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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of scientific computing 11 (1996), S. 179-205 
    ISSN: 1573-7691
    Keywords: Compressible flows ; direct numerical simulation ; essentially non-oscillatory ; parallel processing ; turbulence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Notes: Abstract In this paper, a finite-difference based ENO (essentially nonoscillatory) procedure has been chosen for the direct numerical simulation (DNS) of compressible turbulence. The implementation of the ENO scheme follows the relatively efficient procedure in Shuet al. (1992), but the latter has been modified in the present paper to admit scalar conservation equations and to run on the iPSC/860 Paragon parallel supercomputer. DNS results with our procedure are in excellent agreement with pseudo-spectral and Padé approximation calculations in two and three dimensions. This is the case for a variety of initial conditions for compressible turbulence. The parallel algorithms presented are simple but quite efficient for DNS, with a speedup that approaches the theoretical value. Some of the attractive features include 1) minimum communication whereby a processor only communicates with two neighbors, 2) almost one hundred percent load balancing, 3) a checker-board approach to solve the Poisson equation reduces communication by a factor of approximately 2, and, 4) obtaining turbulence statistics is based on a ‘global collect’ approach, which is implemented to ensure that a single number, rather than a large matrix of numbers, is communicated between processors. The ENO code presented in this paper should be quite useful in its own right, while the parallel implementation should allow the simulation of fairly realistic problems.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 55-62 
    ISSN: 0886-1544
    Keywords: purified tubulin ; computer simulations ; polymer loss ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Microtubules were assembled from purified tubulin in the buffer originally used to study dynamic instability (100 mM PIPES, 2 mM EGTA, 1 mM magnesium, 0.2 mM GTP) and then diluted in the same buffer to study the rate of disassembly. Following a 15-fold dilution, microtubule polymer decreased linearly to about 20% of the starting value in 15 sec. We determined the length distribution of microtubules before dilution, and prepared computer simulations of polymer loss for different assumed rates of disassembly. Our experimental data were consistent with a disassembly rate per microtubules of 60 μm/min. This is the total rate of depolymerization for microtubules in the rapid shortening phase, as determined by light microscopy of individual microtubules (Walker et al.: Journal of Cell Biology 107:1437-1448, 1988). We conclude, therefore, that microtubules began rapid shortening at both ends upon dilution. Moreover, since we could detect no lag between dilution and the onset of rapid disassembly, the transition from elongation to rapid shortening apparently occurred within 1 sec following dilution. Assuming that this transition (catastrophe) involves the loss of the GTP cap, and that cap loss is achieved by the sequential dissociation of GTP-tubulin subunits following dilution, we can estimate the maximum size of the cap based on the kinetic data and model interpretation of Walker et al. The cap is probably shorter than 40 and 20 subunits at the plus and minus ends, respectively.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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