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ABSTRACT: We report experimental observation of the shear thickening oscillation, i.e.
the spontaneous macroscopic oscillation in the shear flow of severe shear
thickening fluid. The shear thickening oscillation is caused by the interplay
between the fluid dynamics and the shear thickening, and has been predicted
theoretically by the present authors using a phenomenological fluid dynamics
model for the dilatant fluid, but never been reported experimentally. Using a
density-matched starch-water mixture, in the cylindrical shear flow of a few
centimeters flow width, we observed strong vibrations of the frequency around
20 Hz, which is consistent with our theoretical prediction.
11/2012;
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ABSTRACT: A dense mixture of granules and liquid often shows a severe shear thickening and is called a dilatant fluid. We construct a fluid dynamics model for the dilatant fluid by introducing a phenomenological state variable for a local state of dispersed particles. With simple assumptions for an equation of the state variable, we demonstrate that the model can describe basic features of the dilatant fluid such as the stress-shear rate curve that represents discontinuous severe shear thickening, hysteresis upon changing shear rate, and instantaneous hardening upon external impact. An analysis of the model reveals that the shear thickening fluid shows an instability in a shear flow for some regime and exhibits the shear thickening oscillation (i.e., the oscillatory shear flow alternating between the thickened and the relaxed states). The results of numerical simulations are presented for one- and two-dimensional systems.
Physical Review E 01/2012; 85(1 Pt 1):011401. · 2.26 Impact Factor
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[show abstract]
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ABSTRACT: Dense mixture of granules and liquid often shows a sever shear thickening and
is called a dilatant fluid. We construct a fluid dynamics model for the
dilatant fluid by introducing a phenomenological state variable for a local
state of dispersed particles. With simple assumptions for an equation of the
state variable, we demonstrate that the model can describe basic features of
the dilatant fluid such as the stress-shear rate curve that represents
discontinuous severe shear thickening, hysteresis upon changing shear rate,
instantaneous hardening upon external impact. Analysis of the model reveals
that the shear thickening fluid shows an instability in a shear flow for some
regime and exhibits {\it the shear thickening oscillation}, i.e. the
oscillatory shear flow alternating between the thickened and the relaxed
states. Results of numerical simulations are presented for one and
two-dimensional systems.
12/2011;
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ABSTRACT: Cultural competition has throughout our history shaped and reshaped the geography of boundaries between humans. Language and culture are intimately connected and linguists often use distinctive keywords to quantify the dynamics of information spreading in societies harboring strong culture centers. One prominent example, which is addressed here, is Kyoto's historical impact on Japanese culture. We construct a minimal model, based on shared properties of linguistic maps, to address the interplay between information flow and geography. We show that spreading of information over Japan in the premodern time can be described by an Eden growth process with noise levels corresponding to coherent spatial patches of sizes given by a single day's walk (~15 km), and that new words appear in Kyoto at times comparable to the time between human generations (~30 yr).
Physical Review E 06/2011; 83(6 Pt 2):066116. · 2.26 Impact Factor
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ABSTRACT: Cultural competition has throughout our history shaped and reshaped the
geography of boundaries between humans. Language and culture are intimately
connected and linguists often use distinctive keywords to quantify the dynamics
of information spreading in societies harbouring strong culture centres. One
prominent example, which is addressed here, is Kyoto's historical impact on
Japanese culture. We construct a first minimal model, based on shared
properties of linguistic maps, to address the interplay between information
flow and geography. In particular, we show that spreading of information over
Japan in the pre-modern time can be described as a Eden growth process, with
noise levels corresponding to coherent spatial patches of sizes given by a
single days walk, and with patch-to-patch communication time comparable to the
time between human generations.
01/2011;
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ABSTRACT: We present a phenomenological fluid dynamics model for a dilatant fluid, i.e. a severe shear thickening fluid, by introducing a state variable. The Navier-Stokes equation is coupled with the state variable field, which evolves in response to the local shear stress as the fluid is sheared. The viscosity is assumed to depend upon the state variable and to diverge at a certain value due to jamming. We demonstrate that the coupling of the fluid dynamics with the shear thickening leads to an oscillatory instability in the shear flow. The model also shows a peculiar response of the fluid to a strong external impact. Comment: 4 pages, 6 figures
10/2010;
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ABSTRACT: We study the configurational properties of single polymers in a theta solvent by Monte Carlo simulation of the bond fluctuation model. The intramolecular structure factor at the theta point is found to be distinctively different from that of the ideal chain. The structure factor shows a hump around q approximately 5/Rg and a dip around q approximately 10/Rg in the Kratky plot with Rg being the radius of gyration. This feature is apparently similar to that in a melt. The theoretical expression by the simple perturbation expansion to the first order in terms of the Mayer function can be fitted to the obtained structure factor quite well, but the second virial coefficient cannot be set to zero.
Physical Review E 11/2009; 80(5 Pt 1):051804. · 2.26 Impact Factor
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ABSTRACT: We numerically study the Loewner driving function Ut of a site percolation cluster boundary on the triangular lattice for p<pc . It is found that Ut shows a drifted random walk with a finite crossover time. Within this crossover time, the averaged driving function Ut shows a scaling behavior -(pc-p)t(nu+1)/2nu with a superdiffusive fluctuation whereas, beyond the crossover time, the driving function Ut undergoes a normal diffusion with Hurst exponent 1/2 but with the drift velocity proportional to (pc-p)nu , where nu=4/3 is the critical exponent for two-dimensional percolation correlation length. The crossover time diverges as (pc-p)-2nu as p-->pc.
Physical Review E 11/2009; 80(5 Pt 1):050102. · 2.26 Impact Factor
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ABSTRACT: We study the configurational properties of single polymers in a theta solvent by Monte Carlo simulation of the bond fluctuation model. The intramolecular structure factor at the theta point is found to be distinctively different from that of the ideal chain. The structure factor shows a hump around $q\sim 5/R_g$ and a dip around $q\sim 10/R_g$ in the Kratky plot with $R_g$ being the radius of gyration. This feature is apparently similar to that in a melt. The theoretical expression by the simple perturbation expansion to the first order in terms of the Mayer function can be fitted to the obtained structure factor quite well, but the second virial coefficient cannot be set to zero. Comment: 8 pages, 7figures
09/2009;
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ABSTRACT: The lytic-lysogenic switch of the temperate lactococcal phage TP901-1 is fundamentally different from that of phage lambda. In phage TP901-1, the lytic promoter P(L) is repressed by CI, whereas repression of the lysogenic promoter P(R) requires the presence of both of the antagonistic regulator proteins, MOR and CI. We model the central part of the switch and compare the two cases for P(R) repression: the one where the two regulators interact only on the DNA and the other where the two regulators form a heteromer complex in the cytoplasm prior to DNA binding. The models are analyzed for bistability, and the predicted promoter repression folds are compared to experimental data. We conclude that the experimental data are best reproduced the latter case, where a heteromer complex forms in solution. We further find that CI sequestration by the formation of MOR:CI complexes in cytoplasm makes the genetic switch robust.
Journal of Molecular Biology 09/2009; 394(1):15-28. · 4.00 Impact Factor
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ABSTRACT: We propose a simple phenomenological model for wet granular media to take into account many particle interaction through liquid in the funicular state as well as two-body cohesive force by a liquid bridge in the pendular state. In the wet granular media with small liquid content, liquid forms a bridge at each contact point, which induces two-body cohesive force due to the surface tension. As the liquid content increases, some liquid bridges merge, and more than two grains interact through a single liquid cluster. In our model, the cohesive force acts between the grains connected by a liquid-gas interface. As the liquid content increases, the number of grains that interact through the liquid increases, but the liquid-gas interface may decrease when liquid clusters are formed. Due to this competition, our model shows that the shear stress has a maximum as a function of the liquid-content. Comment: 6 pages, 8 figures. Discussion is updated. Accepted for publication in EPL
08/2009;
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ABSTRACT: Transcription is regulated through interplay among transcription factors, an RNA polymerase (RNAP), and a promoter. Even for a simple repressive transcription factor that disturbs promoter activity at initial binding of RNAP, its repression level is not determined solely by the dissociation constant of transcription factor but is sensitive to timescales of processes in RNAP. We first analyze the promoter activity under strong repression by a slow binding repressor, in which case transcription events occur in bursts, followed by long quiescent periods while a repressor binds to the operator; the number of transcription events, bursting, and quiescent times are estimated by reaction rates. We then examine interference effect from an opposing promoter, using the correlation function of initiation events for a single promoter. The interference is shown to de-repress the promoter because RNAPs from the opposing promoter most likely encounter the repressor and remove it in case of strong repression. This de-repression mechanism should be especially prominent for the promoters that facilitate fast formation of open complex with the repressor whose binding rate is slower than approximately 1/s. Finally, we discuss possibility of this mechanism for high activity of promoter PR in the hyp-mutant of lambda-phage.
Biophysical Journal 11/2008; 95(9):4228-40. · 3.65 Impact Factor
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ABSTRACT: It has been found in in vitro experiments that cytoskeletal filaments driven by molecular motors show finite diffusion in sliding motion even in the long filament limit [Imafuku, Y. et al. Biophys. J. 1996, 70, 878-886. Noda, N. et al. Biophysics 2005, 1, 45-53]. This anomalous fluctuation can be evidence for cooperativity among the motors in action because fluctuation should be averaged out for a long filament if the action of each motor is independent. In order to understand the nature of the fluctuation in molecular motors, we perform numerical simulations and analyze velocity correlation in three existing models that are known to show some kind of cooperativity and/or large diffusion coefficient, i.e., the Sekimoto-Tawada model [Sekimoto, K.; Tawada, K. Phys. Rev. Lett. 1995, 75, 180], the Prost model [Prost, J. et al. Phys. Rev. Lett. 1994, 72, 2652], and the Duke model [Duke, T. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 2770]. It is shown that the Prost model and the Duke model do not give a finite diffusion in the long filament limit, in spite of the collective action of motors. On the other hand, the Sekimoto-Tawada model has been shown to give a diffusion coefficient that is independent of filament length, but it comes from the long time correlation whose time scale is proportional to filament length, and our simulations show that such a long correlation time conflicts with the experimental time scales. We conclude that none of the three models represent experimental findings. In order to explain the observed anomalous diffusion, we have to search for a mechanism that will allow both the amplitude and the time scale of the velocity correlation to be independent of the filament length.
The Journal of Physical Chemistry B 03/2008; 112(5):1487-93. · 3.70 Impact Factor
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ABSTRACT: We study the effect of precollisional velocity correlations on granular shear flow by molecular dynamics simulations of an inelastic hard sphere system. Comparison of the simulations with kinetic theory reveals that the theory overestimates both the energy dissipation rate and the normal stress in the dense flow region. We find that the relative normal velocity of colliding particles is smaller than that expected from random collisions, and the discrepancies in the dissipation and the normal stress can be adjusted by introducing the idea of the collisional temperature, from which we conclude that the velocity correlation neglected in the kinetic theory is responsible for the discrepancies. Our analysis of the distributions of the precollisional velocity suggests that the correlation grows through multiple inelastic collisions during the time scale of the inverse of the shear rate. As for the shear stress, the discrepancy is also found in the dense region, but it depends strongly on the particle inelasticity.
Physical Review E 04/2007; 75(3 Pt 1):031305. · 2.26 Impact Factor
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ABSTRACT: Based on the invasion percolation model, a lattice model for the sweeping interface dynamics is constructed to describe the pattern forming process by a sweeping interface upon drying the water-granule mixture. The model is shown to produce labyrinthine patterns similar to those found in the experiment[Yamazaki and Mizuguchi, J. Phys. Soc. Jpn. \textbf{69} (2000) 2387]. Upon changing the initial granular density, resulting patterns undergo the percolation transition, but estimated critical exponents are different from those of the conventional percolation. Loopless structure of clusters in the patterns produced by the sweeping dynamics seems to influence the nature of the transition.
07/2006;
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ABSTRACT: We investigate the bulk rheology of dense granular flow down a rough slope, where the density profile has been found to show a plateau except for the boundary layers in simulations [Silbert et al., Phys. Rev. E 64, 051302 (2001)]. It is demonstrated that both the Bagnold scaling and the framework of kinetic theory are applicable in the bulk, which allows us to extract the constitutive relations from simulation data. The detailed comparison of our data with the kinetic theory shows quantitative agreement for the normal and shear stresses, but there exists a slight discrepancy in the energy dissipation, which causes a rather large disagreement in the kinetic theory analysis of the flow.
Physical Review Letters 05/2005; 94(12):128001. · 7.37 Impact Factor
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ABSTRACT: Motivated by the drying pattern experiment by Yamazaki and Mizuguchi[J. Phys. Soc. Jpn. {\bf 69} (2000) 2387], we propose the dynamics of sweeping interface, in which material distributed over a region is swept by a moving interface. A model based on a phase field is constructed and results of numerical simulations are presented for one and two dimensions. Relevance of the present model to the drying experiment is discussed.
04/2005;
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ABSTRACT: Fractal basin structure in the two-dimensional dissipative circle map is examined in detail. Numerically obtained basin appears to be riddling in the parameter region where two periodic orbits co-exist near a boundary crisis, but it is shown to consist of layers of thin bands. Comment: published in J. Phys. Soc. Jpn., 72, 1943-1947 (2003)
09/2003;
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ABSTRACT: The linear stability of rapid granular flow on a slope under gravity against the longitudinal perturbation is analyzed using hydrodynamic equations. It is demonstrated that the steady flow uniform along the flow direction becomes unstable against the long-wavelength perturbations longitudinal to the flow direction for certain parameter ranges to form the density wave, in contrast with the finite wavelength instability against the transverse perturbation (Forterre & Pouliquen 2002). It is shown that the instability can be understood as the the long-wave instability of the kinematic waves in a quasi-one dimensional system. The results are compared with our previous molecular dynamics simulations (Mitarai & Nakanishi 2001), where the spontaneous density wave formation has been found. Comment: 25 pages, 15 figures, submitted to J. Fluid Mech.; larger parameter range investigated, discussions revised
03/2003;
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ABSTRACT: Dynamical behavior of steady granular flow is investigated numerically in the inelastic hard-sphere limit of the soft-sphere model. We find distinctively different limiting behaviors for the two flow regimes, i.e., the collisional flow and the frictional flow. In the collisional flow, the hard-sphere limit is straightforward; the number of collisions per particle per unit time converges to a finite value and the total contact time fraction with other particles goes to zero. For the frictional flow, however, we demonstrate that the collision rate diverges as the power of the particle stiffness so that the time fraction of the multiple contacts remains finite even in the hard-sphere limit, although the contact time fraction for the binary collisions tends to zero.
Physical Review E 03/2003; 67(2 Pt 1):021301. · 2.26 Impact Factor
