Academic literature on the topic 'Filament packings'
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Journal articles on the topic "Filament packings"
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Hall, Douglas M., and Gregory M. Grason. "How geometric frustration shapes twisted fibres, inside and out: competing morphologies of chiral filament assembly." Interface Focus 7, no. 4 (June 16, 2017): 20160140. http://dx.doi.org/10.1098/rsfs.2016.0140.
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Chirality frustrates and shapes the assembly of flexible filaments in rope-like, twisted bundles and fibres by introducing gradients of both filament shape (i.e. curvature) and packing throughout the structure. Previous models of chiral filament bundle formation have shown that this frustration gives rise to several distinct morphological responses, including self-limiting bundle widths, anisotropic domain (tape-like) formation and topological defects in the lateral inter-filament order. In this paper, we employ a combination of continuum elasticity theory and discrete filament bundle simulations to explore how these distinct morphological responses compete in the broader phase diagram of chiral filament assembly. We show that the most generic model of bundle formation exhibits at least four classes of equilibrium structure—finite-width, twisted bundles with isotropic and anisotropic shapes, with and without topological defects, as well as bulk phases of untwisted, columnar assembly (i.e. ‘frustration escape’). These competing equilibrium morphologies are selected by only a relatively small number of parameters describing filament assembly: bundle surface energy, preferred chiral twist and stiffness of chiral filament interactions, and mechanical stiffness of filaments and their lateral interactions. Discrete filament bundle simulations test and verify continuum theory predictions for dependence of bundle structure (shape, size and packing defects of two-dimensional cross section) on these key parameters.
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Madden, T. L., and J. Herzfeld. "Crowding-induced organization of cytoskeletal elements: II. Dissolution of spontaneously formed filament bundles by capping proteins." Journal of Cell Biology 126, no. 1 (July 1, 1994): 169–74. http://dx.doi.org/10.1083/jcb.126.1.169.
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Through calculations of molecular packing constraints in crowded solutions, we have previously shown that dispersions of filament forming proteins and soluble proteins can be unstable at physiological concentrations, such that tight bundles of filaments are formed spontaneously, in the absence of any accessory binding proteins. Here we consider the modulation of this phenomenon by capping proteins. The theory predicts that, by shortening the average filament length, capping alleviates the packing problem. As a result, the dispersed isotropic solution is stable over an expanded range of compositions.
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Riley, Danny A., James L. W. Bain, Joyce L. Thompson, Robert H. Fitts, Jeffrey J. Widrick, Scott W. Trappe, Todd A. Trappe, and David L. Costill. "Thin filament diversity and physiological properties of fast and slow fiber types in astronaut leg muscles." Journal of Applied Physiology 92, no. 2 (February 1, 2002): 817–25. http://dx.doi.org/10.1152/japplphysiol.00717.2001.
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Slow type I fibers in soleus and fast white (IIa/IIx, IIx), fast red (IIa), and slow red (I) fibers in gastrocnemius were examined electron microscopically and physiologically from pre- and postflight biopsies of four astronauts from the 17-day, Life and Microgravity Sciences Spacelab Shuttle Transport System-78 mission. At 2.5-μm sarcomere length, thick filament density is ∼1,012 filaments/μm2 in all fiber types and unchanged by spaceflight. In preflight aldehyde-fixed biopsies, gastrocnemius fibers possess higher percentages (∼23%) of short thin filaments than soleus (9%). In type I fibers, spaceflight increases short, thin filament content from 9 to 24% in soleus and from 26 to 31% in gastrocnemius. Thick and thin filament spacing is wider at short sarcomere lengths. The Z-band lattice is also expanded, except for soleus type I fibers with presumably stiffer Z bands. Thin filament packing density correlates directly with specific tension for gastrocnemius fibers but not soleus. Thin filament density is inversely related to shortening velocity in all fibers. Thin filament structural variation contributes to the functional diversity of normal and spaceflight-unloaded muscles.
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Drenckhahn, D., K. Engel, D. Höfer, C. Merte, L. Tilney, and M. Tilney. "Three different actin filament assemblies occur in every hair cell: each contains a specific actin crosslinking protein." Journal of Cell Biology 112, no. 4 (February 15, 1991): 641–51. http://dx.doi.org/10.1083/jcb.112.4.641.
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The apex of hair cells of the chicken auditory organ contains three different kinds of assemblies of actin filaments in close spatial proximity. These are (a) paracrystals of actin filaments with identical polarity in stereocilia, (b) a dense gellike meshwork of actin filaments forming the cuticular plate, and (c) a bundle of parallel actin filaments with mixed polarities that constitute the circumferential filament belt attached to the cytoplasmic aspect of the zonula adhaerens (ZA). Each different supramolecular assembly of actin filaments contains a specific actin filament cross-linking protein which is unique to that particular assembly. Thus fimbrin appears to be responsible for paracrystallin packing of actin filaments in stereocillia; an isoform of spectrin resides in the cuticular plate where it forms the whisker-like crossbridges, and alpha actinin is the actin crosslinking protein of the circumferential ZA bundle. Tropomyosin, which stabilizes actin filaments, is present in all the actin filament assemblies except for the stereocilia. Another striking finding was that myosin appears to be absent from the ZA ring and cuticular plate of hair cells although present in the ZA ring of supporting cells. The abundance of myosin in the ZA ring of the surrounding supporting cells means that it may be important in forming a supporting tensile cellular framework in which the hair cells are inserted.
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Skubiszak, Ludmila, and Leszek Kowalczyk. "Myosin molecule packing within the vertebrate skeletal muscle thick filaments. A complete bipolar model." Acta Biochimica Polonica 49, no. 4 (December 31, 2002): 829–40. http://dx.doi.org/10.18388/abp.2002_3743.
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Computer modelling related to the real dimensions of both the whole filament and the myosin molecule subfragments has revealed two alternative modes for myosin molecule packing which lead to the head disposition similar to that observed by EM on the surface of the cross-bridge zone of the relaxed vertebrate skeletal muscle thick filaments. One of the modes has been known for three decades and is usually incorporated into the so-called three-stranded model. The new mode differs from the former one in two aspects: (1) myosin heads are grouped into asymmetrical cross-bridge crowns instead of symmetrical ones; (2) not the whole myosin tail, but only a 43-nm C-terminus of each of them is straightened and near-parallel to the filament axis, the rest of the tail is twisted. Concurrent exploration of these alternative modes has revealed their influence on the filament features. The parameter values for the filament models as well as for the building units depicting the myosin molecule subfragments are verified by experimental data found in the literature. On the basis of the new mode for myosin molecule packing a complete bipolar structure of the thick filament is created.
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Gotow, T., T. Tanaka, Y. Nakamura, and M. Takeda. "Dephosphorylation of the largest neurofilament subunit protein influences the structure of crossbridges in reassembled neurofilaments." Journal of Cell Science 107, no. 7 (July 1, 1994): 1949–57. http://dx.doi.org/10.1242/jcs.107.7.1949.
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Phosphorylation-dependent change in electrophoretic mobility is the most unique characteristic of NF-H, the largest molecular mass subunit of the neurofilament. We dephosphorylated NF-H using Escherichia coli alkaline phosphatase, then reassembled it into neurofilaments with NF-M and NF-L, and into NF-H filaments with NF-H alone. We compared these dephosphorylated filaments with control: projections by low-angle rotary-shadow, crossbridges by quick-freeze deep-etch, and core filament packing density by thin-section electron microscopy. Projections in the dephosphorylated filaments were basically similar in structure to those in control, although there was a tendency for them to be wider and less dense, especially in NF-H filaments. Dephosphorylated filaments were still able to form crossbridges between core filaments, but their crossbridges were significantly wider, less dense, more branched and more irregular than crossbridges in control, and core filaments were more densely packed. These structural differences may be brought about by the removal of phosphate groups from NF-H tail and consequent reduction of electrostatic repulsion between adjacent crossbridges extending from the same core filament. The results indicate that phosphorylation of NF-H is necessary for forming well developed crossbridges, straight and at constant intervals, like those of in vivo axonal neurofilaments.
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Trybus, K. M., and S. Lowey. "Assembly of smooth muscle myosin minifilaments: effects of phosphorylation and nucleotide binding." Journal of Cell Biology 105, no. 6 (December 1, 1987): 3007–19. http://dx.doi.org/10.1083/jcb.105.6.3007.
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Small bipolar filaments, or "minifilaments," are formed when smooth muscle myosin is dialyzed against low ionic strength pyrophosphate or citrate/Tris buffers. Unlike synthetic filaments formed at approximately physiological ionic conditions, minifilaments are homogeneous as indicated by their hypersharp boundary during sedimentation velocity. Electron microscopy and hydrodynamic techniques were used to show that 20-22S smooth muscle myosin minifilaments are 380 nm long and composed of 12-14 molecules. By varying solvents, a continuum of different size polymers in the range of 15-30S could be obtained. Skeletal muscle myosin, in contrast, preferentially forms a stable 32S minifilament (Reisler, E., P. Cheung, and N. Borochov. 1986. Biophys. J. 49:335-342), suggesting underlying differences in the assembly properties of the two myosins. Addition of salt to the smooth muscle myosin minifilaments caused unidirectional growth into a longer "side-polar" type of filament, whereas bipolar filaments were consistently formed by skeletal muscle myosin. As with synthetic filaments, addition of 1 mM MgATP caused dephosphorylated minifilaments to dissociate to a mixture of folded monomers and dimers. Phosphorylation of the regulatory light chain prevented disassembly by nucleotide, even though it had no detectable effect on the structure of the minifilament. These results suggest that differences in filament stability as a result of phosphorylation are due largely to conformational changes occurring in the myosin head, and are not due to differences in filament packing.
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Rovner, Arthur S., Patricia M. Fagnant, Susan Lowey, and Kathleen M. Trybus. "The carboxyl-terminal isoforms of smooth muscle myosin heavy chain determine thick filament assembly properties." Journal of Cell Biology 156, no. 1 (January 7, 2002): 113–24. http://dx.doi.org/10.1083/jcb.200107131.
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The alternatively spliced SM1 and SM2 smooth muscle myosin heavy chains differ at their respective carboxyl termini by 43 versus 9 unique amino acids. To determine whether these tailpieces affect filament assembly, SM1 and SM2 myosins, the rod region of these myosin isoforms, and a rod with no tailpiece (tailless), were expressed in Sf 9 cells. Paracrystals formed from SM1 and SM2 rod fragments showed different modes of molecular packing, indicating that the tailpieces can influence filament structure. The SM2 rod was less able to assemble into stable filaments than either SM1 or the tailless rods. Expressed full-length SM1 and SM2 myosins showed solubility differences comparable to the rods, establishing the validity of the latter as a model for filament assembly. Formation of homodimers of SM1 and SM2 rods was favored over the heterodimer in cells coinfected with both viruses, compared with mixtures of the two heavy chains renatured in vitro. These results demonstrate for the first time that the smooth muscle myosin tailpieces differentially affect filament assembly, and suggest that homogeneous thick filaments containing SM1 or SM2 myosin could serve distinct functions within smooth muscle cells.
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Sazzed, Salim, Peter Scheible, Jing He, and Willy Wriggers. "Spaghetti Tracer: A Framework for Tracing Semiregular Filamentous Densities in 3D Tomograms." Biomolecules 12, no. 8 (July 23, 2022): 1022. http://dx.doi.org/10.3390/biom12081022.
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Within cells, cytoskeletal filaments are often arranged into loosely aligned bundles. These fibrous bundles are dense enough to exhibit a certain regularity and mean direction, however, their packing is not sufficient to impose a symmetry between—or specific shape on—individual filaments. This intermediate regularity is computationally difficult to handle because individual filaments have a certain directional freedom, however, the filament densities are not well segmented from each other (especially in the presence of noise, such as in cryo-electron tomography). In this paper, we develop a dynamic programming-based framework, Spaghetti Tracer, to characterizing the structural arrangement of filaments in the challenging 3D maps of subcellular components. Assuming that the tomogram can be rotated such that the filaments are oriented in a mean direction, the proposed framework first identifies local seed points for candidate filament segments, which are then grown from the seeds using a dynamic programming algorithm. We validate various algorithmic variations of our framework on simulated tomograms that closely mimic the noise and appearance of experimental maps. As we know the ground truth in the simulated tomograms, the statistical analysis consisting of precision, recall, and F1 scores allows us to optimize the performance of this new approach. We find that a bipyramidal accumulation scheme for path density is superior to straight-line accumulation. In addition, the multiplication of forward and backward path densities provides for an efficient filter that lifts the filament density above the noise level. Resulting from our tests is a robust method that can be expected to perform well (F1 scores 0.86–0.95) under experimental noise conditions.
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Hasegawa, Kazuya, Ichiro Yamashita, Yuko Mimori-Kiyosue, Ferenc Vonderviszt, and Keiichi Namba. "Molecular Mechanisms of Self-Assembly and Polymorphic Switching of the Bacterial Flagellum." Microscopy and Microanalysis 5, S2 (August 1999): 1034–35. http://dx.doi.org/10.1017/s1431927600018493.
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Bacterial flagellum is a helical filament by means of which bacteria swim. Each filament rotated by the motor at its base works as a screw that propels the cell, but it is not simply a rigid propeller. The filament is normally in a left-handed supercoiled form and several of them form a bundle when bacteria swim. Upon quick reversal of the motor rotation, which occurs every few seconds, the filament switches into a right-handed supercoil, making the filament bundle fall apart and enabling the cell to tumble for its tactic behavior. The filament is a tubular structure formed by helical assembly of single protein, flagellin, whose molecular mass is 51.5 kDa in the case of Salmonella typhimurium, which we study. The supercoiling of the filament is thought to involve two distinct subunit conformations and/or packing, whose mechanism is interesting in terms of conformational distinctness and adaptability of flagellin.To understand the mechanisms of self-assembly and polymorphism of the filament, electron cryomicroscopy (EM) and X-ray fiber diffraction have been used to analyze the structures of two straight filaments with distinct helical symmetries.
Dissertations / Theses on the topic "Filament packings"
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Evans, Myfanwy Ella. "Three-dimensional entanglement: knots, knits and nets." Phd thesis, 2011. http://hdl.handle.net/1885/9502.
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Three-dimensional entanglement, including knots, periodic arrays of woven filaments (weavings) and periodic arrays of interpenetrating networks (nets), forms an integral part of the analysis of structure within the natural sciences. This thesis constructs a catalogue of 3-periodic entanglements via a scaffold of Triply-Periodic Minimal Surfaces (TPMS). The two-dimensional Hyperbolic plane can be wrapped over a TPMS in much the same way as the two-dimensional Euclidean plane can be wrapped over a cylinder. Thus vertices and edges of free tilings of the Hyperbolic plane, which are tilings by tiles of infinite size, can be wrapped over a TPMS to represent vertices and edges of an array in three-dimensional Euclidean space. In doing this, we harness the simplicity of a two-dimensional surface as compared with 3D space to build our catalogue.
We numerically tighten these entangled flexible knits and nets to an ideal conformation that minimises the ratio of edge (or filament) length to diameter. To enable the tightening of periodic entanglements which may contain vertices, we extend the Shrink-On-No-Overlaps algorithm, a simple and fast algorithm for tightening finite knots and links. The ideal geometry of 3-periodic weavings found through the tightening process exposes an interesting physical property: Dilatancy. The cooperative straightening of the filaments with a fixed diameter induces an expansion of the material accompanied with an increase in the free volume of the material. Further, we predict a dilatant rod packing as the structure of the keratin matrix in the corneocytes of mammalian skin, where the dilatant property of the matrix allows the skin to maintain structural integrity while experiencing a large expansion during the uptake of water.
Conference papers on the topic "Filament packings"
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Devra, Rajdeep Singh, Nishkarsh Srivastava, Madhu Vadali, and Amit Arora. "Polymer Filament Extrusion Using LDPE Waste Polymer: Effect of Processing Temperature." In ASME 2022 17th International Manufacturing Science and Engineering Conference. American Society of Mechanical Engineers, 2022. http://dx.doi.org/10.1115/msec2022-85586.
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Abstract Low-density polyethylene (LDPE) is a soft thermoplastic with extensive application as a packing material such as plastic bags, dispensing bottles, milk pouches, etc. Many LDPE bags are used and dumped in landfills every year, leading to millions of tons of persistent waste. In addition, the recycling of LDPE is of no commercial interest due to its low stiffness, poor mechanical properties, and limited commercial application. In the current work, we attempt to recycle milk pouches made of LDPE to create polymer filaments for fused deposition modeling (FDM), thereby adding value to waste plastic by converting it into high-value 3D printer filament. This research examines the feasibility of reclamation of waste LDPE milk pouches as filament for 3D printers and studies the changes in filament’s chemical and mechanical properties when produced at different temperatures. The waste milk pouches are cleaned thoroughly, shredded, and extruded using a single screw extruder at three nozzle temperatures, i.e., 150°C, 180°C, 210°C. The extruded specimens are analyzed using an optical microscope and scanning electron microscope (SEM) for surface texture. The effect of change in process temperature on flow behaviors is also studied by integrating a current sensor and an encoder. Fourier transform infrared spectroscopy (FTIR) analysis is performed on the filaments and the used LDPE milk pouches to compare the chemical bondings of the polymer. The mechanical properties of the extruded filaments are examined using dynamic mechanical analysis (DMA). The morphological analysis, chemical characterization, and mechanical characterization of prepared filaments are presented. The results show that the chemical bondings are intact after extrusion at all the temperatures examined in this work. The surface texture and the mechanical properties are better at higher temperatures owing to better fluidity and are more suitable for fused deposition modeling. Thus, it is possible to valorize waste LDPE milk pouches by transforming them into filaments for 3D printing.
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Hu, Chaohui. "Study on the factors which affecting the conductive anodic filament reliability for packing substrate." In 2017 18th International Conference on Electronic Packaging Technology (ICEPT). IEEE, 2017. http://dx.doi.org/10.1109/icept.2017.8046593.
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