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Kunihiko Kaneko

Publications and source records attributed to Kunihiko Kaneko.

16 recordsLinked to original sources
PubMed2003

On the relation between fluctuation and response in biological systems.

A general relationship between fluctuation and response in a biological system is presented. The fluctuation is given by the variance of some quantity, whereas the response is given as the average change of that quantity for a given parameter change. We propose a relationship where the two are proportional, in a similar way to the fluctuation-dissipation theorem in physics. By studying an evolution experiment where fluorescence of protein in bacteria increases, we confirm our relation by observing a positive correlation between the speed of fluorescence evolution and the phenotypic fluctuation of the fluorescence over clone bacteria. The generality of the relationship as well as its relevance to evolution is discussed.

Biological Evolution↗
PubMed2003

Robust development as a consequence of generated positional information.

The origin and robustness of morphogenesis are studied by dynamical system modeling of a cell society, in which cells possessing internal chemical reaction dynamics interact with each other through their mutual interaction with diffusive chemicals in a two-dimensional medium. It is found that stem-type cells differentiate into various cell types (where a cell 'type' is defined by a type of intra-cellular dynamics) due to a dynamic instability caused by cell-cell interactions in a manner described by the isologous diversification theory. The differentiations are spatially regulated by the concentration of chemicals in the medium, while the chemical concentrations are locally influenced by the intra-cell dynamics. Through this reciprocal relationship, chemical concentrations come to exhibit spatial variation as differentiated cell types begin to emerge, and as a result the regulation exercised by the chemical concentrations become spatially inhomogeneous. This reinforces the process of differentiation, through which spatial patterns of differentiated cells appear. Within this reciprocal relationship, the concentration gradients are read and interpreted by the cell as positional information. A spatial order of cells realized in this process represents a stable state of the system governed by this reciprocal relationship, and that the developmental process through which this state is realized is robust with respect to perturbations. The dependence of the morphogenesis on history and the community effect in cell differentiation are also discussed.

Animals↗
PubMed2003

Recursiveness, switching, and fluctuations in a replicating catalytic network.

A protocell model consisting of mutually catalyzing molecules is studied, in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the numbers of molecules and species, and the path rate, three phases are found: fast switching state without recursive production, recursive production, and itinerancy between the above two states. The number distributions of the molecules in the recursive states are shown to be log-normal except for those species that form a core hypercycle, and are explained with the help of a heuristic argument.

Animals↗
PubMed2003

Spontaneous structure formation in a network of dynamic elements.

To discover the generic behaviors of dynamic networks, we study a coupled map system with variable coupling strength. It is found that this system spontaneously forms various types of network structure according to the parameter values. Depending on the synchronized or desynchronized motion of unit dynamics, the network structure can be either static or dynamic. The separation of units into two groups, one composed of units with a large number of outgoing connections and the other units with little outgoing connections, is observed in dynamic structure. It is revealed that the mechanism for such separation is a positive feedback between unit and connection dynamics.

Journal Article↗
PubMed2003

Dynamical mechanism for the conversion of energy at a molecular scale.

We propose a dynamical mechanism of a molecular machine for energy conversion, by considering a simple model describing the dynamics of two components, the head and the chain. After injection of energy to the head region, the energy is stored at one part for some time, and is used step by step, allowing the head to move directionally along the chain, irrespective of the direction of the input, under a fluctuating environment. Our system can adjust the timing with which the head crosses the energy barrier by taking advantage of internal dynamics and the flexibility of components. Some suggestions are given for molecular machines.

Biophysical Phenomena↗
PubMed2003

Zipf's law in gene expression.

Using data from gene expression databases on various organisms and tissues, including yeast, nematodes, human normal and cancer tissues, and embryonic stem cells, we found that the abundances of expressed genes exhibit a power-law distribution with an exponent close to -1; i.e., they obey Zipf's law. Furthermore, by simulations of a simple model with an intracellular reaction network, we found that Zipf's law of chemical abundance is a universal feature of cells where such a network optimizes the efficiency and faithfulness of self-reproduction. These findings provide novel insights into the nature of the organization of reaction dynamics in living cells.

Animals↗
PubMed2003

Energy conversion by autonomous regulation of chaos: dynamical mechanism of loose coupling.

Inspired by recent experiments of molecular motors, a dynamical systems model for a flexible machine is proposed which converts injected energy to output directional motion. The output amount is distributed broadly, and thus the coupling between input energy and output motion is loose, as in the experiments. This energy conversion is shown to be robust against the change of surrounding environment. Stability analysis on the fixed point solutions of the model is presented, which suggests that transient chaotic motion, induced by temporal three-body motion, is relevant to the energy conversion.

Journal Article↗
PubMed2003

Bifurcation cascade as chaotic itinerancy with multiple time scales.

A coupled chaotic system with a variety of time scales is studied. Under a certain condition, it is shown that a change in fast dynamics can influence slow dynamics with a huge time-scale difference, successively through propagation of correlation over elements. This propagation is given by bifurcation cascade, for which three conditions are found to be essential: strong correlation, bifurcation of fast element dynamics by the change of its parameter, and marginal stability. By using coupled Lorenz equation with multiple time scales, it is shown that chaotic itinerancy (CI) observed there leads for the system to satisfy the three conditions, and the bifurcation cascade occurs. Through the analysis of the CI, characteristic properties of the bifurcation cascade, asymmetry in propagation with regards to the time scale, and the universality of the results are discussed, with possible relevance to biological memory.

Journal Article↗
PubMed2003

Chaotic itinerancy.

Chaotic itinerancy is universal dynamics in high-dimensional dynamical systems, showing itinerant motion among varieties of low-dimensional ordered states through high-dimensional chaos. Discovery, basic features, characterization, examples, and significance of chaotic itinerancy are surveyed.

Journal Article↗
PubMed2002

Dominance of Milnor attractors in globally coupled dynamical systems with more than 7+/-2 degrees of freedom.

The prevalence of Milnor attractors has recently been reported in a class of high-dimensional dynamical systems. We study how this prevalence depends on the number of degrees of freedom by using a globally coupled map and show that the basin fraction of Milnor attractors increases drastically around 5-10 degrees of freedom, saturating for higher numbers of degrees of freedom. It is argued that this dominance of Milnor attractors in the basin arises from a combinatorial explosion of the basin boundaries. In addition, the dominance is also found in a system without permutation symmetry, i.e., a coupled dynamical system of nonidentical elements. Possible relevance to the magic number 7+/-2 in psychology is briefly discussed.

Journal Article↗
PubMed2002

Origin of multicellular organisms as an inevitable consequence of dynamical systems.

The origin of multicellular organisms is studied by considering a cell system that satisfies minimal conditions, that is, a system of interacting cells with intracellular biochemical dynamics, and potentiality in reproduction. Three basic features in multicellular organisms-cellular diversification, robust developmental process, and emergence of germ-line cells-are found to be general properties of such a system. Irrespective of the details of the model, such features appear when there are complex oscillatory dynamics of intracellular chemical concentrations. Cells differentiate from totipotent stem cells into other cell types due to instability in the intracellular dynamics with cell-cell interactions, as explained by our isologous diversification theory (Furusawa and Kaneko, 1998a; Kaneko and Yomo, 1997). This developmental process is shown to be stable with respect to perturbations, such as molecular fluctuations and removal of some cells. By further imposing an adequate cell-type-dependent adhesion force, some cells are released, from which the next generation cell colony is formed, and a multicellular organism life-cycle emerges without any finely tuned mechanisms. This recursive production of multicellular units is stabilized if released cells are few in number, implying the separation of germ cell lines. Furthermore, such an organism with a variety of cellular states and robust development is found to maintain a larger growth speed as an ensemble by achieving a cooperative use of resources, compared to simple cells without differentiation. Our results suggest that the emergence of multicellular organisms is not a "difficult problem" in evolution, but rather is a natural consequence of a cell colony that can grow continuously.

Algorithms↗
PubMed2002

On a kinetic origin of heredity: minority control in a replicating system with mutually catalytic molecules.

As the first step in an investigation of the origin of genetic information, we study how some species of molecules are preserved over cell generations and play an important role in controlling the growth of a cell. We consider a model consisting of protocells. Each protocell contains two mutually catalysing molecule species (X and Y), each of which has catalytically active and inactive types. One of the species Y is assumed to have a slower synthesis speed. Through divisions of the protocells, the system reaches and remains in a state in which there are only a few active Y and almost no inactive Y molecules in most protocells, through the selection of very rare fluctuations. In this state, the active Y molecules are shown to control the behavior of the protocell. The minority molecule species act as the carrier of heredity, due to the relatively discrete nature of its population, in comparison with the majority species which behaves statistically in accordance with the law of large numbers. The minority controlled state may give rise to a selection pressure for mechanisms that ensure the transmission of the minority molecule. Once those mechanisms are in place, the minority molecule becomes the ideal storage device for information to be transmitted across generations, thus giving rise to "genetic information". The relevance of this minority controlled state to evolvability is also discussed.

Animals↗
PubMed2001

Spontaneous structure formation in a network of chaotic units with variable connection strengths.

As a model of temporally evolving networks, we consider a globally coupled logistic map with variable connection weights. The model exhibits self-organization of network structure, reflected by the collective behavior of units. Structural order emerges even without any interunit synchronization of dynamics. Within this structure, units spontaneously separate into two groups whose distinguishing feature is that the first group possesses many outwardly directed connections to the second group, while the second group possesses only a few outwardly directed connections to the first. The relevance of the results to structure formation in neural networks is briefly discussed.

Journal Article↗
PubMed2000

Coupled maps with local and global interactions.

A coupled map lattice model with both local and global couplings is studied as a simple example of hierarchical pattern dynamics with different length scales of interactions. Several phases are classified according to domain structures, degree of chaotic dynamics, distribution function, and power spectra. In particular, a cascade process of formation and collapse of bubbles is found in some parameter regime. The state is characterized by spatiotemporal power-law correlation and few positive Lyapunov exponents. In a two-dimensional case, the state leads to a characteristic spatiotemporal pattern that may be regarded as a dynamic extension of a Turing pattern. The possible relevance to natural patterns is also discussed. (c) 2000 American Institute of Physics.

Journal Article↗
PubMed1992

Evolution of host-parasitoid network through homeochaotic dynamics.

Host-parasitoid systems with evolving mutation rates are studied. By increasing the growth rate of hosts, the diversity of both species is maintained dynamically. For the lower growth rate, diversity is brought about by mere parasitism. The average mutation rate for parasites is elevated to a high value, while that for hosts is suppressed at a low level. For the higher growth rate, the mutation rates for both hosts and parasites are elevated to form a symbiotic cluster connected by on-going mutation. This symbiotic state is sustained through a chaotic oscillation keeping some coherency among species. For a flat landscape for hosts, dynamical clustering of oscillation is observed. Lyapunov spectra of such oscillations show that high dimensional chaos with small positive exponents underlies in the symbiotic state. This weak high dimensional chaos, termed "homeochaos," is essential to the maintenance of symbiosis in ecosystems.

Journal Article↗