{sub 2} fronts at the cold ends of the filaments and their further propagation towards the middle of the filaments; and, regarding the hot central portion of the filaments: an initial stage of silicon dissolution into the tungsten bulk, with a random duration for as-manufactured filaments, followed by the inhomogeneous nucleation of W{sub 5}Si{sub 3} (which is later replaced by WSi{sub 2}) and its further growth towards the filaments core. An electrical model is used to obtain real-time information about the current status of the filaments silicidation process by simply monitoring their R{sub fil}(t) evolution during the HWCVD process. It is shown that implementing an annealing pre-treatment to the filaments leads to a clearly repetitive trend in the monitored R{sub fil}(t) signatures. The influence of hydrogen dilution of silane on the filaments silicidation process is also discussed. - Highlights: • The silicidation process of tungsten filaments at 1900 °C has been elucidated. • The silicidation process is correlated with the electrical resistance evolution. • Hydrogen dilution of silane delays the precipitation of silicides. • A thermal treatment of the filaments makes the silicidation process repeatable. • Raman spectroscopy and EDX analysis allow the tungsten silicides identification.

  10. Tunnel ionization, population trapping, filamentation and applications

    Science.gov (United States)

    Leang Chin, See; Xu, Huailiang

    2016-11-01

    The advances in femtosecond Ti-sapphire laser technology have led to the discovery of a profusion of new physics. This review starts with a brief historical account of the experimental realization of tunnel ionization, followed by high harmonic generation and the prediction of attosecond pulses. Then, the unique phenomenon of dynamic population trapping during the ionization of atoms and molecules in intense laser fields is introduced. One of the consequences of population trapping in the highly excited states is the neutral dissociation into simple molecular fragments which fluoresce. Such fluorescence could be amplified in femtosecond laser filamentation in gases. The experimental observations of filament-induced fluorescence and lasing in the atmosphere and combustion flames are given. Excitation of molecular rotational wave packets (molecular alignment) and their relaxation and revival in a gas filament are described. Furthermore, filament-induced condensation and precipitation inside a cloud chamber is explained. Lastly, a summary and future outlook is given.

  11. Large-Scale Filaments: Newtonian versus Modified Dynamics

    Science.gov (United States)

    Milgrom, Mordehai

    1997-03-01

    Eisenstein, Loeb, & Turner (ELT) have recently proposed a method for estimating the dynamical masses of large-scale filaments, whereby the filament is modeled by an infinite, axisymmetric, isothermal, self-gravitating, radially virialized cylinder, for which ELT derive a global relation between the (constant) velocity dispersion and the total line density. We show that the model assumptions of ELT can be relaxed materially: an exact relation between the rms velocity and the line density can be derived for any infinite cylinder (not necessarily axisymmetric) with an arbitrary constituent distribution function (so isothermality need not be assumed). We also consider the same problem in the context of the modified Newtonian dynamics (MOND). After we compare the scaling properties in the two theories, we study two idealized MOND model filaments, one with assumptions similar to those of ELT, which we can only solve numerically, and another, which we solve in closed form. A preliminary application to the same segment of the Perseus-Pisces filament treated by ELT gives MOND M/L estimates of order 10(M/L)⊙, compared with the Newtonian value M/L ~ 450(H0/100 km s-1 Mpc-1)(M/L)⊙ that ELT find. In spite of the large uncertainties still besetting the analysis, this instance of MOND application is of particular interest because (1) objects of this geometry have not been dealt with before; (2) it pertains to large-scale structure; and (3) the typical accelerations involved are the lowest so far encountered in a semivirialized system--only a few percent of the critical MOND acceleration--leading to a large predicted mass discrepancy.

  12. Morgellons disease: a filamentous borrelial dermatitis

    OpenAIRE

    Middelveen MJ; Stricker RB

    2016-01-01

    Marianne J Middelveen, Raphael B Stricker International Lyme and Associated Diseases Society, Bethesda, MD, USA Abstract: Morgellons disease (MD) is a dermopathy characterized by multicolored filaments that lie under, are embedded in, or project from skin. Although MD was initially considered to be a delusional disorder, recent studies have demonstrated that the dermopathy is associated with tickborne infection, that the filaments are composed of keratin and collagen, and that they resu...

  13. Can we determine the filament chirality by the filament footpoint location or the barb-bearing?

    Science.gov (United States)

    Hao, Qi; Guo, Yang; Fang, Cheng; Chen, Peng-Fei; Cao, Wen-Da

    2016-01-01

    We attempt to propose a method for automatically detecting the solar filament chirality and barb bearing. We first introduce the concept of an unweighted undirected graph and adopt the Dijkstra shortest path algorithm to recognize the filament spine. Then, we use the polarity inversion line (PIL) shift method for measuring the polarities on both sides of the filament, and employ the connected components labeling method to identify the barbs and calculate the angle between each barb and the spine to determine the bearing of the barbs, i.e., left or right. We test the automatic detection method with Hα filtergrams from the Big Bear Solar Observatory (BBSO) Hα archive and magnetograms observed with the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO). Four filaments are automatically detected and illustrated to show the results. The barbs in different parts of a filament may have opposite bearings. The filaments in the southern hemisphere (northern hemisphere) mainly have left-bearing (right-bearing) barbs and positive (negative) magnetic helicity, respectively. The tested results demonstrate that our method is efficient and effective in detecting the bearing of filament barbs. It is demonstrated that the conventionally believed one-to-one correspondence between filament chirality and barb bearing is not valid. The correct detection of the filament axis chirality should be done by combining both imaging morphology and magnetic field observations.

  14. On the nature of star-forming filaments: II. Sub-filaments and velocities

    CERN Document Server

    Smith, Rowan J; Klessen, Ralf S; Fuller, Gary A

    2015-01-01

    We show that hydrodynamic turbulent cloud simulations naturally produce large filaments made up of a network of smaller and coherent sub-filaments. Such simulations resemble observations of filaments and fibres in nearby molecular clouds. The sub-filaments are dynamical features formed at the stagnation points of the turbulent velocity field where shocks dissipate the turbulent energy. They are a ubiquitous feature of the simulated clouds, which appear from the beginning of the simulation and are not formed by gradual fragmentation of larger filaments. Most of the sub-filaments are gravitationally sub-critical and do not fragment into cores, however, there is also a significant fraction of supercritical sub-filaments which break up into star-forming cores. The sub-filaments are coherent along their length, and the residual velocities along their spine show that they are subsonically contracting without any ordered rotation on scales of ~0.1 pc. Accretion flows along the sub-filaments can feed material into st...

  15. Filaments in the Lupus molecular clouds

    CERN Document Server

    Benedettini, M; Pezzuto, S; Elia, D; André, P; Könyves, V; Schneider, N; Tremblin, P; Arzoumanian, D; di Giorgio, A M; Di Francesco, J; Hill, T; Molinari, S; Motte, F; Nguyen-Luong, Q; Palmeirim, P; Rivera-Ingraham, A; Roy, A; Rygl, K L J; Spinoglio, L; Ward-Thompson, D; White, G J

    2015-01-01

    We have studied the filaments extracted from the column density maps of the nearby Lupus 1, 3, and 4 molecular clouds, derived from photometric maps observed with the Herschel satellite. Filaments in the Lupus clouds have quite low column densities, with a median value of $\\sim$1.5$\\times$10$^{21}$ cm$^{-2}$ and most have masses per unit length lower than the maximum critical value for radial gravitational collapse. Indeed, no evidence of filament contraction has been seen in the gas kinematics. We find that some filaments, that on average are thermally subcritical, contain dense cores that may eventually form stars. This is an indication that in the low column density regime, the critical condition for the formation of stars may be reached only locally and this condition is not a global property of the filament. Finally, in Lupus we find multiple observational evidences of the key role that the magnetic field plays in forming filaments, and determining their confinement and dynamical evolution.

  16. Filaments in Simulations of Molecular Cloud Formation

    CERN Document Server

    Gomez, Gilberto C

    2013-01-01

    We report on the filaments that develop self-consistently in a new numerical simulation of cloud formation by colliding flows. As in previous studies, the forming cloud begins to undergo gravitational collapse because it rapidly acquires a mass much larger than the average Jeans mass. Thus, the collapse is hierarchical in nature, proceeding along its shortest dimension first. This naturally produces filaments in cloud, and clumps within the filaments. The filaments are not in equilibrium at any time, but instead are long-lived flow features, through which the gas flows from the cloud to the clumps. The filaments are long-lived because they accrete from their environment while simultaneously accreting onto the clumps within them; they are essentially the locus where the flow changes from accreting in two dimensions to accreting in one dimension. Moreover, the clumps also exhibit a hierarchical nature: the gas in a filament flows onto a main, central clump, but other, smaller-scale clumps form along the infalli...

  17. Filaments in the Lupus molecular clouds

    Science.gov (United States)

    Benedettini, M.; Schisano, E.; Pezzuto, S.; Elia, D.; André, P.; Könyves, V.; Schneider, N.; Tremblin, P.; Arzoumanian, D.; di Giorgio, A. M.; Di Francesco, J.; Hill, T.; Molinari, S.; Motte, F.; Nguyen-Luong, Q.; Palmeirim, P.; Rivera-Ingraham, A.; Roy, A.; Rygl, K. L. J.; Spinoglio, L.; Ward-Thompson, D.; White, G. J.

    2015-10-01

    We have studied the filaments extracted from the column density maps of the nearby Lupus 1, 3, and 4 molecular clouds, derived from photometric maps observed with the Herschel satellite. Filaments in the Lupus clouds have quite low column densities, with a median value of ˜1.5 × 1021 cm-2 and most have masses per unit length lower than the maximum critical value for radial gravitational collapse. Indeed, no evidence of filament contraction has been seen in the gas kinematics. We find that some filaments, that on average are thermally subcritical, contain dense cores that may eventually form stars. This is an indication that in the low column density regime, the critical condition for the formation of stars may be reached only locally and this condition is not a global property of the filament. Finally, in Lupus we find multiple observational evidences of the key role that the magnetic field plays in forming filaments, and determining their confinement and dynamical evolution.

  18. The dynamics of filament assembly define cytoskeletal network morphology

    Science.gov (United States)

    Foffano, Giulia; Levernier, Nicolas; Lenz, Martin

    2016-12-01

    The actin cytoskeleton is a key component in the machinery of eukaryotic cells, and it self-assembles out of equilibrium into a wide variety of biologically crucial structures. Although the molecular mechanisms involved are well characterized, the physical principles governing the spatial arrangement of actin filaments are not understood. Here we propose that the dynamics of actin network assembly from growing filaments results from a competition between diffusion, bundling and steric hindrance, and is responsible for the range of observed morphologies. Our model and simulations thus predict an abrupt dynamical transition between homogeneous and strongly bundled networks as a function of the actin polymerization rate. This suggests that cells may effect dramatic changes to their internal architecture through minute modifications of their nonequilibrium dynamics. Our results are consistent with available experimental data.

  19. Solitons and other waves on a quantum vortex filament

    CERN Document Server

    Van Gorder, Robert A

    2014-01-01

    The quantum form of the local induction approximation (LIA, a model approximating the motion of a thin vortex filament in superfluid) including superfluid friction effects is put into correspondence with a type of cubic complex Ginsburg-Landau equation, in a manner analogous to the Hasimoto map taking the classical LIA into the cubic nonlinear Schr\\"odinger equation. From this formulation, we determine the form and behavior of Stokes waves, 1-solitons, and other traveling wave solutions under normal and binormal friction. The most important of these solutions is the soliton on a quantum vortex filament, which is a natural generalization of the 1-soliton solution constructed mathematically by Hasimoto which motivated subsequent real-world experiments. We also conjecture on the possibility of chaos in such systems, and on the existence more complicated solitons such as breathers.

  20. Otomycosis due to filamentous fungi.

    Science.gov (United States)

    García-Agudo, Lidia; Aznar-Marín, Pilar; Galán-Sánchez, Fátima; García-Martos, Pedro; Marín-Casanova, Pilar; Rodríguez-Iglesias, Manuel

    2011-10-01

    Otomycosis is common throughout the world but barely studied in Spain. Our objective was to determine the microbiological and epidemiological characteristics of this pathology in Cadiz (Spain) between 2005 and 2010. Samples from patients with suspicion of otomycosis underwent a direct microscopic examination and culture on different media for fungi and bacteria. Mycological cultures were incubated at 30°C for at least seven days. Identification of fungi was based on colonial morphology and microscopic examination of fungal structure. From a total of 2,633 samples, microbial growth was present in 1,375 (52.2%) and fungal isolation in 390 (28.4%). We identified 228 yeasts and 184 filamentous fungi (13.4% of positive cultures and 47.2% of otomycosis), associated with yeasts in 22 cases (5.6%). The most frequent species were Aspergillus flavus (42.4%), A. niger (35.9%), A. fumigatus (12.5%), A. candidus (7.1%), A. terreus (1.6%), and Paecilomyces variotii (0.5%). Infection was predominant in men (54.9%) and patients beyond 55 years old (46.8%). The most common clinical symptoms were itching (98.9%), otalgia (59.3%), and hypoacusis (56.0%). Fall season reported the lowest number of cases (20.1%). Incidence of otomycosis and fungi producing otomycosis vary within the distinct geographical areas. In Cadiz, this infection is endemic due to warm temperatures, high humidity, sea bathing, and wind, which contributes to disseminate the conidia. Despite Aspergillus niger has been reported as the main causative agent, A. flavus is predominant in Cadiz. Although infection is usually detected in warm months, we observed a homogeneous occurrence of otomycosis in almost all the seasons.

  1. Tau phosphorylation by GSK-3β promotes tangle-like filament morphology

    Directory of Open Access Journals (Sweden)

    Gamblin Truman C

    2007-06-01

    Full Text Available Abstract Background Neurofibrillary tangles (NFTs are intraneuronal aggregates associated with several neurodegenerative diseases including Alzheimer's disease. These abnormal accumulations are primarily comprised of fibrils of the microtubule-associated protein tau. During the progression of NFT formation, disperse and non-interacting tau fibrils become stable aggregates of tightly packed and intertwined filaments. Although the molecular mechanisms responsible for the conversion of disperse tau filaments into tangles of filaments are not known, it is believed that some of the associated changes in tau observed in Alzheimer's disease, such as phosphorylation, truncation, ubiquitination, glycosylation or nitration, may play a role. Results We have investigated the effects of tau phosphorylation by glycogen synthase kinase-3β (GSK-3β on tau filaments in an in vitro model system. We have found that phosphorylation by GSK-3β is sufficient to cause tau filaments to coalesce into tangle-like aggregates similar to those isolated from Alzheimer's disease brain. Conclusion These results suggest that phosphorylation of tau by GSK-3β promotes formation of tangle-like filament morphology. The in vitro cell-free experiments described here provide a new model system to study mechanisms of NFT development. Although the severity of dementia has been found to correlate with the presence of NFTs, there is some question as to the identity of the neurotoxic agents involved. This model system will be beneficial in identifying intermediates or side reaction products that might be neurotoxic.

  2. Rate-dependent force, intracellular calcium, and action potential voltage alternans are modulated by sarcomere length and heart failure induced-remodeling of thin filament regulation in human heart failure: A myocyte modeling study.

    Science.gov (United States)

    Zile, Melanie A; Trayanova, Natalia A

    2016-01-01

    Microvolt T-wave alternans (MTWA) testing identifies heart failure patients at risk for lethal ventricular arrhythmias at near-resting heart rates (voltage alternans (APV-ALT), the cellular driver of MTWA. Our goal was to uncover the mechanisms linking APV-ALT and FORCE-ALT in failing human myocytes and to investigate how the link between those alternans was affected by pacing rate and by physiological conditions such as sarcomere length and heart failure induced-remodeling of mechanical parameters. To achieve this, a mechanically-based, strongly coupled human electromechanical myocyte model was constructed. Reducing the sarcoplasmic reticulum calcium uptake current (Iup) to 27% was incorporated to simulate abnormal calcium handling in human heart failure. Mechanical remodeling was incorporated to simulate altered thin filament activation and crossbridge (XB) cycling rates. A dynamical pacing protocol was used to investigate the development of intracellular calcium concentration ([Ca]i), voltage, and active force alternans at different pacing rates. FORCE-ALT only occurred in simulations incorporating reduced Iup, demonstrating that alternans in the intracellular calcium concentration (CA-ALT) induced FORCE-ALT. The magnitude of FORCE-ALT was found to be largest at clinically relevant pacing rates (<110 bpm), where APV-ALT was smallest. We found that the magnitudes of FORCE-ALT, CA-ALT and APV-ALT were altered by heart failure induced-remodeling of mechanical parameters and sarcomere length due to the presence of myofilament feedback. These findings provide important insight into the relationship between heart-failure-induced electrical and mechanical alternans and how they are altered by physiological conditions at near-resting heart rates.

  3. Potential fields of merging and splitting filaments in air

    Institute of Scientific and Technical Information of China (English)

    Ma Yuan-Yuan; Lu Xin; Xi Ting-Ting; Hao Zuo-Qiang; Gong Qi-Huang; Zhang Jie

    2007-01-01

    Two interacting light filaments with different initial phases propagating in air are investigated numerically by using a ray tracing method. The evolution of the rays of a filament is governed by a potential field. During propagation, the two potential wells of the two filaments can merge into one or repel each other, depending on the initial phase difference between the two filaments. The study provides a simple description of the interacting filaments.

  4. The effect of cosmic web filaments on the properties of groups and their central galaxies

    Science.gov (United States)

    Poudel, A.; Heinämäki, P.; Tempel, E.; Einasto, M.; Lietzen, H.; Nurmi, P.

    2017-01-01

    Context. The nature versus nurture scenario in galaxy and group evolution is a long-standing problem not yet fully understood on cosmological scales. Aims: We study the properties of groups and their central galaxies in different large-scale environments defined by the luminosity density field and the cosmic web filaments. Methods: We use the luminosity density field constructed using 8 h-1 Mpc smoothing to characterize the large-scale environments. We use the Bisous model to extract the filamentary structures in different large-scale environments. We study the properties of galaxy groups as a function of their dynamical mass in different large-scale environments. Results: We find differences in the properties of central galaxies and their groups in and outside of filaments at fixed halo and large-scale environments. In high-density environments, the group mass function has higher number densities in filaments compared to that outside of filaments towards the massive end. The relation is the opposite in low-density environments. At fixed group mass and large-scale luminosity density, mass-to-light ratios show that groups in filaments are slightly more luminous than those outside of filaments. At fixed group mass and large-scale luminosity density, central galaxies in filaments have redder colors, higher stellar masses, and lower specific star formation rates than those outside of filaments. However, the differences in central galaxy and group properties in and outside of filaments are not clear in some group mass bins. We show that the differences in central galaxy properties are due to the higher abundances of elliptical galaxies in filaments. Conclusions: Filamentary structures in the cosmic web are not simply visual associations of galaxies, but rather play an important role in shaping the properties of groups and their central galaxies. The differences in central galaxy and group properties in and outside of cosmic web filaments are not simple effects related

  5. Filament-length-controlled elasticity in 3D fiber networks.

    Science.gov (United States)

    Broedersz, C P; Sheinman, M; Mackintosh, F C

    2012-02-17

    We present a model for disordered 3D fiber networks to study their linear and nonlinear elasticity. In contrast to previous 2D models, these 3D networks with binary crosslinks are underconstrained with respect to fiber stretching elasticity, suggesting that bending may dominate their response. We find that such networks exhibit a bending-dominated elastic regime controlled by fiber length, as well as a crossover to a stretch-dominated regime for long fibers. Finally, by extending the model to the nonlinear regime, we show that these networks become intrinsically nonlinear with a vanishing linear response regime in the limit of flexible or long filaments.

  6. Nonlinear mechanisms to Rogue events in the process of interaction between optical filaments

    CERN Document Server

    Kovachev, L M

    2015-01-01

    We investigate two types of nonlinear interaction between collinear femtosecond laser pulses with power slightly above the critical for self-focusing $P_{cr}$. In the first case we study energy exchange between filaments. The model describes this process through degenerate four-photon parametric mixing (FPPM) scheme and requests initial phase difference between the waves. When there are no initial phase difference between the pulses, the FPPM process does not work. In this case it is obtained the second type of interaction as merging between two, three or four filaments in a single filament with higher power. It is found that in the second case the interflow between the filaments has potential of interaction due to cross-phase modulation (CPM).

  7. Measuring cohesion between macromolecular filaments, one pair at a time: Depletion-induced microtubule binding

    CERN Document Server

    Hilitski, Feodor; Cajamarca, Luis; Hagan, Michael F; Grason, Gregory M; Dogic, Zvonimir

    2014-01-01

    In presence of non-adsorbing polymers, colloidal particles experience a ubiquitous attractive interactions induced by the depletion mechanism. We measure the depletion interaction between a pair of microtubule filaments by a method that combines optical trapping, single molecule imaging and umbrella sampling. By quantifying the dependence of filament cohesion on both polymer concentration and solution ionic strength, we demonstrate that the minimal model of depletion based, on the Asakura-Oosawa theory, fails to describe the experimental data. By measuring the cohesion strength in two- and three- filament bundles we verify pairwise additivity of the depletion interaction for the specific experimental conditions. The described experimental technique can be used to measure pairwise interactions between various biological or synthetic filaments, thus complementing information extracted from bulk osmotic stress experiments.

  8. PDGF induces reorganization of vimentin filaments.

    Science.gov (United States)

    Valgeirsdóttir, S; Claesson-Welsh, L; Bongcam-Rudloff, E; Hellman, U; Westermark, B; Heldin, C H

    1998-07-30

    In this study we demonstrate that stimulation with platelet-derived growth factor (PDGF) leads to a marked reorganization of the vimentin filaments in porcine aortic endothelial (PAE) cells ectopically expressing the PDGF beta-receptor. Within 20 minutes after stimulation, the well-spread fine fibrillar vimentin was reorganized as the filaments aggregated into a dense coil around the nucleus. The solubility of vimentin upon Nonidet-P40-extraction of cells decreased considerably after PDGF stimulation, indicating that PDGF caused a redistribution of vimentin to a less soluble compartment. In addition, an increased tyrosine phosphorylation of vimentin was observed. The redistribution of vimentin was not a direct consequence of its tyrosine phosphorylation, since treatment of cells with an inhibitor for the cytoplasmic tyrosine kinase Src, attenuated phosphorylation but not redistribution of vimentin. These changes in the distribution of vimentin occurred in conjunction with reorganization of actin filaments. In PAE cells expressing a Y740/751F mutant receptor that is unable to bind and activate phosphatidylinositol 3'-kinase (PI3-kinase), the distribution of vimentin was virtually unaffected by PDGF stimulation. Thus, PI3-kinase is important for vimentin reorganization, in addition to its previously demonstrated role in actin reorganization. The small GTPase Rac has previously been shown to be involved downstream of PI3-kinase in the reorganization of actin filaments. In PAE cells overexpressing dominant negative Rac1 (N17Rac1), no change in the fine fibrillar vimentin network was seen after PDGF-BB stimulation, whereas in PAE cells overexpressing constitutively active Rac1 (V12Rac1), there was a dramatic change in vimentin filament organization independent of PDGF stimulation. These data indicate that PDGF causes a reorganization of microfilaments as well as intermediate filaments in its target cells and suggest an important role for Rac downstream of PI3-kinase in

  9. Filament Activation in Response to Magnetic Flux Emergence and Cancellation in Filament Channels

    CERN Document Server

    Li, Ting; Ji, Haisheng

    2015-01-01

    We make a comparative analysis for two filaments that showed quite different activation in response to the flux emergence within the filament channels. The observations from the Solar Dynamics Observatory (SDO) and Global Oscillation Network Group (GONG) are carried out to analyze the two filaments on 2013 August 17-20 and September 29. The first event showed that the main body of the filament was separated into two parts when an active region (AR) emerged with a maximum magnetic flux of about 6.4*10^21 Mx underlying the filament. The close neighborhood and common direction of the bright threads in the filament and the open AR fan loops suggest similar magnetic connectivity of these two flux systems. The equilibrium of the filament was not destroyed within 3 days after the start of the emergence of the AR. To our knowledge, similar observations have never been reported before. In the second event, the emerging flux occurred nearby a barb of the filament with a maximum magnetic flux of 4.2*10^20 Mx, about one ...

  10. Biophysically realistic filament bending dynamics in agent-based biological simulation.

    Science.gov (United States)

    Alberts, Jonathan B

    2009-01-01

    An appealing tool for study of the complex biological behaviors that can emerge from networks of simple molecular interactions is an agent-based, computational simulation that explicitly tracks small-scale local interactions--following thousands to millions of states through time. For many critical cell processes (e.g. cytokinetic furrow specification, nuclear centration, cytokinesis), the flexible nature of cytoskeletal filaments is likely to be critical. Any computer model that hopes to explain the complex emergent behaviors in these processes therefore needs to encode filament flexibility in a realistic manner. Here I present a numerically convenient and biophysically realistic method for modeling cytoskeletal filament flexibility in silico. Each cytoskeletal filament is represented by a series of rigid segments linked end-to-end in series with a variable attachment point for the translational elastic element. This connection scheme allows an empirically tuning, for a wide range of segment sizes, viscosities, and time-steps, that endows any filament species with the experimentally observed (or theoretically expected) static force deflection, relaxation time-constant, and thermal writhing motions. I additionally employ a unique pair of elastic elements--one representing the axial and the other the bending rigidity- that formulate the restoring force in terms of single time-step constraint resolution. This method is highly local -adjacent rigid segments of a filament only interact with one another through constraint forces-and is thus well-suited to simulations in which arbitrary additional forces (e.g. those representing interactions of a filament with other bodies or cross-links / entanglements between filaments) may be present. Implementation in code is straightforward; Java source code is available at www.celldynamics.org.

  11. Biophysically realistic filament bending dynamics in agent-based biological simulation.

    Directory of Open Access Journals (Sweden)

    Jonathan B Alberts

    Full Text Available An appealing tool for study of the complex biological behaviors that can emerge from networks of simple molecular interactions is an agent-based, computational simulation that explicitly tracks small-scale local interactions--following thousands to millions of states through time. For many critical cell processes (e.g. cytokinetic furrow specification, nuclear centration, cytokinesis, the flexible nature of cytoskeletal filaments is likely to be critical. Any computer model that hopes to explain the complex emergent behaviors in these processes therefore needs to encode filament flexibility in a realistic manner. Here I present a numerically convenient and biophysically realistic method for modeling cytoskeletal filament flexibility in silico. Each cytoskeletal filament is represented by a series of rigid segments linked end-to-end in series with a variable attachment point for the translational elastic element. This connection scheme allows an empirically tuning, for a wide range of segment sizes, viscosities, and time-steps, that endows any filament species with the experimentally observed (or theoretically expected static force deflection, relaxation time-constant, and thermal writhing motions. I additionally employ a unique pair of elastic elements--one representing the axial and the other the bending rigidity- that formulate the restoring force in terms of single time-step constraint resolution. This method is highly local -adjacent rigid segments of a filament only interact with one another through constraint forces-and is thus well-suited to simulations in which arbitrary additional forces (e.g. those representing interactions of a filament with other bodies or cross-links / entanglements between filaments may be present. Implementation in code is straightforward; Java source code is available at www.celldynamics.org.

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

    Science.gov (United States)

    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

  13. Hydrodynamic interactions of sheets vs filaments: Synchronization, attraction, and alignment

    Science.gov (United States)

    Olson, Sarah D.; Fauci, Lisa J.

    2015-12-01

    The synchronization of nearby sperm flagella as they swim in a viscous fluid was observed nearly a century ago. In the early 1950s, in an effort to shed light on this intriguing phenomenon, Taylor initiated the mathematical analysis of the fluid dynamics of microorganism motility. Since then, models have investigated sperm hydrodynamics where the flagellum is treated as a waving sheet (2D) or as a slender waving filament (3D). Here, we study the interactions of two finite length, flexible filaments confined to a plane in a 3D fluid and compare these to the interactions of the analogous pair of finite, flexible sheets in a 2D fluid. Within our computational framework using regularized Stokeslets, this comparison is easily achieved by choosing either the 2D or 3D regularized kernel to compute fluid velocities induced by the actuated structures. We find, as expected, that two flagella swimming with a symmetric beatform will synchronize (phase-lock) on a fast time scale and attract towards each other on a longer time scale in both 2D and 3D. For a symmetric beatform, synchronization occurs faster in 2D than 3D for sufficiently stiff swimmers. In 3D, a greater enhancement in efficiency and swimming velocity is observed for attracted swimmers relative to the 2D case. We also demonstrate the tendency of two asymmetrically beating filaments in a 3D fluid to align — in tandem — exhibiting an efficiency boost for the duration of their sustained alignment.

  14. Swimming speeds of filaments in viscous fluids with resistance

    Science.gov (United States)

    Ho, Nguyenho; Olson, Sarah D.; Leiderman, Karin

    2016-04-01

    Many microorganisms swim in a highly heterogeneous environment with obstacles such as fibers or polymers. To better understand how this environment affects microorganism swimming, we study propulsion of a cylinder or filament in a fluid with a sparse, stationary network of obstructions modeled by the Brinkman equation. The mathematical analysis of swimming speeds is investigated by studying an infinite-length cylinder propagating lateral or spiral displacement waves. For fixed bending kinematics, we find that swimming speeds are enhanced due to the added resistance from the fibers. In addition, we examine the work and the torque exerted on the cylinder in relation to the resistance. The solutions for the torque, swimming speed, and work of an infinite-length cylinder in a Stokesian fluid are recovered as the resistance is reduced to zero. Finally, we compare the asymptotic solutions with numerical results for the Brinkman flow with regularized forces. The swimming speed of a finite-length filament decreases as its length decreases and planar bending induces an angular velocity that increases linearly with added resistance. The comparisons between the asymptotic analysis and computation give insight on the effect of the length of the filament, the permeability, and the thickness of the cylinder in terms of the overall performance of planar and helical swimmers.

  15. Natural products from filamentous fungi and production by heterologous expression.

    Science.gov (United States)

    Alberti, Fabrizio; Foster, Gary D; Bailey, Andy M

    2017-01-01

    Filamentous fungi represent an incredibly rich and rather overlooked reservoir of natural products, which often show potent bioactivity and find applications in different fields. Increasing the naturally low yields of bioactive metabolites within their host producers can be problematic, and yield improvement is further hampered by such fungi often being genetic intractable or having demanding culturing conditions. Additionally, total synthesis does not always represent a cost-effective approach for producing bioactive fungal-inspired metabolites, especially when pursuing assembly of compounds with complex chemistry. This review aims at providing insights into heterologous production of secondary metabolites from filamentous fungi, which has been established as a potent system for the biosynthesis of bioactive compounds. Numerous advantages are associated with this technique, such as the availability of tools that allow enhanced production yields and directing biosynthesis towards analogues of the naturally occurring metabolite. Furthermore, a choice of hosts is available for heterologous expression, going from model unicellular organisms to well-characterised filamentous fungi, which has also been shown to allow the study of biosynthesis of complex secondary metabolites. Looking to the future, fungi are likely to continue to play a substantial role as sources of new pharmaceuticals and agrochemicals-either as producers of novel natural products or indeed as platforms to generate new compounds through synthetic biology.

  16. Detecting multi-scale filaments in galaxy distribution

    Science.gov (United States)

    Tempel, Elmo

    2014-05-01

    The main feature of the spatial large-scale galaxy distribution is its intricate network of galaxy filaments. This network is spanned by the galaxy locations that can be interpreted as a three-dimensional point distribution. The global properties of the point process can be measured by different statistical methods, which, however, do not describe directly the structure elements. The morphology of the large-scale structure, on the other hand, is an important property of the galaxy distribution. Here, we apply an object point process with interactions (the Bisous model) to trace and extract the filamentary network in the presently largest galaxy redshift survey, the Sloan Digital Sky Survey (SDSS data release 10). We search for multi-scale filaments in the galaxy distribution that have a radius of about 0.5, 1.0, 2.0, and 4.0 h -1 Mpc. We extract the spines of the filamentary network and divide the detected network into single filaments.

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

    Science.gov (United States)

    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.

  18. High Throughput Screening for Drugs that Modulate Intermediate Filament Proteins

    Science.gov (United States)

    Sun, Jingyuan; Groppi, Vincent E.; Gui, Honglian; Chen, Lu; Xie, Qing; Liu, Li

    2016-01-01

    Intermediate filament (IF) proteins have unique and complex cell and tissue distribution. Importantly, IF gene mutations cause or predispose to more than 80 human tissue-specific diseases (IF-pathies), with the most severe disease phenotypes being due to mutations at conserved residues that result in a disrupted IF network. A critical need for the entire IF-pathy field is the identification of drugs that can ameliorate or cure these diseases, particularly since all current therapies target the IF-pathy complication, such as diabetes or cardiovascular disease, rather than the mutant IF protein or gene. We describe a high throughput approach to identify drugs that can normalize disrupted IF proteins. This approach utilizes transduction of lentivirus that expresses green-fluorescent-protein-tagged keratin 18 (K18) R90C in A549 cells. The readout is drug ‘hits’ that convert the dot-like keratin filament distribution, due to the R90C mutation, to a wildtype-like filamentous array. A similar strategy can be used to screen thousands of compounds and can be utilized for practically any IF protein with a filament-disrupting mutation, and could therefore potentially target many IF-pathies. ‘Hits’ of interest require validation in cell culture then using in vivo experimental models. Approaches to study the mechanism of mutant-IF normalization by potential drugs of interest are also described. The ultimate goal of this drug screening approach is to identify effective and safe compounds that can potentially be tested for clinical efficacy in patients. PMID:26795471

  19. Nylon filament coated with paraffin for intraluminal permanent middle cerebral artery occlusion in rats.

    Science.gov (United States)

    Zuo, Xia-Lin; Wu, Ping; Ji, Ai-Min

    2012-06-21

    A variety of intraluminal nylon filament has been used in rat middle cerebral artery occlusion (MCAO) models. However the lesion extent and its reproducibility vary among laboratories. The properties of nylon filament play a part of reasons for these variations. In the present study, we used paraffin-coated nylon filament for rat MCAO model, tested the effects and advanced improvement for making the rat MCAO. Forty male Sprague-Dawley (SD) rats were randomized into two groups, MCAO with traditional uncoated nylon filament (uMCAO) and MCAO with paraffin-coated nylon filament (cMCAO), three rats as normal group and sham group respectively. Assessment included mortality rates, model success rates, neurological deficit evaluation, and infarct volume. The study showed two rats died in uMCAO group, no rat died in cMCAO group within the 12h. The model success rate of uMCAO was 100%, while the uMCAO group was 55% (n=20, two died within 12h, seven rats were excluded as the brain slices showed no TTC staining due to subarachanoid hemorrhage). Neurological evaluation demonstrated group cMCAO had more worse neurological outcomes than group uMCAO, and the difference was statistically signification (pparaffin-coated nylon filament intraluminal occlusion provide better occlusion of middle cerebral artery than the uncoated nylon filament, improve the consistent of model, and raise the success rate to reduce the number of experimental animals. These positive results are much encouraging and interesting. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  20. Free-Space Nonlinear Beam Combining Towards Filamentation

    CERN Document Server

    Rostami, Shermineh; Kepler, Daniel; Baudelet, Matthieu; Litchinitser, Natalia M; Richardson, Martin

    2016-01-01

    Multi-filamentation opens new degrees of freedom for manipulating electromagnetic waves in air. However, without control, multiple filament interactions, including attraction, repulsion or fusion often result in formation of complex disordered filament distributions. Moreover, high power beams conventionally used in multi-filament formation experiments often cause significant surface damage. The growing number of applications for laser filaments requires fine control of their formation and propagation. We demonstrate, experimentally and theoretically, that the attraction and fusion of ultrashort beams with initial powers below the critical value enable the eventual formation of a filament downstream. Filament formation is delayed to a predetermined distance in space, avoiding optical damage to external beam optics while still enabling robust filaments with controllable properties as if formed from a single high power beam. This paradigm introduces new opportunities for filament engineering eliminating the nee...

  1. Unwinding motion of a twisted active-region filament

    CERN Document Server

    Yan, X L; Liu, J H; Kong, D F; Xu, C L

    2014-01-01

    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 June 22, 2010. 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 is consisted of twisted magnetic field lines. The total twist of the filament is at least 5$\\pi$ obtained by using 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 magn...

  2. Cosmic walls and filaments formation in modified Chaplygin gas cosmology

    CERN Document Server

    Karbasi, S

    2016-01-01

    We want to study the perturbation growth of an initial seed of an ellipsoidal shape in Top-Hat collapse model of structure formation in the Modified Chaplygin gas cosmology. Considering reasonable values of the constants and the parameters of the model under study, it is shown that a very small deviation from spherical symmetry (ellipsoidal geometry) in the initial seed leads to a final highly non-spherical structure which can be considered as a candidate for justifying already known cosmological structures as cosmic walls and filaments.

  3. Filament attachment dynamics in actin-based propulsion

    CERN Document Server

    Katz, J I

    2005-01-01

    Theory and experiment have established that F-actin filaments are strongly attached to the intracellular parasites (such as Listeria) they propel with ``comet tails''. We consider the implications of these observations for propulsion. By calculating the motion produced in various models of attachment and comparing to experiment we demonstrate that the attachment must be sliding rather than hinged. By modeling experiments on ActA-coated spheres we draw conclusions regarding the interaction between F-actin and their surfaces that may also be applicable to living systems.

  4. Femtosecond filamentation in air and higher-order nonlinearities

    CERN Document Server

    Kolesik, M; Moloney, J V

    2010-01-01

    According to a recent experiment, the instantaneous electronic Kerr effect in air exhibits a strong intensity dependence, the nonlinear refractive index switching sign and crossing over from a self-focusing to a de-focusing nonlinearity. A subsequent theoretical work has demonstrated that this has paradigm-changing consequences for the understanding of filamentation in air, so it is important to subject the idea of higher-order nonlinearities to stringent tests. Here we use numerical modeling to propose an experiment capable of discriminating between the standard and the new intensity-dependent Kerr-effect models.

  5. Oscillating Filaments: I - Oscillation and Geometrical Fragmentation

    CERN Document Server

    Gritschneder, Matthias; Burkert, Andreas

    2016-01-01

    We study the stability of filaments in equilibrium between gravity and internal as well as external pressure using the grid based AMR-code RAMSES. A homogeneous, straight cylinder below a critical line mass is marginally stable. However, if the cylinder is bent, e.g. with a slight sinusoidal perturbation, an otherwise stable configuration starts to oscillate, is triggered into fragmentation and collapses. This previously unstudied behavior allows a filament to fragment at any given scale, as long as it has slight bends. We call this process `geometrical fragmentation'. In our realization the spacing between the cores matches the wavelength of the sinusoidal perturbation, whereas up to now, filaments were thought to be only fragmenting on the characteristical scale set by the mass-to-line ratio. Using first principles, we derive the oscillation period as well as the collapse timescale analytically. To enable a direct comparison with observations, we study the line-of-sight velocity for different inclinations. ...

  6. Heterologous expression of cellobiohydrolases in filamentous fungi

    DEFF Research Database (Denmark)

    Zoglowek, Marta; Lübeck, Peter S.; Ahring, Birgitte K.

    2015-01-01

    Cellobiohydrolases are among the most important enzymes functioning in the hydrolysis of crystalline cellulose, significantly contributing to the efficient biorefining of recalcitrant lignocellulosic biomass into biofuels and bio-based products. Filamentous fungi are recognized as both well...... into valuable products. However, due to low cellobiohydrolase activities, certain fungi might be deficient with regard to enzymes of value for cellulose conversion, and improving cellobiohydrolase expression in filamentous fungi has proven to be challenging. In this review, we examine the effects of altering...... promoters, signal peptides, culture conditions and host post-translational modifications. For heterologous cellobiohydrolase production in filamentous fungi to become an industrially feasible process, the construction of site-integrating plasmids, development of protease-deficient strains and glycosylation...

  7. Role of coherent resonant nonlinear processes in the ultrashort KrF laser pulse propagation and filamentation in air

    Energy Technology Data Exchange (ETDEWEB)

    Smetanin, I.V.; Levchenko, A.O.; Shutov, A.V.; Ustinovskii, N.N. [P.N. Lebedev Physical Institute of Russian Academy of Sciences, 53 Leninskii pr., 119991 Moscow (Russian Federation); Zvorykin, V.D. [P.N. Lebedev Physical Institute of Russian Academy of Sciences, 53 Leninskii pr., 119991 Moscow (Russian Federation); National Research Nuclear University “MEPhI”, 31 Kashirskoe sh., 115409 Moscow (Russian Federation)

    2016-02-15

    Recent experiments on multiple filamentation of sub-picosecond terawatt-level KrF laser pulse in air and multi-photon ionization of air revealed an extremely low electron density in filaments, which is out of the conventional filamentation model considering Kerr self-focusing and plasma de-focusing. We propose here the coherent resonant scattering and ionization processes at the pulse durations significantly less than the polarization relaxation time to be possible explanation of the observed filamentation peculiarities. Namely, we argue that the plasma production results from the resonance enhanced (2+1)-photon ionization of the oxygen molecules through the two-photon excitation of the 3s metastable Rydberg state. Coherent Raman self-scattering at rotational transitions of nitrogen molecules provides self-induced focusing of the ultrashort UV laser pulse and filament formation.

  8. The Drosophila formin Fhos is a primary mediator of sarcomeric thin-filament array assembly

    Science.gov (United States)

    Shwartz, Arkadi; Dhanyasi, Nagaraju; Schejter, Eyal D; Shilo, Ben-Zion

    2016-01-01

    Actin-based thin filament arrays constitute a fundamental core component of muscle sarcomeres. We have used formation of the Drosophila indirect flight musculature for studying the assembly and maturation of thin-filament arrays in a skeletal muscle model system. Employing GFP-tagged actin monomer incorporation, we identify several distinct phases in the dynamic construction of thin-filament arrays. This sequence includes assembly of nascent arrays after an initial period of intensive microfilament synthesis, followed by array elongation, primarily from filament pointed-ends, radial growth of the arrays via recruitment of peripheral filaments and continuous barbed-end turnover. Using genetic approaches we have identified Fhos, the single Drosophila homolog of the FHOD sub-family of formins, as a primary and versatile mediator of IFM thin-filament organization. Localization of Fhos to the barbed-ends of the arrays, achieved via a novel N-terminal domain, appears to be a critical aspect of its sarcomeric roles. DOI: http://dx.doi.org/10.7554/eLife.16540.001 PMID:27731794

  9. An Imaging and Spectral Study of Ten X-Ray Filaments around the Galactic Center

    CERN Document Server

    Lu, F J; Lou, Y -Q

    2007-01-01

    We report the detection of 10 new X-ray filaments using the data from the {\\sl Chandra} X-ray satellite for the inner $6^{\\prime}$ ($\\sim 15$ parsec) around the Galactic center (GC). All these X-ray filaments are characterized by non-thermal energy spectra, and most of them have point-like features at their heads that point inward. Fitted with the simple absorbed power-law model, the measured X-ray flux from an individual filament in the 2-10 keV band is $\\sim 2.8\\times10^{-14}$ to $10^{-13}$ ergs cm$^{-2}$ s$^{-1}$ and the absorption-corrected X-ray luminosity is $\\sim 10^{32}-10^{33}$ ergs s$^{-1}$ at a presumed distance of 8 kpc to the GC. We speculate the origin(s) of these filaments by morphologies and by comparing their X-ray images with the corresponding radio and infrared images. On the basis of combined information available, we suspect that these X-ray filaments might be pulsar wind nebulae (PWNe) associated with pulsars of age $10^3 \\sim 3\\times 10^5$ yr. The fact that most of the filament tails po...

  10. Relation between halo spin and cosmic-web filaments at z ≃ 3

    Science.gov (United States)

    González, Roberto E.; Prieto, Joaquin; Padilla, Nelson; Jimenez, Raul

    2017-02-01

    We investigate the spin evolution of dark matter haloes and their dependence on the number of connected filaments from the cosmic web at high redshift (spin-filament relation hereafter). To this purpose, we have simulated 5000 haloes in the mass range 5 × 109 h-1 M⊙ to 5 × 1011 h-1 M⊙ at z = 3 in cosmological N-body simulations. We confirm the relation found by Prieto et al. (2015) where haloes with fewer filaments have larger spin. We also found that this relation is more significant for higher halo masses, and for haloes with a passive (no major mergers) assembly history. Another finding is that haloes with larger spin or with fewer filaments have their filaments more perpendicularly aligned with the spin vector. Our results point to a picture in which the initial spin of haloes is well described by tidal torque theory and then gets subsequently modified in a predictable way because of the topology of the cosmic web, which in turn is given by the currently favoured Lambda cold dark matter (LCDM) model. Our spin-filament relation is a prediction from LCDM that could be tested with observations.

  11. Molecular mechanism of Ena/VASP-mediated actin-filament elongation.

    Science.gov (United States)

    Breitsprecher, Dennis; Kiesewetter, Antje K; Linkner, Joern; Vinzenz, Marlene; Stradal, Theresia E B; Small, John Victor; Curth, Ute; Dickinson, Richard B; Faix, Jan

    2011-02-01

    Ena/VASP proteins are implicated in a variety of fundamental cellular processes including axon guidance and cell migration. In vitro, they enhance elongation of actin filaments, but at rates differing in nearly an order of magnitude according to species, raising questions about the molecular determinants of rate control. Chimeras from fast and slow elongating VASP proteins were generated and their ability to promote actin polymerization and to bind G-actin was assessed. By in vitro TIRF microscopy as well as thermodynamic and kinetic analyses, we show that the velocity of VASP-mediated filament elongation depends on G-actin recruitment by the WASP homology 2 motif. Comparison of the experimentally observed elongation rates with a quantitative mathematical model moreover revealed that Ena/VASP-mediated filament elongation displays a saturation dependence on the actin monomer concentration, implying that Ena/VASP proteins, independent of species, are fully saturated with actin in vivo and generally act as potent filament elongators. Moreover, our data showed that spontaneous addition of monomers does not occur during processive VASP-mediated filament elongation on surfaces, suggesting that most filament formation in cells is actively controlled.

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

    Science.gov (United States)

    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.

  13. Production of recombinant proteins by filamentous fungi.

    Science.gov (United States)

    Ward, Owen P

    2012-01-01

    The initial focus of recombinant protein production by filamentous fungi related to exploiting the extraordinary extracellular enzyme synthesis and secretion machinery of industrial strains, including Aspergillus, Trichoderma, Penicillium and Rhizopus species, was to produce single recombinant protein products. An early recognized disadvantage of filamentous fungi as hosts of recombinant proteins was their common ability to produce homologous proteases which could degrade the heterologous protein product and strategies to prevent proteolysis have met with some limited success. It was also recognized that the protein glycosylation patterns in filamentous fungi and in mammals were quite different, such that filamentous fungi are likely not to be the most suitable microbial hosts for production of recombinant human glycoproteins for therapeutic use. By combining the experience gained from production of single recombinant proteins with new scientific information being generated through genomics and proteomics research, biotechnologists are now poised to extend the biomanufacturing capabilities of recombinant filamentous fungi by enabling them to express genes encoding multiple proteins, including, for example, new biosynthetic pathways for production of new primary or secondary metabolites. It is recognized that filamentous fungi, most species of which have not yet been isolated, represent an enormously diverse source of novel biosynthetic pathways, and that the natural fungal host harboring a valuable biosynthesis pathway may often not be the most suitable organism for biomanufacture purposes. Hence it is expected that substantial effort will be directed to transforming other fungal hosts, non-fungal microbial hosts and indeed non microbial hosts to express some of these novel biosynthetic pathways. But future applications of recombinant expression of proteins will not be confined to biomanufacturing. Opportunities to exploit recombinant technology to unravel the

  14. Reduced filamentation in high power semiconductor lasers

    DEFF Research Database (Denmark)

    Skovgaard, Peter M. W.; McInerney, John; O'Brien, Peter

    1999-01-01

    High brightness semiconductor lasers have applications in fields ranging from material processing to medicine. The main difficulty associated with high brightness is that high optical power densities cause damage to the laser facet and thus require large apertures. This, in turn, results in spatio...... in the optical field causes spatial hole-burning and thus filamentation. To reduce filamentation we propose a new, relatively simple design based on inhomogeneous pumping in which the injected current has a gradual transverse profile. We confirm the improved laser performance theoretically and experimentally...

  15. Filament stretching rheometer: inertia compensation revisited

    DEFF Research Database (Denmark)

    Szabo, Peter; McKinley, Gareth H.

    2003-01-01

    The necessary inertia compensation used in the force balance for the filament stretching rheometer is derived for an arbitrary frame of reference. This enables the force balance to be used to extract correctly the extensional viscosity from measurements of the tensile force at either end of the e......The necessary inertia compensation used in the force balance for the filament stretching rheometer is derived for an arbitrary frame of reference. This enables the force balance to be used to extract correctly the extensional viscosity from measurements of the tensile force at either end...

  16. On the nature of star-forming filaments: I. Filament morphologies

    CERN Document Server

    Smith, Rowan J; Klessen, Ralf S

    2014-01-01

    We use a suite of high resolution molecular cloud simulations carried out with the moving mesh code Arepo to explore the nature of star-forming filaments. The simulated filaments are identified and categorised from column density maps in the same manner as for recent Herschel observations. When fit with a Plummer-like profile the filaments are in excellent agreement with observations, and have shallow power-law profiles of p~2.2 without the need for magnetic support. The derived filament widths depend on the data range that is fitted. When data within 1 pc of the filament centre is fitted with a Gaussian function, the average FWHM is ~0.3 pc, in agreement with predictions for accreting filaments. However, if the fit is constructed using only data within 0.35 pc of the centre, in order to better match the procedure used to derive filament widths from Herschel observations, the resulting FWHM is only ~0.2 pc. This value is larger than that measured in IC 5146 and Taurus, but is similar to that found in the Plan...

  17. Elasticity of 3D networks with rigid filaments and compliant crosslinks

    CERN Document Server

    Heidemann, Knut M; Rehfeldt, Florian; Schmidt, Christoph F; Wardetzky, Max

    2014-01-01

    Disordered filamentous networks with compliant crosslinks exhibit a low linear elastic shear modulus at small strains, but stiffen dramatically at high strains. Experiments have shown that the elastic modulus can increase by up to three orders of magnitude while the networks withstand relatively large stresses without rupturing. Here, we perform an analytical and numerical study on model networks in three dimensions. Our model consists of a collection of randomly oriented rigid filaments connected by flexible crosslinks that are modeled as wormlike chains. Due to zero probability of filament intersection in three dimensions, our model networks are by construction prestressed in terms of initial tension in the crosslinks. We demonstrate how the linear elastic modulus can be related to the prestress in these network. Under the assumption of affine deformations in the limit of infinite crosslink density, we show analytically that the nonlinear elastic regime in 1- and 2-dimensional networks is characterized by p...

  18. Undulatory locomotion of finite filaments: lessons from Caenorhabditis elegans

    Science.gov (United States)

    Berman, R. S.; Kenneth, O.; Sznitman, J.; Leshansky, A. M.

    2013-07-01

    Undulatory swimming is a widespread propulsion strategy adopted by many small-scale organisms including various single-cell eukaryotes and nematodes. In this work, we report a comprehensive study of undulatory locomotion of a finite filament using (i) approximate resistive force theory (RFT) assuming a local nature of hydrodynamic interaction between the filament and the surrounding viscous liquid and (ii) particle-based numerical computations taking into account the intra-filament hydrodynamic interaction. Using the ubiquitous model of a propagating sinusoidal waveform, we identify the limit of applicability of the RFT and determine the optimal propulsion gait in terms of (i) swimming distance per period of undulation and (ii) hydrodynamic propulsion efficiency. The occurrence of the optimal swimming gait maximizing hydrodynamic efficiency at finite wavelength in particle-based computations diverges from the prediction of the RFT. To compare the model swimmer powered by sine wave undulations to biological undulatory swimmers, we apply the particle-based approach to study locomotion of the model organism nematode Caenorhabditis elegans using the swimming gait extracted from experiments. The analysis reveals that even though the amplitude and the wavenumber of undulations are similar to those determined for the best performing sinusoidal swimmer, C. elegans overperforms the latter in terms of both displacement and hydrodynamic efficiency. Further comparison with other undulatory microorganisms reveals that many adopt waveforms with characteristics similar to the optimal model swimmer, yet real swimmers still manage to beat the best performing sine-wave swimmer in terms of distance covered per period. Overall our results underline the importance of further waveform optimization, as periodic undulations adopted by C. elegans and other organisms deviate considerably from a simple sine wave.

  19. The Origin of Solar Filament Plasma Inferred from In Situ Observations of Elemental Abundances

    Science.gov (United States)

    Song, H. Q.; Chen, Y.; Li, B.; Li, L. P.; Zhao, L.; He, J. S.; Duan, D.; Cheng, X.; Zhang, J.

    2017-02-01

    Solar filaments/prominences are one of the most common features in the corona, which may lead to energetic coronal mass ejections (CMEs) and flares when they erupt. Filaments are about 100 times cooler and denser than the coronal material, and physical understanding of their material origin remains controversial. Two types of scenarios have been proposed: one argues that the filament plasma is brought into the corona from photosphere or chromosphere through a siphon or evaporation/injection process, while the other suggests that the material condenses from the surrounding coronal plasma due to thermal instability. The elemental abundance analysis is a reasonable clue to constrain the models, as the siphon or evaporation/injection model would predict that the filament material abundances are close to the photospheric or chromospheric ones, while the condensation model should have coronal abundances. In this Letter, we analyze the elemental abundances of a magnetic cloud that contains the ejected filament material. The corresponding filament eruption occurred on 1998 April 29, accompanying an M6.8 class soft X-ray flare located at the heliographic coordinates S18E20 (NOAA 08210) and a fast halo CME with the linear velocity of 1374 km s‑1 near the Sun. We find that the abundance ratios of elements with low and high first ionization potential such as Fe/O, Mg/O, and Si/O are 0.150, 0.050, and 0.070, respectively, approaching their corresponding photospheric values 0.065, 0.081, and 0.066, which does not support the coronal origin of the filament plasma.

  20. An atomistic study on configuration, mechanics and growth of nanoscale filaments

    Science.gov (United States)

    Shahabi, Alireza

    The objective of this dissertation is to study the characteristics of nanoscale materials as a function of their configuration and to investigate the nanoscale production methods, which enable us to tune their properties. Interplay between structure and function in atomically thin crystalline nanofilaments is sensitive to their conformations, size, and defect densities. At the nanoscale, dimensional confinement often creates a strong correlation between their physical properties and geometrical shape, and this is particularly important as their physical properties both influence, and are influenced by their conformations and structure. In the first part of the thesis, we focus on conformations of ultra-thin and ultra-long nanoscale filaments. As the synthesis lengths approach their persistence length, their conformational behavior is not unlike semi-flexible filaments. However, the ability to control their configuration is still limited and the exact relation between geometry and functions are yet to be explored. In this dissertation, we develop a novel approach to create and control the conformation of nanotubes, nanoribbons and nanowires as a method to tuning their properties. Our approach is based on controlling the boundary constraints on these nanofilaments by applying twist and displacement to their ends. We develop conformational phase diagrams by performing all-atom molecular dynamics simulations. We observe the formation of scrolled and folded nanostructures in graphene nanoribbons, and well-defined plectonemes in carbon nanotubes and silicon nanowires. We develop a stability analysis using minimization of bend and twist energies stored in the conformations, suitably modified by the long range van der Waals interactions. Our theoretical predictions are in good agreement with the molecular dynamics simulation results. In the case of graphene nanoribbons, we further investigate the effect of unpassivated edges on their structural evolution. The soft

  1. A generic model for lipid monolayers, bilayers, and membranes

    CERN Document Server

    Schmid, F; Lenz, O; West, B

    2007-01-01

    We describe a simple coarse-grained model which is suited to study lipid layers and their phase transitions. Lipids are modeled by short semiflexible chains of beads with a solvophilic head and a solvophobic tail component. They are forced to self-assemble into bilayers by a computationally cheap `phantom solvent' environment. The model reproduces the most important phases and phase transitions of monolayers and bilayers. Technical issues such as Monte Carlo parallelization schemes are briefly discussed.

  2. The exo-metabolome in filamentous fungi

    DEFF Research Database (Denmark)

    Thrane, Ulf; Andersen, Birgitte; Frisvad, Jens Christian

    2007-01-01

    Filamentous fungi are a diverse group of eukaryotic microorganisms that have a significant impact on human life as spoilers of food and feed by degradation and toxin production. They are also most useful as a source of bulk and fine chemicals and pharmaceuticals. This chapter focuses on the exo...

  3. The Apis mellifera filamentous virus genome

    Science.gov (United States)

    A complete reference genome of the Apis mellifera Filamentous virus (AmFV) was determined using Illumina Hiseq sequencing. The AmFV genome is a double strand DNA molecule of approximately 498’500 nucleotides with a GC content of 50.8%. It encompasses 251 non overlapping open reading frames (ORFs), e...

  4. Filament eruption with apparent reshuffle of endpoints

    CERN Document Server

    Filippov, Boris

    2014-01-01

    Filament eruption on 30 April - 1 May 2010, which shows the reconnection of one filament leg with a region far away from its initial position, is analyzed. Observations from three viewpoints are used for as precise as possible measurements of endpoint coordinates. The northern leg of the erupting prominence loop 'jumps' laterally to the latitude lower than the latitude of the originally southern endpoint. Thus, the endpoints reshuffled their positions in the limb view. Although this behaviour could be interpreted as the asymmetric zipping-like eruption, it does not look very likely. It seems more likely to be reconnection of the flux-rope field lines in its northern leg with ambient coronal magnetic field lines rooted in a quiet region far from the filament. From calculations of coronal potential magnetic field, we found that the filament before the eruption was stable for vertical displacements, but was liable to violation of the horizontal equilibrium. This is unusual initiation of an eruption with combinat...

  5. Linear viscoelastic characterization from filament stretching rheometry

    DEFF Research Database (Denmark)

    Wingstrand, Sara Lindeblad; Alvarez, Nicolas J.; Hassager, Ole

    viscoelasticity well into the nonlinear regime. Therefore at present, complete rheological characterization of a material requires two apparatuses: a shear and an extensional rheometer. This work is focused on developing a linear viscoelastic protocol for the filament stretching rheometer (FSR) in order...

  6. Filament stretching rheometry of polymer melts

    DEFF Research Database (Denmark)

    Hassager, Ole; Nielsen, Jens Kromann; Rasmussen, Henrik Koblitz

    2005-01-01

    The Filament Stretching Rheometry (FSR) method developed by Sridhar, McKinley and coworkers for polymer solutions has been extended to be used also for polymer melts. The design of a melt-FSR will be described and differences to conventional melt elongational rheometers will be pointed out. Results...

  7. Filament stretching rheometry of polymer melts

    DEFF Research Database (Denmark)

    Hassager, Ole; Nielsen, Jens Kromann; Rasmussen, Henrik Koblitz

    2005-01-01

    The Filament Stretching Rheometry (FSR) method developed by Sridhar, McKinley and coworkers for polymer solutions has been extended to be used also for polymer melts. The design of a melt-FSR will be described and differences to conventional melt elongational rheometers will be pointed out. Results...

  8. Featured Image: A Filament Forms and Erupts

    Science.gov (United States)

    Kohler, Susanna

    2017-06-01

    This dynamic image of active region NOAA 12241 was captured by the Solar Dynamics Observatorys Atmospheric Imaging Assembly in December 2014. Observations of this region from a number of observatories and instruments recently presented by Jincheng Wang (University of Chinese Academy of Sciences) and collaborators reveal details about the formation and eruption of a long solar filament. Wang and collaborators show that the right part of the filament formed by magnetic reconnection between two bundles of magnetic field lines, while the left part formed as a result of shearing motion. When these two parts interacted, the filament erupted. You can read more about the teams results in the article linked below. Also, check out this awesome video of the filament formation and eruption, again by SDO/AIA:http://cdn.iopscience.com/images/0004-637X/839/2/128/Full/apjaa6bf3f1_video.mp4CitationJincheng Wang et al 2017 ApJ 839 128. doi:10.3847/1538-4357/aa6bf3

  9. Filamentous bacteria transport electrons over centimetre distances

    DEFF Research Database (Denmark)

    Pfeffer, Christian; Larsen, Steffen; Song, Jie

    2012-01-01

    across centimetre-wide zones. Here we present evidence that the native conductors are long, filamentous bacteria. They abounded in sediment zones with electric currents and along their length they contained strings with distinct properties in accordance with a function as electron transporters. Living...

  10. Simulation optimization of filament parameters for uniform depositions of diamond films on surfaces of ultra-large circular holes

    Science.gov (United States)

    Wang, Xinchang; Shen, Xiaotian; Sun, Fanghong; Shen, Bin

    2016-12-01

    Chemical vapor deposition (CVD) diamond films have been widely applied as protective coatings on varieties of anti-frictional and wear-resistant components, owing to their excellent mechanical and tribological properties close to the natural diamond. In applications of some components, the inner hole surface will serve as the working surface that suffers severe frictional or erosive wear. It is difficult to realize uniform depositions of diamond films on surfaces of inner holes, especially ultra-large inner holes. Adopting a SiC compact die with an aperture of V80 mm as an example, a novel filament arrangement with a certain number of filaments evenly distributed on a circle is designed, and specific effects of filament parameters, including the filament number, arrangement direction, filament temperature, filament diameter, circumradius and the downward translation, on the substrate temperature distribution are studied by computational fluid dynamics (CFD) simulations based on the finite volume method (FVM), adopting a modified computational model well consistent with the actual deposition environment. Corresponding temperature measurement experiments are also conducted to verify the rationality of the computational model. From the aspect of depositing uniform boron-doped micro-crystalline, undoped micro-crystalline and undoped fine-grained composite diamond (BDM-UMC-UFGCD) film on such the inner hole surface, filament parameters as mentioned above are accurately optimized and compensated by orthogonal simulations. Moreover, deposition experiments adopting compensated optimized parameters and some typical contrastive parameters are also accomplished for further verifying the rationality of the computational model and the correctness of the compensation coefficient 0.7 defined for the downward translation determined by simulations. More importantly, on the basis of more simulations and verification tests, a general filament arrangement model suitable for V50-120 mm

  11. Interaction of Two Filament Channels of Different Chiralities

    CERN Document Server

    Joshi, Navin Chandra; Schmieder, Brigitte; Magara, Tetsuya; Moon, Young-Jae; Uddin, Wahab

    2016-01-01

    We present observations of interactions between the two filament channels of different chiralities and associated dynamics that occurred during 2014 April 18 -- 20. While two flux ropes of different helicity with parallel axial magnetic fields can only undergo a bounce interaction when they are brought together, the observations at the first glance show that the heated plasma is moving from one filament channel to the other. The SDO/AIA 171 A observations and the PFSS magnetic field extrapolation reveal the presence of fan-spine magnetic configuration over the filament channels with a null point located above them. Three different events of filament activations, partial eruptions, and associated filament channel interactions have been observed. The activation initiated in one filament channel seems to propagate along the neighbour filament channel. We believe that the activation and partial eruption of the filaments bring the field lines of flux ropes containing them closer to the null point and trigger the m...

  12. Assembly characteristics of plant keratin intermediate filaments in vitro

    Institute of Scientific and Technical Information of China (English)

    闵光伟; 杨澄; 佟向军; 翟中和

    1999-01-01

    After selective extraction and purification, plant keratin intermediate filaments were reassembled in vitro. Scanning tunneling microscope (STM) and transmission electron microscope (TEM) micrographs showed that acidic keratins and basic keratins can assemble into dimers and further into 10 nm filaments in vitro. In higher magnification images, it can be seen that fully assembled plant keratin intermediate filaments consist of several thinner filaments of 3 nm in diameter, which indicates the formation of protofilaments in the assembly processes. One of the explicit features of plant keratin intermediate filaments is a 24—25 nm periodic structural repeat alone the axis of beth the 10 nm filaments and protofilaments. The periodic repeat is one of the fundamental characteristic of all intermediate filaments, and demonstrates the half staggered arrangement of keratin molecules within the filaments.

  13. Evidence for Small-Scale Filamentation and Dynamics in the Solar Corona

    Science.gov (United States)

    Warren, H.

    2004-05-01

    Observations with the Transition Region and Coronal Explorer (TRACE) have revealed that the solar corona is both highly dynamic and highly filamented. In this talk I will discuss how dynamics and filamentation play an important role in explaining some of the observational properties of the Sun's atmosphere. TRACE observations have shown, for example, that many relatively cool ( ˜1 MK), long-lived active region loops have density and temperature profiles that are difficult to reconcile with static models. By modeling these loops as a sequence of impulsively heated filaments, in contrast, it is possible to account for the high densities, flat temperature profiles, and the temporal evolution of these structures. A similar approach to modeling the evolution of flare emission yields much better agreement with observation than treating the flare as a single loop.

  14. Ion-neutral friction and accretion-driven turbulence in self-gravitating filaments

    CERN Document Server

    Hennebelle, Patrick

    2013-01-01

    Recent Herschel observations have confirmed that filaments are ubiquitous in molecular clouds and suggest that irrespectively of the column density, there is a characteristic width of about 0.1 pc whose physical origin remains unclear. We develop an analytical model that can be applied to self-gravitating accreting filaments. It is based on one hand on the virial equilibrium of the central part of the filament and on the other hand on energy balance between the turbulence driven by accretion onto the filament and dissipation. We consider two dissipation mechanisms the turbulent cascade and the ion-neutral friction. Our model predicts that the width of the filament inner part is almost independent of the column density and leads to values comparable to what is inferred observationally if dissipation is due to ion-neutral friction. On the contrary turbulent dissipation leads to a structure that is bigger and depends significantly on the column density. Our model provides a reasonable physical explanation which ...

  15. Characterization of 3D filament dynamics in a MAST SOL flux tube geometry

    Science.gov (United States)

    Walkden, N. R.; Dudson, B. D.; Fishpool, G.

    2013-10-01

    Non-linear simulations of filament propagation in a realistic MAST SOL flux tube geometry using the BOUT++ fluid modelling framework show an isolation of the dynamics of the filament in the divertor region from the midplane region due to three features of the magnetic geometry; the variation of magnetic curvature along the field line, the expansion of the flux tube and strong magnetic shear. Of the three effects, the latter two lead to a midplane ballooning feature of the filament, whilst the former leads to a ballooning around the X-points. In simulations containing all three effects the filament is observed to balloon at the midplane, suggesting that the role of curvature variation is sub-dominant to the flux expansion and magnetic shear. The magnitudes of these effects are all strongest near the X-point which leads to the formation of parallel density gradients. The filaments simulated, which represent filaments in MAST, are identified as resistive ballooning, meaning that their motion is inertially limited, not sheath limited. Parallel density gradients can drive the filament towards a Boltzmann response when the collisionalityof the plasma is low. The results here show that the formation of parallel density gradients is a natural and inevitable consequence of a realistic magnetic geometry and therefore the transition to the Boltzmann response is a consequence of the use of realistic magnetic geometry and does not require initializing specifically varying background profiles as in slab simulations. The filaments studied here are stable to the linear resistive drift-wave instability but are subject to the non-linear effects associated with the Boltzmann response, particularly Boltzmann spinning. The Boltzmann response causes the filament to spin on an axis. In later stages of its evolution a non-linear turbulent state develops where the vorticity evolves into a turbulent eddy field on the same length scale as the parallel current. The transition from interchange

  16. Mechanical Probing of the Intermediate Filament-Rich Caenorhabditis Elegans Intestine.

    Science.gov (United States)

    Jahnel, Oliver; Hoffmann, Bernd; Merkel, Rudolf; Bossinger, Olaf; Leube, Rudolf E

    2016-01-01

    It is commonly accepted that intermediate filaments have an important mechanical function. This function relies not only on intrinsic material properties but is also determined by dynamic interactions with other cytoskeletal filament systems, distinct cell adhesion sites, and cellular organelles which are fine-tuned by multiple signaling pathways. While aspects of these properties and processes can be studied in vitro, their full complexity can only be understood in a viable tissue context. Yet, suitable and easily accessible model systems for monitoring tissue mechanics at high precision are rare. We show that the dissected intestine of the genetic model organism Caenorhabditis elegans fulfills this requirement. The 20 intestinal cells, which are arranged in an invariant fashion, are characterized by a dense subapical mesh of intermediate filaments that are attached to the C. elegans apical junction. We present procedures to visualize details of the characteristic intermediate filament-junctional complex arrangement in living animals. We then report on methods to prepare intestines with a fully intact intermediate filament cytoskeleton and detail procedures to assess their viability. A dual micropipette assay is described to measure mechanical properties of the dissected intestine while monitoring the spatial arrangement of the intermediate filament system. Advantages of this approach are (i) the high reproducibility of measurements because of the uniform architecture of the intestine and (ii) the high degree of accessibility allowing not only mechanical manipulation of an intact tissue but also control of culture medium composition and addition of drugs as well as visualization of cell structures. With this method, examination of worms carrying mutations in the intermediate filament system, its interacting partners and its regulators will become feasible.

  17. Flexible ferromagnetic filaments and the interface with biology

    Energy Technology Data Exchange (ETDEWEB)

    Erglis, K.; Belovs, M. [University of Latvia, Zellu 8, Riga LV-1002 (Latvia); Cebers, A. [University of Latvia, Zellu 8, Riga LV-1002 (Latvia)], E-mail: aceb@tesla.sal.lv

    2009-04-15

    Flexible ferromagnetic filaments are studied both theoretically and experimentally. Two main deformation modes of the filament at magnetic field inversion are theoretically described and observed experimentally by using DNA-linked chains of ferromagnetic particles. Anomalous orientation of ferromagnetic filaments perpendicular to AC field with a frequency which is high enough is predicted and confirmed experimentally. By experimental studies of magnetotactic bacteria it is demonstrated how these properties of ferromagnetic filaments may be used to measure the flexibility of the chain of magnetosomes.

  18. Responsibility of a Filament Eruption for the Initiation of a Flare, CME, and Blast Wave, and its Possible Transformation into a Bow Shock

    CERN Document Server

    Grechnev, V V; Kuzmenko, I V; Kochanov, A A; Chertok, I M; Kalashnikov, S S

    2014-01-01

    Multi-instrument observations of two filament eruptions on 24 February and 11 May 2011 suggest the following updated scenario for eruptive flare, CME and shock wave evolution. An initial destabilization of a filament results in stretching out of magnetic threads belonging to its body and rooted in the photosphere along the inversion line. Their reconnection leads to i) heating of parts of the filament or its environment, ii) initial development of the flare arcade cusp and ribbons, and iii) increasing similarity of the filament to a curved flux rope and its acceleration. Then the pre-eruption arcade enveloping the filament gets involved in reconnection according to the standard model and continues to form the flare arcade and ribbons. The poloidal magnetic flux in the curved rope developing from the filament progressively increases and forces its toroidal expansion. This flux rope impulsively expands and produces an MHD disturbance, which rapidly steepens into a shock. The shock passes through the arcade expa...

  19. Architecture and fine structure of gill filaments in the brown mussel, perna perna

    CSIR Research Space (South Africa)

    Gregory, MA

    1996-10-01

    Full Text Available attention was paid to filament architecture, enervation of filaments, number and type of cells populating filament epithelia and variations in epithelial cell morphotogy and cilia ultra structure. Filament shape was maintained by thickened chitin...

  20. Synthesis, structure and luminescent properties of halogenated isophthalic acid-directed frameworks in virtue of flexible and semiflexible N-containing ligands

    Science.gov (United States)

    Pan, Yong-Mei; Dong, Bao-Xia; Tang, Meng; Wu, Yi-Chen; Bu, Fan-Yan; Liu, Wen-Long; Teng, Yun-Lei

    2017-07-01

    Four three-dimensional (3D) coordination complexes on the basis of 4-halogenated isophthalic acid and two types of flexible and semiflexible N-donor ligands, formulated as {[Zn(bix)(4-Br-ip)]·H2O}n (1), {[Co(bix)(4-Br-ip)]·0.5H2O}n (2), [Zn(bbi)(4-Br-ip)]n (3) and [Co(bbi)(4-Cl-ip)]n (4), (4-Br-H2ip = 4-bromoisophthalic acid, 4-Cl-H2ip = 4-chloroisophthalic acid, bix = 1,4-bis(imidazol-1-yl-methyl)benzene, bbi = 1,1‧-(1,4-butanediyl)bis(imidazole)), have been synthesized and characterized by elemental analyses, IR spectra, single-crystal and powder X-ray diffraction analyses. Compounds 1 and 2 possess the same 4-connected 66 net. Compounds 3 and 4 are isostructural and exhibit the 4-connected 412 topology. The thermal stabilities for 1-4 and photoluminescence properties for the d10 metal centers were discussed in detail.

  1. Amplitude scaling for interchange motions of plasma filaments

    CERN Document Server

    Kube, R; Garcia, O E

    2016-01-01

    We numerically study the interchange motion of seeded plasma blobs in a reduced two-field fluid model. If we neglect the compression of the electric drift in the model, the maximal radial center-of-mass velocity V of the filament follows the familiar square-root scaling V ~ (\\Delta n/N)^1/2, where \\Delta n is the blob amplitude and N is the background density. When including compression of the electric drift to account for an inhomogeneous magnetic field, the numerical simulations reveal that the maximal blob velocity depends linearly on its initial amplitude, V ~ \\Delta n/N. When the relative initial amplitude of the filament exceeds approximately unity we recover the square root velocity scaling. We explain the observed scaling laws in t erms of the conserved energy integrals of the model equations. The compression term leads to a constraint on the maximum kinetic energy of the blob, which is not present if the drift compression is ignored. If the compression term is included, only approximately half of the...

  2. CHIRALITY OF HIGH-LATITUDE FILAMENTS OVER SOLAR CYCLE 23

    Energy Technology Data Exchange (ETDEWEB)

    Yeates, A. R. [Department of Mathematical Sciences, Durham University, Durham, DH1 3LE (United Kingdom); Mackay, D. H., E-mail: anthony.yeates@durham.ac.uk, E-mail: duncan@mcs.st-and.ac.uk [School of Mathematics and Statistics, University of St Andrews, St Andrews, KY16 9SS (United Kingdom)

    2012-07-10

    A non-potential quasi-static evolution model coupling the Sun's photospheric and coronal magnetic fields is applied to the problem of filament chirality at high latitudes. For the first time, we run a continuous 15 year simulation, using bipolar active regions determined from US National Solar Observatory, Kitt Peak magnetograms between 1996 and 2011. Using this simulation, we are able to address the outstanding question of whether magnetic helicity transport from active latitudes can overcome the effect of differential rotation at higher latitudes. Acting alone, differential rotation would produce high-latitude filaments with opposite chirality to the majority type in each hemisphere. We find that differential rotation can indeed lead to opposite chirality at high latitudes, but only for around 5 years of the solar cycle following the polar field reversal. At other times, including the rising phase, transport of magnetic helicity from lower latitudes overcomes the effect of in situ differential rotation, producing the majority chirality even on the polar crowns at polar field reversal. These simulation predictions will allow for future testing of the non-potential coronal model. The results indicate the importance of long-term memory and helicity transport from active latitudes when modeling the structure and topology of the coronal magnetic field at higher latitudes.

  3. The titin A-band rod domain is dispensable for initial thick filament assembly in zebrafish.

    Science.gov (United States)

    Myhre, J Layne; Hills, Jordan A; Prill, Kendal; Wohlgemuth, Serene L; Pilgrim, David B

    2014-03-01

    The sarcomeres of skeletal and cardiac muscle are highly structured protein arrays, consisting of thick and thin filaments aligned precisely to one another and to their surrounding matrix. The contractile mechanisms of sarcomeres are generally well understood, but how the patterning of sarcomeres is initiated during early skeletal muscle and cardiac development remains uncertain. Two of the most widely accepted hypotheses for this process include the "molecular ruler" model, in which the massive protein titin defines the length of the sarcomere and provides a scaffold along which the myosin thick filament is assembled, and the "premyofibril" model, which proposes that thick filament formation does not require titin, but that a "premyofibril" consisting of non-muscle myosin, α-actinin and cytoskeletal actin is used as a template. Each model posits a different order of necessity of the various components, but these have been difficult to test in vivo. Zebrafish motility mutants with developmental defects in sarcomere patterning are useful for the elucidation of such mechanisms, and here we report the analysis of the herzschlag mutant, which shows deficits in both cardiac and skeletal muscle. The herzschlag mutant produces a truncated titin protein, lacking the C-terminal rod domain that is proposed to act as a thick filament scaffold, yet muscle patterning is still initiated, with grossly normal thick and thin filament assembly. Only after embryonic muscle contraction begins is breakdown of sarcomeric myosin patterning observed, consistent with the previously noted role of titin in maintaining the contractile integrity of mature sarcomeres. This conflicts with the "molecular ruler" model of early sarcomere patterning and supports a titin-independent model of thick filament organization during sarcomerogenesis. These findings are also consistent with the symptoms of human titin myopathies that exhibit a late onset, such as tibial muscular dystrophy.

  4. Choreography for nucleosomes: the conformational freedom of the nucleosomal filament and its limitations.

    Science.gov (United States)

    Engelhardt, Mogens

    2007-01-01

    Eukaryotic DNA is organized into nucleosomes by coiling around core particles of histones, forming a nucleosomal filament. The significance for the conformation of the filament of the DNA entry/exit angle (alpha) at the nucleosome, the angle of rotation (beta) of nucleosomes around their interconnecting DNA (linker DNA) and the length of the linker DNA, has been studied by means of wire models with straight linkers. It is shown that variations in alpha and beta endow the filament with an outstanding conformational freedom when alpha is increased beyond 60-90 degrees, owing to the ability of the filament to change between forward right-handed and backward left-handed coiling. A wealth of different helical and looped conformations are formed in response to repeated beta sequences, and helical conformations are shown to be able to contract to a high density and to associate pairwise into different types of double fibers. Filaments with random beta sequences are characterized by relatively stable loop clusters connected by segments of higher flexibility. Displacement of core particles along the DNA in such fibers, combined with limited twisting of the linkers, can generate the beta sequence necessary for compaction into a regular helix, thus providing a model for heterochromatinization.

  5. Actin filaments as the fast pathways for calcium ions involved in auditory processes

    Indian Academy of Sciences (India)

    Miljko V Sataric; Dalibor L Sekulic; Bogdan M Sataric

    2015-09-01

    We investigated the polyelectrolyte properties of actin filaments which are in interaction with myosin motors, basic participants in mechano-electrical transduction in the stereocilia of the inner ear. Here, we elaborated a model in which actin filaments play the role of guides or pathways for localized flow of calcium ions. It is well recognized that calcium ions are implicated in tuning of actin-myosin cross-bridge interaction, which controls the mechanical property of hair bundle. Actin filaments enable much more efficient delivery of calcium ions and faster mechanism for their distribution within the stereocilia. With this model we were able to semiquantitatively explain experimental evidences regarding the way of how calcium ions tune the mechanosensitivity of hair cells.

  6. The two-speed genomes of filamentous pathogens: waltz with plants.

    Science.gov (United States)

    Dong, Suomeng; Raffaele, Sylvain; Kamoun, Sophien

    2015-12-01

    Fungi and oomycetes include deep and diverse lineages of eukaryotic plant pathogens. The last 10 years have seen the sequencing of the genomes of a multitude of species of these so-called filamentous plant pathogens. Already, fundamental concepts have emerged. Filamentous plant pathogen genomes tend to harbor large repertoires of genes encoding virulence effectors that modulate host plant processes. Effector genes are not randomly distributed across the genomes but tend to be associated with compartments enriched in repetitive sequences and transposable elements. These findings have led to the 'two-speed genome' model in which filamentous pathogen genomes have a bipartite architecture with gene sparse, repeat rich compartments serving as a cradle for adaptive evolution. Here, we review this concept and discuss how plant pathogens are great model systems to study evolutionary adaptations at multiple time scales. We will also introduce the next phase of research on this topic.

  7. A CIRCULAR-RIBBON SOLAR FLARE FOLLOWING AN ASYMMETRIC FILAMENT ERUPTION

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Chang; Deng, Na; Lee, Jeongwoo; Wang, Haimin [Space Weather Research Laboratory, New Jersey Institute of Technology, University Heights, Newark, NJ 07102-1982 (United States); Liu, Rui [CAS Key Laboratory of Geospace Environment, Department of Geophysics and Planetary Sciences, University of Science and Technology of China, Hefei 230026 (China); Pariat, Étienne [LESIA, Observatoire de Paris, PSL Research University, CNRS, Sorbonne Universits, UPMC Univ. Paris 06, Univ. Paris Diderot, Sorbonne Paris Cité, F-92190 Meudon (France); Wiegelmann, Thomas [Max-Planck-Institut für Sonnensystemforschung, Justus-von-Liebig Weg 3, D-37077 Göttingen (Germany); Liu, Yang [W. W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305-4085 (United States); Kleint, Lucia, E-mail: chang.liu@njit.edu [University of Applied Sciences and Arts Northwestern Switzerland, Bahnhofstrasse 6, 5210 Windisch (Switzerland)

    2015-10-20

    The dynamic properties of flare ribbons and the often associated filament eruptions can provide crucial information on the flaring coronal magnetic field. This Letter analyzes the GOES-class X1.0 flare on 2014 March 29 (SOL2014-03-29T17:48), in which we found an asymmetric eruption of a sigmoidal filament and an ensuing circular flare ribbon. Initially both EUV images and a preflare nonlinear force-free field model show that the filament is embedded in magnetic fields with a fan-spine-like structure. In the first phase, which is defined by a weak but still increasing X-ray emission, the western portion of the sigmoidal filament arches upward and then remains quasi-static for about five minutes. The western fan-like and the outer spine-like fields display an ascending motion, and several associated ribbons begin to brighten. Also found is a bright EUV flow that streams down along the eastern fan-like field. In the second phase that includes the main peak of hard X-ray (HXR) emission, the filament erupts, leaving behind two major HXR sources formed around its central dip portion and a circular ribbon brightened sequentially. The expanding western fan-like field interacts intensively with the outer spine-like field, as clearly seen in running difference EUV images. We discuss these observations in favor of a scenario where the asymmetric eruption of the sigmoidal filament is initiated due to an MHD instability and further facilitated by reconnection at a quasi-null in corona; the latter is in turn enhanced by the filament eruption and subsequently produces the circular flare ribbon.

  8. Rheology of Active Filament Solutions

    OpenAIRE

    Liverpool, T. B.; Marchetti, M. Cristina

    2006-01-01

    We study the viscoelasticity of an active solution of polar biofilaments and motor proteins. Using a molecular model, we derive the constitutive equations for the stress tensor in the isotropic phase and in phases with liquid crystalline order. The stress relaxation in the various phases is discussed. Contractile activity is responsible for a spectacular difference in the viscoelastic properties on opposite sides of the order-disorder transition.

  9. Liquid crystal domains and thixotropy of filamentous actin suspensions.

    Science.gov (United States)

    Kerst, A; Chmielewski, C; Livesay, C; Buxbaum, R E; Heidemann, S R

    1990-06-01

    The thixotropic properties of filamentous actin suspensions were examined by a step-function shearing protocol. Samples of purified filamentous actin were sheared at 0.2 sec-1 in a cone and plate rheometer. We noted a sharp stress overshoot upon the initiation of shear, indicative of a gel state, and a nearly instantaneous drop to zero stress upon cessation of shear. Stress-overshoot recovery was almost complete after 5 min of "rest" before samples were again sheared at 0.2 sec-1. Overshoot recovery increased linearly with the square root of rest time, suggesting that gel-state recovery is diffusion limited. Actin suspensions subjected to oscillatory shearing at frequencies from 0.003 to 30 radians/sec confirmed the existence of a 5-min time scale in the gel, similar to that for stress-overshoot recovery. Flow of filamentous actin was visualized by polarized light observations. Actin from 6 mg/ml to 20 mg/ml showed the "polycrystalline" texture of birefringence typical for liquid crystal structure. At shear rates less than 1 sec-1, flow occurred by the relative movement of irregular, roughly ellipsoidal actin domains 40-140 microns long; the appearance was similar to moving ice floes. At shear rates greater than 1 sec-1, domains decreased in size, possibly by frictional interactions among domains. Eventually domains flow in a "river" of actin aligned by the flow. Our observations confirm our previous domain-friction model for actin rheology. The similarities between the unusual flow properties of actin and cytoplasm argue that cytoplasm also may flow as domains.

  10. Atomic resolution probe for allostery in the regulatory thin filament

    Science.gov (United States)

    Williams, Michael R.; Lehman, Sarah J.; Tardiff, Jil C.; Schwartz, Steven D.

    2016-01-01

    Calcium binding and dissociation within the cardiac thin filament (CTF) is a fundamental regulator of normal contraction and relaxation. Although the disruption of this complex, allosterically mediated process has long been implicated in human disease, the precise atomic-level mechanisms remain opaque, greatly hampering the development of novel targeted therapies. To address this question, we used a fully atomistic CTF model to test both Ca2+ binding strength and the energy required to remove Ca2+ from the N-lobe binding site in WT and mutant troponin complexes that have been linked to genetic cardiomyopathies. This computational approach is combined with measurements of in vitro Ca2+ dissociation rates in fully reconstituted WT and cardiac troponin T R92L and R92W thin filaments. These human disease mutations represent known substitutions at the same residue, reside at a significant distance from the calcium binding site in cardiac troponin C, and do not affect either the binding pocket affinity or EF-hand structure of the binding domain. Both have been shown to have significantly different effects on cardiac function in vivo. We now show that these mutations independently alter the interaction between the Ca2+ ion and cardiac troponin I subunit. This interaction is a previously unidentified mechanism, in which mutations in one protein of a complex indirectly affect a third via structural and dynamic changes in a second to yield a pathogenic change in thin filament function that results in mutation-specific disease states. We can now provide atom-level insight that is potentially highly actionable in drug design. PMID:26957598

  11. Microrheology of single microtubule filaments and synthesized cytoskeletal networks

    Science.gov (United States)

    Koch, Matthias; Rohrbach, Alexander

    2015-03-01

    The ability to sense and respond to external mechanical forces is crucial for cells in many processes such as cell growth and division. Common models on mechanotransduction rely on the conversion of mechanical stimuli to chemical signals in the cell periphery and their translocation by diffusion (passive) or molecular motors (active). These processes are rather slow (~ seconds) and it has been argued that the cytoskeleton itself might be able to transport a mechanical signal within microseconds via stress waves. Microtubules are the stiffest component of the cytoskeleton and thus ideal candidates for this purpose. We study the frequency dependent response of single microtubule filaments and small networks thereof in a bottom-up approach using several (N =2-10) time-multiplexed optical tweezers together with back focal plane interferometry. Small synthesized networks with a defined geometry are constructed using trapped Neutravidin beads as anchor points for biotinylated filaments. The network is then probed by a defined oscillation of one anchor (actor). The frequency dependent response of the remaining beads (sensors) is analyzed experimentally and modeled theoretically over a wide frequency range.

  12. Intergalactic Filaments as Isothermal Gas Cylinders

    CERN Document Server

    Harford, A Gayler

    2010-01-01

    Using a cosmological simulation at redshift 5, we find that the baryon-rich cores of intergalactic filaments radiating from galaxies commonly form isothermal gas cylinders. The central gas density is typically about 500 times the cosmic mean total density, and the temperature is typically 1-2 times 10^4 K, just above the Lyman alpha cooling floor. These findings argue that the hydrodynamic properties of the gas are more important than the dark matter in determining the structure. Filaments form a major pipeline for the transport of gas into the centers of galaxies. Since the temperature and ionization state of the gas completely determine the mass per unit length of an isothermal gas cylinder, our findings suggest a constraint upon gas transport into galaxies by this mechanism.

  13. Morgellons disease: a filamentous borrelial dermatitis

    Science.gov (United States)

    Middelveen, Marianne J; Stricker, Raphael B

    2016-01-01

    Morgellons disease (MD) is a dermopathy characterized by multicolored filaments that lie under, are embedded in, or project from skin. Although MD was initially considered to be a delusional disorder, recent studies have demonstrated that the dermopathy is associated with tickborne infection, that the filaments are composed of keratin and collagen, and that they result from proliferation of keratinocytes and fibroblasts in epithelial tissue. Culture, histopathological and molecular evidence of spirochetal infection associated with MD has been presented in several published studies using a variety of techniques. Spirochetes genetically identified as Borrelia burgdorferi sensu stricto predominate as the infective agent in most of the Morgellons skin specimens studied so far. Other species of Borrelia including Borrelia garinii, Borrelia miyamotoi, and Borrelia hermsii have also been detected in skin specimens taken from MD patients. The optimal treatment for MD remains to be determined. PMID:27789971

  14. Morgellons disease: a filamentous borrelial dermatitis.

    Science.gov (United States)

    Middelveen, Marianne J; Stricker, Raphael B

    2016-01-01

    Morgellons disease (MD) is a dermopathy characterized by multicolored filaments that lie under, are embedded in, or project from skin. Although MD was initially considered to be a delusional disorder, recent studies have demonstrated that the dermopathy is associated with tickborne infection, that the filaments are composed of keratin and collagen, and that they result from proliferation of keratinocytes and fibroblasts in epithelial tissue. Culture, histopathological and molecular evidence of spirochetal infection associated with MD has been presented in several published studies using a variety of techniques. Spirochetes genetically identified as Borrelia burgdorferi sensu stricto predominate as the infective agent in most of the Morgellons skin specimens studied so far. Other species of Borrelia including Borrelia garinii, Borrelia miyamotoi, and Borrelia hermsii have also been detected in skin specimens taken from MD patients. The optimal treatment for MD remains to be determined.

  15. Merging and energy exchange between optical filaments

    Energy Technology Data Exchange (ETDEWEB)

    Georgieva, D. A., E-mail: dgeorgieva@tu-sofia.bg [Faculty of Applied Mathematics and Computer Science, Technical University of Sofia, 8 Kliment Ohridski Blvd., 1000 Sofia (Bulgaria); Kovachev, L. M. [Institute of Electronics, Bulgarian Academy of Sciences, 72 Tzarigradcko Chaussee Blvd., 1784 Sofia (Bulgaria)

    2015-10-28

    We investigate nonlinear interaction between collinear femtosecond laser pulses with power slightly above the critical for self-focusing P{sub cr} trough the processes of cross-phase modulation (CPM) and degenerate four-photon parametric mixing (FPPM). When there is no initial phase difference between the pulses we observe attraction between pulses due to CPM. The final result is merging between the pulses in a single filament with higher power. By method of moments it is found that the attraction depends on the distance between the pulses and has potential character. In the second case we study energy exchange between filaments. This process is described through FPPM scheme and requests initial phase difference between the waves.

  16. Motion of current filaments in avalanching PIN diodes

    Science.gov (United States)

    Xingrong, Ren; Changchun, Chai; Zhenyang, Ma; Yintang, Yang; Liping, Qiao; Chunlei, Shi; Lihua, Ren

    2013-04-01

    The motion of current filaments in avalanching PIN diodes has been investigated in this paper by 2D transient numerical simulations. The simulation results show that the filament can move along the length of the PIN diode back and forth when the self-heating effect is considered. The voltage waveform varies periodically due to the motion of the filament. The filament motion is driven by the temperature gradient in the filament due to the negative temperature dependence of the impact ionization rates. Contrary to the traditional understanding that current filamentation is a potential cause of thermal destruction, it is shown in this paper that the thermally-driven motion of current filaments leads to the homogenization of temperature in the diode and is expected to have a positive influence on the failure threshold of the PIN diode.

  17. COMPLEX FLARE DYNAMICS INITIATED BY A FILAMENT–FILAMENT INTERACTION

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Chunming; McAteer, R. T. James [Department of Astronomy, New Mexico State University, NM 88003 (United States); Liu, Rui [CAS Key Laboratory of Geospace Environment, Department of Geophysics and Planetary Sciences, University of Science and Technology of China, Hefei 230026 (China); Alexander, David [Department of Physics and Astronomy, Rice University, TX 77005 (United States); Sun, Xudong, E-mail: czhu@nmsu.edu [W. W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305 (United States)

    2015-11-01

    We report on an eruption involving a relatively rare filament–filament interaction on 2013 June 21, observed by SDO and STEREO-B. The two filaments were separated in height with a “double-decker” configuration. The eruption of the lower filament began simultaneously with a descent of the upper filament, resulting in a convergence and direct interaction of the two filaments. The interaction was accompanied by the heating of surrounding plasma and an apparent crossing of a loop-like structure through the upper filament. The subsequent coalescence of the filaments drove a bright front ahead of the erupting structures. The whole process was associated with a C3.0 flare followed immediately by an M2.9 flare. Shrinking loops and descending dark voids were observed during the M2.9 flare at different locations above a C-shaped flare arcade as part of the energy release, giving us unique insight into the flare dynamics.

  18. The Dark Matter filament between Abell 222/223

    Science.gov (United States)

    Dietrich, Jörg P.; Werner, Norbert; Clowe, Douglas; Finoguenov, Alexis; Kitching, Tom; Miller, Lance; Simionescu, Aurora

    2016-10-01

    Weak lensing detections and measurements of filaments have been elusive for a long time. The reason is that the low density contrast of filaments generally pushes the weak lensing signal to unobservably low scales. To nevertheless map the dark matter in filaments exquisite data and unusual systems are necessary. SuprimeCam observations of the supercluster system Abell 222/223 provided the required combination of excellent seeing images and a fortuitous alignment of the filament with the line-of-sight. This boosted the lensing signal to a detectable level and led to the first weak lensing mass measurement of a large-scale structure filament. The filament connecting Abell 222 and Abell 223 is now the only one traced by the galaxy distribution, dark matter, and X-ray emission from the hottest phase of the warm-hot intergalactic medium. The combination of these data allows us to put the first constraints on the hot gas fraction in filaments.

  19. Topological Aspect of Knotted Vortex Filaments in Excitable Media

    Institute of Scientific and Technical Information of China (English)

    REN Ji-Rong; ZHU Tao; DUAN Yi-Shi

    2008-01-01

    Scroll waves exist ubiquitously in three-dimensional excitable media.The rotation centre can be regarded as a topological object called the vortex filament.In three-dimensional space,the vortex filaments usually form closed loops,and can be even linked and knotted.We give a rigorous topological description of knotted vortex filaments.By using the Φ-mapping topological current theory,we rewrite the topological current form of the charge density of vortex filaments,and using this topological current we reveal that the Hopf invariant of vortex filaments is just the sum of the linking and self-linking numbers of the knotted vortex filaments.We think that the precise expression of the Hopf invariant may imply a new topological constraint on knotted vortex filaments.

  20. Adhesion Transition of Flexible Filaments

    Science.gov (United States)

    Evans, Arthur; Lauga, Eric

    2009-03-01

    As forays into fabrication and self-assembly venture to increasingly small length scales, the role of adhesion events between material elements of the system must be closely scrutinized. This area of study is typically dominated by investigations into capillary adhesion, but relatively recent interest in carbon nanotubes and biomimetic devices have spurred interest in intermolecular forces as another source of micro- and nano-scale adhesion. We present here a far-field model for ``dry'' adhesion. We consider a small number N of flexible beams interacting with each other via a typical Lennard-Jones 6-12 potential, and describe the behavior of the system as the ratio of bending rigidity to beam-beam attraction is reduced. Applications ranging from fibrillar systems to the comparatively stiff carbon nanotubes are discussed.