Details of a Researcher - Kobayashi Yasuaki

Robust network clocks: Design of genetic oscillators as a complex combinatorial optimization problem Reviewed

Yasuaki Kobayashi, Tatsuo Shibata, Yoshiki Kuramoto, Alexander S. Mikhailov

PHYSICAL REVIEW E 83 ( 6 ) 060901(R) 2011.06

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER PHYSICAL SOC

Complex combinatorial optimization can be used to design network systems having desired dynamics and that are robust against structural perturbations. Here genetic networks exhibiting limit-cycle oscillations with prescribed periods and, furthermore, that are robust against the deletion of links and nodes or the application of noise are constructed. Large ensembles of robust genetic clocks with different periods could thus be obtained, and some of their statistical properties have been investigated. Similar methods can be used to design robust network oscillators of various origins.

DOI： 10.1103/PhysRevE.83.060901

Evolutionary design of oscillatory genetic networks Reviewed

Y. Kobayashi, T. Shibata, Y. Kuramoto, A. S. Mikhailov

EUROPEAN PHYSICAL JOURNAL B 76 ( 1 ) 167 - 178 2010.07

Language：English Publishing type：Research paper (scientific journal) Publisher：SPRINGER

The present study is devoted to the design and statistical investigations of dynamical gene expression networks. In our model problem, we aim to design genetic networks which would exhibit stable periodic oscillations with a prescribed temporal period. While no rational solution of this problem is available, we show that it can be effectively solved by running a computer evolution of the network models. In this process, structural rewiring mutations are applied to the networks with inhibitory interactions between genes and the evolving networks are selected depending on whether, after a mutation, they closer approach the targeted dynamics. We show that, by using this method, networks with required oscillation periods, varying by up to three orders of magnitude, can be constructed by changing the architecture of regulatory connections between the genes. Statistical properties of designed networks, including motif distributions and Laplacian spectra, are considered.

DOI： 10.1140/epjb/e2010-00200-9

Design principle of multi-cluster and desynchronized states in oscillatory media via nonlinear global feedback Reviewed

Yasuaki Kobayashi, Hiroshi Kori

NEW JOURNAL OF PHYSICS 11 033018 2009.03

Language：English Publishing type：Research paper (scientific journal) Publisher：IOP PUBLISHING LTD

A theoretical framework is developed for the precise control of spatial patterns in oscillatory media using nonlinear global feedback, where a proper form of the feedback function corresponding to a specific pattern is predicted through the analysis of a phase diffusion equation with global coupling. In particular, feedback functions that generate the following spatial patterns are analytically given: (i) 2-cluster states with an arbitrary population ratio, (ii) equally populated multi-cluster states and (iii) a desynchronized state. Our method is demonstrated numerically by using the Brusselator model in the oscillatory regime. Experimental realization is also discussed.

DOI： 10.1088/1367-2630/11/3/033018

Aggregated spots and waving loops in a reaction-advection-diffusion system with a global coupling Reviewed

Y Kobayashi, M Sano

PHYSICAL REVIEW E 73 ( 1 ) 015104(R) 2006.01

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER PHYSICAL SOC

We construct a phenomenological model describing aggregated spots and a loop structure. Our model is based on the Gray-Scott model which is supplemented with a global coupling term and advection terms. One of the species makes a field proportional to its concentration, which induces the advection. By numerically investigating the model, we show that the system has a transition from aggregated spots to a loop which wanders around chaotically or reaches a stationary state. Relation to a similar transition observed in a recent gas discharge experiment [S. Nasuno, Chaos 13, 3 (2003)] is discussed.

DOI： 10.1103/PhysRevE.73.015104

Formation of a loop structure in a reaction-advection-diffusion model Reviewed

Y Kobayashi, M Sano

PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT 161 ( 161 ) 236 - 239 2006

Language：English Publishing type：Research paper (scientific journal) Publisher：PROGRESS THEORETICAL PHYSICS PUBLICATION OFFICE

We construct a reaction-advection-diffusion model which shows a transition of patterns from aggregated spots to a closed loop structure, which has been observed in a recent gas-discharge experiment. Our model is based on the Gray-Scott model which is supplemented with a global coupling term due to an experimental constraint and advection terms which is induced by the discharge current.

DOI： 10.1143/PTPS.161.236

Anomalous collective diffusion in one-dimensional driven granular media Reviewed

Y Kobayashi, M Sano

JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 73 ( 10 ) 2697 - 2700 2004.10

Language：English Publishing type：Research paper (scientific journal) Publisher：PHYSICAL SOC JAPAN

We numerically investigate the nonequilibrium steady state of a one-dimensional rarefied granular system in which each particle is driven by Gaussian white noise and subject to inelastic mutual collisions. We find that the dynamic structure factor S(q, t) decays as exp(-Dq(2)t(2)), which is in marked contrast to the usual Fickian behavior exp(-Dq(2)t). Employing newly obtained S(q, t), we demonstrate that the static spatial correlation function and the one-point time correlation function obey the same scaling behavior.

DOI： 10.1143/JPSJ.73.2697