K. Kaneko's Recent Works (2000-)

Year 2010

A. Kamimura and K. Kaneko ``Reproduction of a Protocell by Replication of Minority Molecule in Catalytic Reaction Network", submitted. html

T. Kurikawa and K. Kaneko, '' Learning Shapes Spontaneous Activity Itinerating over Memorized States" submitted to PLoS Computational Biology.

K. Kaneko, ''Proportionality between Variances in Gene Expression Induced by Noise and Mutation: Consequence of Evolutionary Robustness'' submitted.

A. Awazu and K. Kaneko ``Discreteness-Induced Slow Relaxation in Reversible Catalytic Reaction Networks'' Phys Rev. E 81(2010), 051920 PDF

A. Nakajima, T.Isshiki, K. Kaneko and S. Ishihara " "Robustness under functional constraint: The genetic network for temporal expression in Drosophila neurogenesis", PLoS Computational Biology, 6(2010)e1000760. html

T. Sugawara and K. Kaneko " ''Chemophoresis; Spatial coordination driven by chemical gradient" submitted to Phys. Rev. E

M. Inoue and K. Kaneko " ''Dynamics.of Coupled Adatpive Elements: Bursting and Intermitteny Oscillations Generated by Frustration in the Network " Phys. Rev. E 81, 026203 (2010), PDF

B. Lehner and K. Kaneko " ''A macroscopic relationship between fluctuation and response in biology" submitted.

D. Shimaoka and K. Kaneko, ``Dynamical systems modeling of continuous flash suppression ", submitted

Year 2009

B. Pfeuty and K. Kaneko " ''The combination of positive and negative feedback loops confers exquisite flexibility to biochemical switches'' Physical Biology, 6 (2009) 046013 PDF

A. Sakata, K Hukushima, and K. Kaneko " '' A statistical-mechanical study of evolution of robustness in noisy environment" Phys. Rev. E.80, (2009) 051919. PDF

A. Awazu and K. Kaneko `` ``Glassy" Relaxation in Catalytic Reaction Networks" Phys Rev. E, 80, 041931 (2009) PDF

A. Awazu and K. Kaneko `` Self-organized criticality of a catalytic reaction network under flow" PDF Phys. Rev. E.80, 010902(R) 2009 (Rapid Communication).

S.Tsuru, J.Ichinose, T. Sakurai, A.Kashiwagi, B-W. Ying, K. Kaneko, and T. Yomo " ``Noisy cell growth rate leads to fluctuating protein concentration in bacteria" Physical Biology 6 (2009) 036015 PDF Supplement

K. Kaneko " ``Relationship among Phenotypic Plasticity, Genetic and Epigenetic Fluctuations, Robustness, and Evolovability; Waddington's Legacy revisited under the Spirit of Einstein" J Biological Science, 34 (2009) 529-542 PDF

C. Furusawa and K. Kaneko, ``Chaotic Expression Dynamics Implies Pluripotency: When Theory and Experimentation Meet", Biology Direct 4 (2009) 17; html ;

H. Yoshida and K. Kaneko, `` Unified description of regeneration by coupled dynamical systems theory: Intercalary/segmented regeneration in insect legs'' Developmental Dynamics 238 (2009) 1974-1983; PDF

A. Sakata, K Hukushima, and K. Kaneko " '' Funnel landscape and mutational robustness as a result of evolution under thermal noise'', Phys. Rev. Lett., 102 (2009) 148101 PDF

Y.Ito, H.Toyota, K. Kaneko, and T. Yomo " ``How Selection affects Phenotypic Fluctuation" Molecular Systems Biology, 5 (2009) 264; html (Main text) ; html (Supporting Information)

Year 2008

B. Pfeuty, T. David-Pfeuty, and K. Kaneko " ``Underlying Principles of cell fate determination during G1 phase of the mammalian cell cycle", Cell Cycle 7 (2008) 1-13 PDF

K. Kaneko "Shaping Robust System Through Evolution", Chaos, 18 (2008) 026112 PDF

K. Kaneko and C. Furusawa "Relevance of Phenotypic Noise to Adaptation and Evolution" (review) IET Systems Biology, 2 (2008) 234-246. PDF html

K. Kaneko and C. Furusawa "Consistency Principle in Biological Dynamical Systems" Theory in Biosciences, 127 (2008) 195-204. PDF

A. Nakajima and K. Kaneko " Regulative Differentiation as Bifurcation of Interacting Cell Population" J. Theor Biol. 253 (2008) 779-787 PDF

M. Inoue and K. Kaneko " ``Conditions for self-consistent aggregation by chemotactic particles", Phys. Rev. E 77, 041916 (2008) PDF

K. Kaneko, K. Sato, T. Michiue, K. Okabayashi, K. Ohnuma, H. Danno, and M. Asashima " `` Developmental Potential Describing Morphogenesis in vivo and in vitro" J Experimental Zoology B 310 (2008) 492-503 PDF

K. Fujimoto, S. Ishihara, and K. Kaneko " ``Network Evolution of Body Plans", PLoS ONE, 3 (2008) e2772 html

C. Furusawa and K. Kaneko, ``A generic mechanism for adaptive gowth rate regulation", PLoS Computationa Biology, 4(2008) e3 html (selected in Faculty of 1000 Biology http://www.f1000biology.com/article/id/1104005 )

T. Toyota, K. Takakura, Y. Kageyama, K. Kurihara, N. Maru, K. Ohnuma, K. Kaneko, and T. Sugawara" Flow Cytometric Investigation of Self-Reproducing Giant Multilamellar Vesicles " Langmuir,24 (2008) 3037-3044

Year 2007

B. Pfeuty and K. Kaneko, ``Minimal requirements for a robust cell size control in eukaryotic cells" Physical Biology, 4 (2007) 194-204 PDF

A. Awazu and K. Kaneko " ``Discretenss-induced Transition in Catalytic Reaction Networks", Phys Rev. E76, 041915 (2007) PDF

K. Kaneko, Evolution of Robustness to Noise and Mutation in Gene Expression Dynamics, PLoS One(2007) 2 e434. html

K. Sato and K. Kaneko, ``Evolution Equation of Phenotype Distribution: General Formulation and Application to Error Catastrophe", Phys. Rev. E75 (2007) 061909 PDF

Y. Watanabe and K. Kaneko, ``State Generation by Transient Truncation in Coupled Threshold Dynamics", Phys. Rev. E., 75 (2007) 016206 PDF

Y. Togashi and K. Kaneko, " Switching Dynamics in reaction Networks Induced by Molecular Discreteness". J Phys. Condens. Matt. 19,(2007) 065150 (10p)

Year 2006

A. Kashiwagi, I. Urabe, K. Kaneko and T. Yomo " Adaptive response of a gene network to environmental changes by attractor selection " PLOS ONE 1 (2006) e49 html (selected for Faculty of 1000 Biology )

D. Lawson, H.J. Jensen and K. Kaneko, "Diversity as a product of interspecial interactions" J theor. Biol. 243(2006) 299-307 PDF

M. Inoue and K. Kaneko, Condition for Intra-cellular Adaptive Dynamics for Chemotaxis, Phys. Rev. E., 74 (2006) 011903 PDF

K. Sato and K. Kaneko, "On the Distribution of State Values of Reproducing Cells" Physical Biology 3 (2006) 74-82 PDF

H. Morita and K. Kaneko, "Collective oscillation in a Hamiltonian dynamical system" Phys. Rev. Lett.96 (2006) 050602, PDF

S. Ishihara and K. Kaneko, "Turing pattern with proportion preservation", J. Theo. Biol. 238 (2006) 683-693 PDF

K. Kaneko and C. Furusawa, "An Evolutionary Relationship between Genetic Variation and Phenotypic Fluctuation", J. Theo. Biol. 240 (2006) 78-86 PDF

C.Furusawa and K. Kaneko "Morphogenesis, Plasticity, and Irreversibility" International Journal Developmental Biology, 50 (2006) 223-232 PDF

C.Furusawa and K. Kaneko "Evolutionary origin of power-laws in Biochemical Reaction Network; embedding abundance distribution into topology" Phys. Rev. E 73, (2006) 011912PDF

A. Ponzi, A. Yasutomi and K. Kaneko Complex Dynamical Behavior in Economic Production Networks, Journal of Economic Behavior and Organization, 61 (2006) 729-749 PDF

Year 2005

K. Kaneko "Inter-Intra Molecular Dynamics as an Iterated Function System" J. Phys. Soc. Japan 74 (2005), 2386-2390 PDF

S. Ishihara and K. Kaneko"Magic number 7 $\pm$ 2 in networks of threshold dynamics", Phys. Rev. Lett., 94(2005) 058102 PDF

H. Morita and K. Kaneko" Roundabout relaxation: collective excitation requires a detour to equilibrium " ,Phys. Rev. Lett., 94 (2005) 087203 PDF gzipped PS

C. Furusawa, T. Suzuki, A. Kashiwagi, T. Yomo, and K. Kaneko " Ubiquity of Log-normal Distributions in Intra-cellular Reaction Dynamics " BIOPHYSICS, 1(2005) 25 PDF

K. Kaneko" On Recursive Production and Evolvabilty of Cells: Catalytic Reaction Network Approach " Adv. Chem. Phys. , 130 (2005) 543-598 (pdf file )

H. Yoshida, C.Furusawa and K. Kaneko "Selection of initial condition for recursive production of multicellular organisms" J. theor. Biol.233, (2005) 501-514 PDF

H. Takagi and K. Kaneko "Dynamical Systems Basis of Metamorphosis: Diversity and Plasticity of Cellular States in Reaction Diffusion Netowork" Journal of Theoretical Biology, 234, (2005) 173-186PDF

Y. Togashi and K. Kaneko "Discreteness-induced Stochastic Steady State in Reaction Diffusion Systems: Self-consistent Analysis and Stochastic Simulations" Physica D 205(2005) 87-99 PDF

F. Willeboordse and K. Kaneko" Externally controlled attractor selection in a high-dimensional system " Phys. Rev. E. , 72 (2005) 026207 (pdf file )

S. Honjo and K. Kaneko " "Structure of Resonances and Transport in Multidimensional Hamiltonian Dynamical Systems", Adv.Chem.Phys.,130 (2005) 437-463

Year 2004

K. Fujimoto and K. Kaneko " Convective Instability with Time Scale Translation of the Transmitted Disturbance " Physica D, 196, 67-89. 2004 (pdf file )

Y. Togashi and K. Kaneko" Molecular discreteness in reaction-diffusion systems yields steady states not seen in the continuum limit. " Phys. Rev. E, 70, 020901(R). 2004.(pdf file )

A.Awazu and K. Kaneko " Is relaxation to equilibrium hindered by transient dissipative structures in closed systems? " Phys. Rev. Lett. 92 (2004) 258302(pdf file )

K. Kaneko " Constructive and Dynamical Systems Aphttp://chaos.c.u-tokyo.ac.jp/papers/proach to Life " Proceedings of Modelling and Theory in Biological systems , Function and Regulation of Cellular Systems:Experiments and Models,213-224, ed. by A.Deutsch, M.Falcke, J.Howard, W.Zimmermann(Birkhaeuser Verlag Basel) (pdf file )

N. Nakagawa and K. Kaneko " Autonomous Energy Transducer: Proposition, Example, Basic Characteristics " Physica A 338 (2004) 511-536 (pdf file )

Year 2003

H. Morita and K. Kaneko " Self-Organized Bottleneck in Energy Relaxation " Europhys. Lett., 66(2003) 198-204 (pdf file )

K. Sato, Y. Ito, T. Yomo, and K. Kaneko " On the Relation between Fluctuation and Response in Biological Systems " Proc. Nat. Acad. Sci. USA 100 (2003) 14086-14090 (pdf file )

K. Kaneko and I. Tsuda " Chaotic Itinerancy" Chaos, 13 (2003) 926-936 (pdf file )

K. Kaneko " Recursiveness, Switching, and Fluctuations in a Replicating Catalytic Network" Phys. Rev.E. 68 (2003) 031909 (pdf file )

K. Fujimoto and K. Kaneko " Bifurcation cascade realized by Chaotic Itinerancy" Chaos 13 (2003) 1041-1056

N. Nakagawa and K. Kaneko, and T. Komatsu " Energy Conversion by Autonomous Regulation of Chaos: Dynamical Mechanism of Loose Coupling" Chaos, 13 (2003) 1032-1040 (pdf file )

K. Fujimoto and K. Kaneko, "How Fast Elements can Affect Slow Dynamics" Physica D 180 (2003) 1-16. (pdf file )

Y. Togashi and K. Kaneko " Alteration of Chemical Concentrations through Discreteness-Induced Transitions in Small Autocatalytic Systems" J.Phys.Soc. Japan 72 (2003)62-68 (pdf file )

C. Furusawa and K. Kaneko " Zipf's law in Gene Expression " Phys. Rev. Lett., 90 (2003) 088102 (pdf file )
(selected in Faculty of 1000 Biology as hidden jewel )

C. Furusawa and K. Kaneko " Robust Development as a Consequence of Generated Positional Information " J. Theor. Biol. 224 (2003) 413-435 (pdf file )

K. Kaneko " Recursiveness and Evolvability in Mutually Catalytic Reaction System "Adv. in Complex Systems, Vol.6 (2003)79-92 (pdf file )

J. Ito and K. Kaneko " Spontaneous structure formation in a network of dynamic elements " Phys Rev E 67 (2003) 046226 (pdf file )

N. Nakagawa and K. Kaneko " A dynamic mechanism of energy conversion to a mechanical work " Phys. Rev. E 67 (2003) 040901(R) (pdf file )

A. Ponzi, A. Yasutomi, and K. Kaneko " A Nonlinear model of Economic Production Processes, " Physica A 324 (2003) 372-379.(pdf file )

N. Kataoka and K. Kaneko " Dynamical Networks in Function Dynamics" Physica D 181 (2003) 235-251 (pdf file )

T. Shibata and K. Kaneko " Coupled Map Gas: structure formation and dynamics of interacting mobile elements with internal dynamics " Physica D 181(2003) 197-214 (pdf file )

T. Yamamoto and K. Kaneko"Tile Automaton in the well-mixed medium" Physica D 181 (2003) 252-273 (pdf file )

Year 2002

K. Kaneko " Dominance of Minlnor attractors in Globally Coupled Dynamical Systems with more than 7 +- 2 degrees of freedom (retitled from `Magic Number 7 +- 2 in Globally Coupled Dynamical Systems') " Phys. Rev. E.66, 055201(R) 2002 (pdf file )

C. Furusawa and K. Kaneko " Origin of Multicellular Organisms as an Inevitable Consequence of Dynamical Systems " Anatomical Record, 268 (2002) 327-342 (pdf file )

K. Kaneko " Symbiotic Sympatric Speciation: Compliance with Interaction-driven Phenotype Differentiation from a Single Genotype " Population Ecology, 44 (2002) 71-85 (pdf file )

K. Kaneko " Kinetic Origin of Heredity in a Replicating System with a Catalytic Network " J Biol. Phys., 28 (2002) 781-792 (pdf file )

H. Takagi and K. Kaneko " Pattern Dynamics of a Multi-Component Reaction-Diffusion System:Differentiation of Replicating Spots " Int. J. Bifurcation and Chaos, 11 (2002) 2579-2598 (pdf file )

J. Ito and K. Kaneko " Spontaneous structure formation in a network of chaotic units with variable connection strengths " Phys. Rev. Lett., 88 (2002) 028701-1 (pdf file )

S. Ishihara and K. Kaneko " Simple dynamical system model of history dependent phenomena " J. Phys. Soc. Jpn, 71 (2002) 2357-2360 (pdf file )

K. Kaneko and T. Yomo" On a kinetic origin of heredity :minority control in replicating molecules " J. Theor. Biol. 214 (2002) 563-576 (nlin.AO/0105031) (pdf file )

K. Kaneko and T. Yomo "Genetic Diversification through Interaction-driven Phenotype Differentiation" Evol Eco. Res., 4 (2002) 317-350 (pdf file )

K. Kaneko " From Coupled Dynamical Systems to Biological Irreversibility" " Adv. in Chem. Phys. 122 (2002) 53-73

E. Akiyama and K. Kaneko"Dynamical Systems Game Theory II" Phsyica D 167 (2002) 36-71 (pdf file )

Year 2001

C. Furusawa and K. Kaneko"Theory of Robustness of Irreversible Differentiation in a Stem Cell System: Chaos Hypothesis" J. Theor. Biol. 209 (2001) 395-416 (pdf file )

Y. Togashi and K. Kaneko,"Transitions Induced by the Discreteness of Molecules in a Small Autocatalytic System" Phys. Rev. Lett., 86 (2001) 2459-2462 (pdf file )

N. Nakagawa and K. Kaneko, "Relaxation, the Boltzmann-Jeans Conjecture and Chaos"" Phys. Rev. E 64., (2001) 055205(R) (pdf file )

Y. Takahashi, N. Kataoka, K. Kaneko, and T. Namiki" Function Dynamics" Jap J. J. Appl. Math., 18 (2001) 405-423 (pdf file )

H. Takagi and K. Kaneko"Differentiation and Replication of Spots in a Reaction Diffusion System with Many Chemicals", Europhys. Lett. 56 (2001) 145-151 (pdf file )

Naoto Kataoka and Kunihiko Kaneko ``Functional Dynamics II: Syntactic structure", submitted to Phsyica D 149 (2001) 174-196 (pdf file )

A. Saito and K. Kaneko, ``Inaccessibility and Undecidability in Computation, Geometry and Dynamical Systems", Physica D 155 (2001) 1-33 (pdf file )

Koichi Fujimoto and Kunihiko Kaneko ``Sensitive boundary condition dependence of noise-sustained structure" Phys. Rev. E. 63 (2001) 036128 (pdf file )

Year 2000

C. Furusawa and K. Kaneko" Complex Orgnization in multicullarity as a necessity in evolution" Artificial Life, 6(2000) 265-281 (pdf file )

H. Takagi, K. Kaneko, and T. Yomo"Evolution of genetic code through isologous diversification of cellular states" Artificial Life 6(2000) 283-305 (pdf file )

N. Nakagawa, K. Kaneko and T.S. Komatsu,"Long-term Relaxation of a Composite System in Partial Contact with a Heat Bath",J. Phys. Soc. Jpn, 69 (2000) 3214-3222 (pdf file )

Naoto Kataoka, Kunihiko Kaneko, "Natural language from functional dynamics", Biosystems 57 (2000) 1-11 (pdf file )

A new approach to syntax and semantics of language is presented as a form of function dynamics, which is studied both analytically and numerically. The iteration of the function dynamics leads to articulation and formation of rules, which depend on each other. A hierarchy of meta-rules as rules of rules also emerges through the iteration when the initial function is suitably embedded. Iteration of a model with dialogue between two function dynamics is shown to generate a higher level structure.

Kunihiko Kaneko and Tetsuya Yomo ``Sympatric Speciation: compliance with phenotype diversification from a single genotype ", Proc. Roy. Soc. B, 267 (2000) 2367-2373 (pdf file )

A novel mechanism for sympatric speciation that takes into account complex bio-processes within each individual organism is proposed. According to dynamical systems theory, organisms with identical genotypes can possess differentiated physiological states and may coexist `symbiotically' through appropriate mutual interaction. With mutations, the phenotypically differentiated organisms gradually come to possess distinct genotypes, while maintaining their symbiotic relationship. This symbiotic speciation is robust against sexual recombination, because offspring of mixed parentage, with intermediate genotypes, are less fit than their parents. This leads to sterility of the hybrid. Accordingly, a basis for mating preference also arises.

Naoto Kataoka and Kunihiko Kaneko ``Functional Dynamics I : Articulation Process", Physica D 138 (2000) 225-250 (pdf file )

The articulation process of dynamical networks is studied with a functional map, a minimal model for the dynamic change of relationships through iteration. The model is a dynamical system of a function $f$, not of variables, having a self-reference term $f \circ f$, introduced by recalling that operation in a biological system is often applied to itself, as is typically seen in rules in the natural language or genes. Starting from an inarticulate network, two types of fixed points are formed as an invariant structure with iterations. The function is folded with time, until it has finite or infinite piecewise-flat segments of fixed points, regarded as articulation. For an initial logistic map, attracted functions are classified into step, folded step, fractal, and random phases, according to the degree of folding. Oscillatory dynamics are also found, where function values are mapped to several fixed points periodically. The significance of our results to prototype categoriz ation in language is discussed.

C. Furusawa and K. Kaneko ``Origin of complexity in multicellular organisms", Phys. Rev. Lett. 84 (2000) 6130-6133 (pdf file )

Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems can exhibit complex pattern formation with spontaneous cell differentiation. Such systems employ a `cooperative' use of resources and maintain a larger growth speed than simple cell systems, which exist in a homogeneous state and behave 'selfishly'. The relevance of the diversity of chemicals and reaction dynamics to the growth of a multicellular organism is demonstrated. Chaotic biochemical dynamics are found to provide the multi-potency of stem cells.

Naoko Nakagawa and Kunihiko Kaneko, ``Energy Storage in a Hamiltonian System in Partial Contact with a Heat Bath", J. Phys. Soc. Jpn. 69 (2000) 1255-1258, (pdf file )

To understand the mechanism allowing for long-term storage of excess energy in proteins, we study a Hamiltonian system consisting of several coupled pendula in partial contact with a heat bath. It is found that energy storage is possible when the motion of each pendulum switches between oscillatory (vibrational) and rotational (phase-slip) modes. The storage time increases almost exponentially to the square root of the injected energy. The relevance of our mechanism to protein motors is discussed.

Junji Ito and Kunihiko Kaneko, ``Self-organized hierarchical structure in a plastic network of chaotic units" Neural Networks, 13 (2000) 275-281, (also available at http://arXiv.org/abs/cond-mat/9911416)

Formation of a layered structure is studied in a globally coupled map of chaotic units with a plastic coupling strength that changes depending on the states of units globally and an external input. In the parameter region characterized by weakly chaotic and desynchronized dynamics, units spontaneously form a hierarchical structure due to the influence of the input, with regards to the coupling strength. This hierarchical structure is not fixed in time, and is successively reorganized. It is found that the distribution of lifetimes of the structure obeys a power law. The possible relevance of the present result to information processing in the brain is briefly discussed.

Eizo Akiyama, Kunihiko Kaneko, ``Dynamical Systems Game Theory and Dynamics of Games,'' Physica D 147 (2000) 221-258 (pdf file )

A theoretical framework we call dynamical systems game is presented, in which the game itself can change due to the influence of players' behaviors and states. That is, the nature of the game itself is described as a dynamical system. The relation between game dynamics and the evolution of strategies is discussed by applying this framework. Computer experiments are carried out for simple one-person games to demonstrate the evolution of dynamical systems with the effective use of dynamical resources.

Kunihiko Kaneko and Chikara Furusawa ``Robust and Irreversible Development in Cell Society as a General Consequence of Intra-Inter Dynamics", Physica A 280 (2000) 22-33 (pdf file )

A dynamical systems scenario for developmental cell biology is proposed, based on numerical studies of a system with interacting units with internal dynamics and reproduction. Diversification, formation of discrete and recursive types, and rules for differentiation are found as a natural consequence of such a system. ``Stem cells" that either proliferate or differentiate to different types stochastically are found to appear when intra-cellular dynamics are chaotic. Robustness of the developmental process against microscopic and macroscopic perturbations is shown to be a natural consequence of such intra-inter dynamics, while irreversibility in developmental process is discussed in terms of the gain of stability, loss of diversity and chaotic instability.

N.B. Ouchi and K. Kaneko ``Coupled Map with Local and Global interactions", Chaos 10 (2000) 359-365

A coupled map lattice model both with 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 Turing pattern. Possible relevance to natural patterns is also discussed.

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