arXiv subjects

Hiizu Nakanishi

Publications and source records attributed to Hiizu Nakanishi.

At least 19 recordsLinked to original sources

arXiv2021

Fold analysis of crumpled sheet using micro computed tomography

Hand crumpled paper balls involve intricate structure with a network of creases and vertices, yet show simple scaling properties, which suggests self-similarity of the structure. We investigate the internal structure of crumpled papers by the micro computed tomography (micro-CT) without destroying or unfolding them. From the reconstructed three dimensional data, we examine several power laws for the crumpled square sheets of paper of the sizes $L=50\sim 300$ mm, and obtain the mass fractal dimension $D_M = 2.7\pm 0.1$ by the relation between the mass and the radius of gyration of the balls, and the fractal dimension $2.5\lesssim d_f \lesssim 2.8$ for the internal structure of each crumpled paper ball by the box counting method in the real space and the structure factors in the Fourier space; The data for the paper sheets are consistent with $D_M = d_f$, suggesting that the self-similarity in the structure of each crumpled ball gives rise to the similarity among the balls with different sizes. We also examine the cellophane sheets and the aluminium foils of the size $L=200$ mm and obtain $2.6\lesssim d_f\lesssim 2.8$ for both of them. The micro-CT also allows us to reconstruct 3-d structure of a line drawn on the crumpled sheets of paper. The Hurst exponent for the root mean square displacement along the line is estimated as $H\approx 0.9$ for the length scale shorter than the scale of the radius of gyration, beyond which the line structure becomes more random with $H\sim 0.5$.

cond-mat.soft↗

arXiv2020

Stabilization of straight longitudinal dune under bimodal wind with large directional variation

It has been observed that the direction in which a sand dune extends its crest line depends on seasonal variation of wind direction; when the variation is small, the crest line develops more or less perpendicularly to the mean wind direction to form a transverse dune with some undulation. In the case of bimodal wind with a large relative angle, however, the dune extends its crest along the mean wind direction and evolves into an almost straight longitudinal dune. Motivated by these observations, we investigate the dynamical stability of isolated dunes using the crest line model, where the dune dynamics is represented by its crest line motion. First, we extend the previous linear stability analysis under the unidirectional wind to the case with non-zero slant angle between the wind direction and the normal direction of the crest line, and show that the stability diagram does not depend on the slant angle. Secondly, we examine how the linear stability is affected by the seasonal changes of wind direction in the case of bimodal wind with equal strength and duration. For the transverse dune, we find that the stability is virtually the same with that for the unidirectional wind as long as the dune evolution during a season is small. On the other hand, in the case of the longitudinal dune, the dispersions of the growth rates for the perturbation are drastically different from those of the unidirectional wind, and we find that the largest growth rate is always located at $k = 0$. This is because the growth of the perturbation with $k \ne 0$ is canceled by the alternating wind from opposite sides of the crest line even though it grows during each duration period of the bimodal wind.

cond-mat.soft↗

arXiv2017

Rattleback dynamics and its reversal time of rotation

A rattleback is a rigid, semi-elliptic toy which exhibits unintuitive behavior; when it is spun in one direction, it soon begins pitching and stops spinning, then it starts to spin in the opposite direction, but in the other direction, it seems to spin just steadily. This puzzling behavior results from the slight misalignment between the principal axes for the inertia and those for the curvature; the misalignment couples the spinning with the pitching and the rolling oscillations. It has been shown that under the no-slip condition and without dissipation the spin can reverse in both directions, and Garcia and Hubbard obtained the formula for the time required for the spin reversal $t_r$ [Proc. R. Soc. Lond. A 418, 165-197 (1988) ]. In this work, we reformulate the rattleback dynamics in a physically transparent way and reduce it to a three-variable dynamics for spinning, pitching, and rolling. We obtain an expression of the Garcia-Hubbard formula for $t_r$ by a simple product of four factors: (1) the misalignment angle, (2) the difference in the inverses of inertia moment for the two oscillations, (3) that in the radii for the two principal curvatures, and (4) the squared frequency of the oscillation. We perform extensive numerical simulations to examine validity and limitation of the formula, and find that (1) the Garcia-Hubbard formula is good for both spinning directions in the small spin and small oscillation regime, but (2) in the fast spin regime especially for the steady direction, the rattleback may not reverse and shows a rich variety of dynamics including steady spinning, spin wobbling, and chaotic behavior reminiscent of chaos in a dissipative system.

physics.class-ph↗

arXiv2017

Compressive response and helix formation of a semi flexible polymer confined in a nanochannel

Configurations of a single semiflexible polymer is studied when it is pushed into a nanochannel in the case where the polymer persistence length $l_p$ is much longer than the channel diameter $D$, i.e. $l_p/D \gg 1$. Using numerical simulations, we show that the polymer undergoes a sequence of recurring structural transitions upon longitudinal compression, i.e. random deflection along the channel, helix going around the channel wall, double-fold random deflection, double-fold helix, etc. We find that the helix transition can be understood as buckling of deflection segments, and the initial helix formation takes place at very small compression with no appreciable weak compression regime of the random deflection polymer.

cond-mat.stat-mech↗

arXiv2016

Negative pressure in shear thickening band of a dilatant fluid

We perform experiments and numerical simulations to investigate spatial distribution of pressure in a sheared dilatant fluid of the Taylor-Couette flow under a constant external shear stress. In a certain range of shear stress, the flow undergoes the shear thickening oscillation around 20 Hz. We find that, during the oscillation, a localized thickened band rotates around the axis with the flow. {Based upon experiments and numerical simulations, we show that a major part of the thickened band is under negative pressure even in the case of discontinuous shear thickening}, which indicates that the thickening is caused by Reynolds dilatancy; the dilatancy causes the negative pressure in interstitial fluid, which generates contact structure in the granular medium., then frictional resistance hinders rearrangement of the structure and solidifies the medium.

physics.flu-dyn↗

arXiv2015

Dynamics of microdroplets over the surface of hot water

When drinking a cup of coffee under the morning sunshine, you may notice white membranes of steam floating on the surface of the hot water. They stay notably close to the surface and appear to almost stick to it. Although the membranes whiffle because of the air flow of rising steam, peculiarly fast splitting events occasionally occur. They resemble cracking to open slits approximately 1 mm wide in the membranes, and leave curious patterns. We studied this phenomenon using a microscope with a high-speed video camera and found intriguing details: i) the white membranes consist of fairly monodispersed small droplets of the order of 10 $μ\,{\rm m}$; ii) they levitate above the water surface by 10$\sim$100 $μ{\rm m}$; iii) the splitting events are a collective disappearance of the droplets, which propagates as a wave front of the surface wave with a speed of 1$\sim$2 m/s; and iv) these events are triggered by a surface disturbance, which results from the disappearance of a single droplet.

cond-mat.soft↗

arXiv2014

Dynamical Scaling of Polymerized Membranes

Monte Carlo simulations have been performed to analyze the sub-diffusion dynamics of a tagged monomer in self-avoiding polymerized membranes in the flat phase. By decomposing the mean square displacement into the out-of-plane ($\parallel$) and the in-plane ($\perp$) components, we obtain good data collapse with two distinctive diffusion exponents $2 α_{\parallel} = 0.36 \pm 0.01$ and $2 α_{\perp} = 0.21 \pm 0.01$, and the roughness exponents $ζ_{\parallel} = 0.6 \pm 0.05$ and $ζ_{\perp} = 0.25 \pm 0.05 $, respectively for each component. Their values are consistent with the relation from the rotational symmetry. We derive the generalized Langevin equations to describe the sub-diffusional behaviors of a tagged monomer in the intermediate time regime where the collective effect of internal modes in the membrane dominate the dynamics to produce negative memory kernels with a power-law. We also briefly discuss how the long-range hydrodynamic interactions alter the exponents.

cond-mat.soft↗

arXiv2013

Hamilton-Jacobi method for molecular distribution function in a chemical oscillator

Using the Hamilton-Jacobi method, we solve chemical Fokker-Planck equations within the Gaussian approximation and obtain a simple and compact formula for a conditional probability distribution. The formula holds in general transient situations, and can be applied not only for a steady state but also for a oscillatory state. By analyzing the long time behavior of the solution in the oscillatory case, we obtain the phase diffusion constant along the periodic orbit and the steady distribution perpendicular to it. A simple method for numerical evaluation of these formulas are devised, and they are compared with Monte Carlo simulations in the case of Brusselator as an example. Some results are shown to be identical to previously obtained expressions.

cond-mat.stat-mech↗

arXiv2013

Experimental observation of shear thickening oscillation

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.

physics.flu-dyn↗

arXiv2013

Inelastic collapse in one-dimensional driven systems under gravity

We study the inelastic collapse in the one-dimensional $N$-particle systems in the situation where the system is driven from below under the gravity. We investigate the hard-sphere limit of the inelastic soft-sphere systems by numerical simulations to find how the collision rate per particle $n_{coll}$ increases as a function of the elastic constant of the sphere $k$ when the restitution coefficient $e$ is kept constant. For the systems with large enough $N \agt 20$, we find three regimes in $e$ depending on the behavior of $n_{coll}$ in the hard-sphere limit: (i) uncollapsing regime for $1 \ge e > e_{c1}$, where $n_{coll}$ converges to a finite value, (ii) logarithmically collapsing regime for $e_{c1} > e > e_{c2}$, where $n_{coll}$ diverges as $n_{coll} \sim \log k$, and (iii) power-law collapsing regime for $e_{c2} > e > 0$, where $n_{coll}$ diverges as $n_{coll} \sim k^α$ with an exponent $α$ that depends on $N$. The power-law collapsing regime shrinks as $N$ decreases and seems not to exist for the system with N=3 while, for large $N$, the size of the uncollapsing and the logarithmically collapsing regime decreases as $e_{c1} \simeq 1-2.6/N$ and $e_{c2} \simeq 1-3.0/N$. We demonstrate that this difference between large and small systems exists already in the inelastic collapse without the external drive and the gravity.

cond-mat.soft↗

arXiv2012

Transcription fluctuation effects on biochemical oscillations

Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules involved are small, ii) there are typically only a couple of genes in a cell with a finite regulation time scale. Due to the fluctuations caused by these features, the system behavior can be quite different from the one obtained by rate equations, because the rate equations ignore molecular fluctuations and thus are exact only in the infinite molecular number limit. The molecular fluctuations on a free-running circadian system have been studied by Gonze et al. (2002) by introducing a scale parameter $Ω$ for the system size. They consider, however, only the first effect, assuming that the gene process is fast enough for the second effect to be ignored, but this has not been examined systematically yet. In this work, we study fluctuation effects due to the finite gene regulation time by introducing a new scale parameter $τ$, which we take as the unbinding time of a nuclear protein from the gene. We focus on the case where the fluctuations due to small molecular numbers can be ignored. In simulations on the same system studied by Gonze et al., we find the system is sensitive to the fluctuation in the transcription regulation; the period of oscillation fluctuates about 30 min even when the regulation time scale $τ$ is around 30 s, that is even smaller than 1/1000 of its circadian period. We also demonstrate that the distribution width for the oscillation period and the amplitude scales with $\sqrtτ$, and the correlation time of the oscillation scales with $1/τ$ in the small $τ$ regime. The relative fluctuations for the period are about half of that for the amplitude, namely, the periodicity is more stable than the amplitude.

q-bio.MN↗

arXiv2011

Fluid dynamics of dilatant fluid

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.

cond-mat.soft↗

arXiv2011

Modelling the Spatial Dynamics of Culture Spreading in the Presence of Cultural Strongholds

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.

physics.soc-ph↗

arXiv2010

Fluid dynamics and jamming in a dilatant fluid

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.

cond-mat.soft↗

arXiv2009

Simple Model for Wet Granular Materials with Liquid Clusters

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.

cond-mat.soft↗

arXiv2009

Loewner driving functions for off-critical percolation clusters

We numerically study the Loewner driving function U_t of a site percolation cluster boundary on the triangular lattice for p shows a scaling behavior -(p_c-p) t^{(ν+1)/2ν} with a superdiffusive fluctuation whereas, beyond the crossover time, the driving function U_t undergoes a normal diffusion with Hurst exponent 1/2 but with the drift velocity proportional to (p_c-p)^ν, where ν= 4/3 is the critical exponent for two-dimensional percolation correlation length. The crossover time diverges as (p_c-p)^{-2ν} as p\to p_c.

cond-mat.stat-mech↗

arXiv2009

Non-ideal behavior of intramolecular structure factor of dilute polymers in a theta solvent

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.

cond-mat.soft↗

arXiv2009

Modeling of the genetic switch of bacteriophage TP901-1: A heteromer of CI and MOR ensures robust bistability

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 PL is repressed by CI whereas repression of the lysogenic promoter PR 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 PR 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.

q-bio.MN↗