arXiv subjects

Kenichi Yoshikawa

Publications and source records attributed to Kenichi Yoshikawa.

At least 19 recordsLinked to original sources

arXiv2015

Discrimination of time-dependent inflow properties with a cooperative dynamical system

Many physical, chemical and biological systems exhibit a cooperative or sigmoidal response with respect to the input. In biochemistry, such behavior is called an allosteric effect. Here we demonstrate that a system with such properties can be used to discriminate the amplitude or frequency of an external periodic perturbation or input. Numerical simulations performed for a model sigmoidal kinetics illustrate that there exists a narrow range of frequencies and amplitudes within which the system evolves toward significantly different states. Therefore, observation of system evolution should provide information about the characteristics of the perturbation. The discrimination properties for periodic perturbation are generic. They can be observed in various dynamical systems and for different types of periodic perturbation. \end{abstract}

nlin.AO↗

arXiv2015

Anomalous roughening of forced radial imbibition in a porous medium

We report forced radial imbibition of water in a porous medium in a Hele-Shaw cell. Washburn's law is confirmed in our experiment. Radial imbibition follows scaling dynamics and shows anomalous roughening dynamics when the front invades the porous medium. The roughening dynamics depend on the flow rate of the injected fluid. The growth exponents increase linearly with an increase in the flow rate while the roughness exponents decrease with an increase in the flow rate. Roughening dynamics of radial imbibition is markedly different from one dimensional imbibition with a planar interface window. Such difference caused by geometric change suggests that "universality class" for the interface growth is not universal.

physics.flu-dyn↗

arXiv2015

Roughening dynamics of spontaneous radial imbibition

We performed an experimental observation on the spontaneous imbibition of water in a porous media in a radial Hele-Shaw cell and confirmed Washburn's law, where r is distance and t is time. Spontaneous imbibition with a radial interface window followed scaling dynamics when the front invaded into the porous media. We found a growth exponent (\b{eta}=0.6) that was independent of the pressure applied at the liquid inlet. The roughness exponent decreased with an increase in pressure. The roughening dynamics of two dimensional spontaneous radial imbibition obey Family-Vicsek scaling, which is different from that with a one-dimensional planar interface window.

physics.flu-dyn↗

arXiv2014

Order Estimates for the Exact Lugannani-Rice Expansion

The Lugannani-Rice formula is a saddlepoint approximation method for estimating the tail probability distribution function, which was originally studied for the sum of independent identically distributed random variables. Because of its tractability, the formula is now widely used in practical financial engineering as an approximation formula for the distribution of a (single) random variable. In this paper, the Lugannani-Rice approximation formula is derived for a general, parametrized sequence of random variables and the order estimates of the approximation are given.

q-fin.CP↗

arXiv2013

Self-organized Archimedean Spiral Pattern: Regular Bundling of Fullerene through Solvent Evaporation

We report the spontaneous generation of an Archimedean spiral pattern of fullerene via the evaporation of solvent. The self-organized spiral pattern exhibited equi-spacing on the order of micrometer between neighboring stripes. The characteristics of the spirals, such as the spacing between stripes, the number of stripes and the band width of stripes, could be controlled by tuning the thickness of the liquid bridge and the concentration of solution. The mechanism of pattern formation is interpreted in terms of a specific traveling wave on the liquid-solid interface accompanied by a stick-slip process of the contact line.

cond-mat.soft↗

arXiv2012

Interface dynamics under nonequilibrium conditions: from a self-propelled droplet to dynamic pattern evolution

In this article, we describe the instability of a contact line under nonequilibrium conditions mainly based on the results of our recent studies. Two experimental examples are presented: the self-propelled motion of a liquid droplet and spontaneous dynamic pattern formation. For the self-propelled motion of a droplet, we introduce an experiment in which a droplet of aniline sitting on an aqueous layer moves spontaneously at an air-water interface. The spontaneous symmetry breaking of Marangoni-driven spreading causes regular motion. In a circular Petri dish, the droplet exhibits either beeline motion or circular motion. On the other hand, we show the emergence of a dynamic labyrinthine pattern caused by dewetting of a metastable thin film from the air-water interface. The contact line between the organic phase and aqueous phase forms a unique spatio-temporal pattern characterized as a dynamic labyrinthine. Motion of the contact line is controlled by diffusion processes. We propose a theoretical model to interpret essential aspects of the observed dynamic behavior.

physics.flu-dyn↗

arXiv2012

Self-Propelled Motion of a Droplet Induced by Marangoni-driven Spreading

We report the generation of directed self-propelled motion of a droplet of aniline oil with a velocity on the order of centimeters per second on an aqueous phase. It is found that, depending on the initial conditions, the droplet shows either circular or beeline motion in a circular Petri dish. The motion of a droplet depends on volume of the droplet and concentration of solution. The velocity decreases when volume of the droplet and concentration of solution increase. Such unique motion is discussed in terms of Marangoni-driven spreading under chemical nonequilibrium. The simulation reproduces the mode of motion in a circular Petri dish.

physics.flu-dyn↗

arXiv2012

Dynamic Labyrinthine Pattern in an Active Liquid Film

We report the generation of a dynamic labyrinthine pattern in an active alcohol film. A dynamic labyrinthine pattern is formed along the contact line of air/pentanol/aqueous three phases. The contact line shows a clear time-dependent change with regard to both perimeter and area of a domain. An autocorrelation analysis of time-development of the dynamics of the perimeter and area revealed a strong geometric correlation between neighboring patterns. The pattern showed autoregressive behavior. The behavior of the dynamic pattern is strikingly different from those of stationary labyrinthine patterns. The essential aspects of the observed dynamic pattern are reproduced by a diffusion-controlled geometric model.

physics.flu-dyn↗

arXiv2012

Anomalous Roughening of Curvature-Driven Growth With a Variable Interface Window

We studied the curvature-driven roughening of a disk domain pattern with a variable interface window. The relaxation of interface is driven by negative surface tension . When a domain boundary propagates radially at a constant rate, we found that evolution of interface roughness follows scaling dynamic behavior. The local growth exponents are substantially different from the global exponents. Curvature-driven roughening belongs to a new class of anomalous roughening dynamics. However, a different surface tension leads to different global exponents. This is different from that of interface evolution with a fixed-size window, which has universal exponent. The variable growth window leads to a new class of anomalous roughening dynamics.

nlin.CD↗

arXiv2012

Mode bifurcation on the rythmic motion of a micro-droplet under stationary DC electric field

Accompanied by the development of microfabrication techniques, such as MEMS and micro-TAS, there has been increasing interests on the methodology to generate a desired motion on a micro object in a solution environment. It is well know that the principle to create an electric motor in a macroscopic scale is not applicable to a micro system because of the enhancement of sticky interaction and higher viscosity in micrometer sized system. On the other hand, living organisms generate various motions under isothermal condition in a well-regulated manner. Despite the past intensive studies, the underlying mechanism of the biological molecular motors has not been unveiled yet. Under such development stage of science and technology at the present, we are performing the study toward real-world modeling on the emergence of regular motion in micro system. In this paper, we report a novel experimental system on the generation of regular movement, such as periodic go-back motion and circular motion, for a micro object under DC electric field.

cond-mat.mes-hall↗

arXiv2012

The probability of double-strand breaks in giant DNA decreases markedly as the DNA concentration increases

DNA double-strand breaks (DSBs) represent a serious source of damage for all living things and thus there have been many quantitative studies of DSBs both in vivo and in vitro. Despite this fact, the processes that lead to their production have not yet been clearly understood, and there is no established theory that can account for the statistics of their production, in particular, the number of DSBs per base pair per unit Gy, here denoted by P1, which is the most important parameter for evaluating the degree of risk posed by DSBs. Here, using the single-molecule observation method with giant DNA molecules (166 kbp), we evaluate the number of DSBs caused by gamma-ray irradiation. We find that P1 is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. A simple model that accounts for the marked decrease of P1 shows that it is necessary to consider the characteristics of giant DNA molecules as semiflexible polymers to interpret the intrinsic mechanism of DSBs.

q-bio.BM↗

arXiv2010

How does torsional rigidity affect the wrapping transition of a semiflexible chain around a spherical core?

We investigated the effect of torsional rigidity of a semiflexible chain on the wrapping transition around a spherical core, as a model of nucleosome, the fundamental unit of chromatin. Through molecular dynamics simulation, we show that the torsional effect has a crucial effect on the chain wrapping around the core under the topological constraints. In particular, the torsional stress (i) induces the wrapping/unwrapping transition, and (ii) leads to a unique complex structure with an antagonistic wrapping direction which never appears without the topological constraints. We further examine the effect of the stretching stress for the nucleosome model, in relation to the unique characteristic effect of the torsional stress on the manner of wrapping.

cond-mat.soft↗

arXiv2010

Finite-Width Bundle is Most Stable in a Solution with Salt

We applied the mean-field approach to a columnar bundle assembled by the parallel arrangement of stiff polyelectrolyte rods in a salt bath. The electrostatic potential can be divided into two regions: inside the bundle for condensed counter-ions, and outside the bundle for free small ions. To determine the distribution of condensed counter-ions inside the bundle, we use a local self-consistent condition that depends on the charge density, the electrostatic potential, and the net polarization. The results showed that, upon bundle formation, the electric charge of polyelectrolytes, even those inside the bundle, tend to survive in an inhomogeneous manner, and thus their width remains finite under thermal equilibrium because of the long-range effect of charge instability.

cond-mat.soft↗

arXiv2009

Self-Sustained Collective Oscillation Generated in an Array of Non-Oscillatory Cells

Oscillations represent a ubiquitous phenomenon in biological systems. The conventional models of biological periodic oscillations are usually proposed as interconnecting transcriptional feedback loops. Some specific proteins function as transcription factors, which in turn negatively regulate the expression of the genes that encode those "clock protein". These loops may lead to rhythmic changes in gene expression of a cell. In the case of multi-cellular tissue, the collective oscillation is often obtained from synchronization of these cells, which manifest themselves as autonomous oscillators. In contrast, here, we propose a different scenario for the occurrence of collective oscillation in a multi-cellular system independent of oscillation, neither intrinsically oscillatory cells nor periodic external stimulation. It is a coupling induced oscillation, with the consideration of wave propagation due to the intracellular communication.

nlin.PS↗

arXiv2008

Chain Length Dependence on Folding Transition of a Semiflexible Homo-polymer Chain: Appearance of a Core-Shell Structure

The folding transition of single, long semiflexible polymers was studied with special emphasis on the chain length effect using Monte Carlo simulations. While a relatively short chain (10-25 Kuhn segments) undergoes a large discrete transiton between swollen coil and compact toroid conformations, a long chain (50 Kuhn segments) exhibits an intrachain segregated state between the disordered coil and ordered toroid.

cond-mat.soft↗

arXiv2008

Contraction-induced cluster formation in cardiac cell culture

Evolution of the spatial arrangement of cells in a primary culture of cardiac tissue derived from newborn rats was studied experimentally over extended period. It was found that cells attract each other spontaneously to form a clustered structure over the timescale of several days. These clusters exhibit spontaneous rhythmic contraction and have been confirmed to consist of cardiac muscle cells. Addition of a contraction inhibitor (2,3-butanedione-2-monoxime) to the culture medium resulted in the inhibition of both the spontaneous contractions exhibited by the cells as well as the formation of clusters. Furthermore, the formation of clusters is suppressed when high concentrations of collagen are used for coating the substratum to which the cells adhere. From these experimental observations, it was deduced that the cells are mechanically stressed by the tension associated with repeated contractions and that this results in the cells becoming compact and attracting each other, finally resulting in the formation of clusters. This process can be interpreted as modulation of a cellular network by the activity associated with contraction, which could be employed to control cellular networks by modifying the dynamics associated with the contractions in cardiac tissue culture.

q-bio.CB↗

arXiv2007

Core-shell structures in single flexible-semiflexible block copolymers: Finding the free energy minimum for the folding transition

We investigate the folding transition of a single diblock copolymer consisting of a semiflexible and a flexible block. We obtain a {\it Saturn-shaped} core-shell conformation in the folded state, in which the flexible block forms a core and the semiflexible block wraps around it. We demonstrate two distinctive features of the core-shell structures: (i) The kinetics of the folding transition in the copolymer are significantly more efficient than those of a semiflexible homopolymer. (ii) The core-shell structure does not depend on the transition pathway.

cond-mat.soft↗

arXiv2007

Elucidation of Conformational Hysteresis on a Giant DNA

The conformational behavior of a giant DNA mediated by condensing agents in the bulk solution has been investigated through experimental and theoretical approaches. Experimentally, a pronounced conformational hysteresis is observed for folding and unfolding processes, by increasing and decreasing the concentration of condensing agent PEG (Polyethylene glycol), respectively. To elucidate the observed hysteresis, a semiflexible chain model is studied by using Monte Carlo simulations for the coil-globule transition. In the simulations, the hysteresis loop emerges for stiff enough chains, indicating distinct pathways for folding and unfolding processes. Also, our results show that globular state is thermodynamically more stable than coiled state in the hysteresis loop. Our findings suggest that increasing chain stiffness may reduce the chain conformations relevant to the folding pathway, which impedes the folding process.

cond-mat.soft↗