arXiv subjects

Kunihiko Kaneko

Publications and source records attributed to Kunihiko Kaneko.

At least 145 records · Page 8Linked to original sources

arXiv2003

Autonomous Energy Transducer: Proposition, Example, Basic Characteristics

We propose a concept of autonomous energy transducer at a molecular scale, where output is produced with small input energy, of the same order of the thermal energy, without restriction of magnitude or timing of input, and without any control after the input. As an example that satisfies these requisites, a dynamical systems model with several degrees of freedom is proposed, which transduces input energy to output motion on the average. It is shown that this transduction is robust and the coupling between the input and output is generally loose. How this transducer works is analyzed in terms of dynamical systems theory, where chaotic dynamics of the internal degrees of freedom, as well as duration of active state which is self-organized with the energy flow, is essential. We also discuss possible relationships to enzyme dynamics or protein motors.

cond-mat↗

arXiv2003

Is Arnold diffusion relevant to global diffusion?

Global diffusion of Hamiltonian dynamical systems is investigated by using a coupled standard maps. Arnold web is visualized in the frequency space, using local rotation numbers, while Arnold diffusion and resonance overlaps are distinguished by the residence time distributions at resonance layers. Global diffusion in the phase space is shown to be accelerated by diffusion across overlapped resonances generated by the coupling term, rather than Arnold diffusion along the lower-order resonances. The former plays roles of hubs for transport in the phase space, and accelerate the diffusion.

nlin.CD↗

arXiv2003

Self-Organized Bottleneck in Energy Relaxation

We study an energy relaxation process after many degrees of freedom are excited in a Hamiltonian system with a large number of degrees of freedom. Bottlenecks of relaxation, where relaxations of the excited elements are drastically slowed down, are discovered. By defining an internal state for the excited degrees of freedom, it is shown that the drastic slowing down occurs when the internal state is in a critical state. The relaxation dynamics brings the internal state into the critical state, and the critical bottleneck of relaxation is self-organized. Relevance of our result to relaxation phenomena in condensed matters or large molecules is briefly discussed.

cond-mat.stat-mech↗

arXiv2003

Prevalence of Milnor Attractors and Chaotic Itinerancy in 'High'-dimensional Dynamical Systems

Dominance of Milnor attractors in high-dimensional dynamical systems is reviewed, with the use of globally coupled maps. From numerical simulations, the threshold number of degrees of freedom for such prevalence of Milnor attractors is suggested to be $5 \sim 10$, which is also estimated from an argument of combinatorial explosion of basin boundaries. Chaotic itinerancy is revisited from the viewpoint of Milnor attractors. Relevance to neural networks is discussed.

nlin.CD↗

arXiv2003

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 path rate, the numbers of molecules and species, 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.

cond-mat↗

arXiv2002

Transitions Induced by the Discreteness of Molecules in a Small Autocatalytic System

Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of molecule species alternately in the autocatalytic reaction loop. Phase transition to this state with the change of the system size and flow is studied, while a single-molecule switch of the molecule distributions is reported. Relevance of the results to intracellular processes are briefly discussed.

physics.bio-ph↗

arXiv2002

Alteration of Chemical Concentrations through Discreteness-Induced Transitions in Small Autocatalytic Systems

We study an autocatalytic system consisting of several interacting chemical species. We observe a strong dependence of the concentrations of the chemicals on the size of the system. This dependence is caused by the discrete nature of the molecular concentrations. Two basic mechanisms responsible for them are identified and elucidated. The relevance of the transitions to processes in biochemical systems and in micro-reactors is briefly discussed.

physics.bio-ph↗

arXiv2002

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 intra-cellular 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.

physics.bio-ph↗

arXiv2002

Dynamic Relationship between Diversity and Plasticity of Cell types in Multi-cellular State

Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species space' to model intra-cellular chemical reaction dynamics. Then, by considering the cell division and death of such cells, developmental process from a single cell is studied. Cell differentiation process is found to occur through instability in transient dynamics and cell-cell interaction. In a long time behavior, extinction of multiple cells is repeated, which leads to itinerancy over successive quasi-stable multi-cellular states consisting of different types of cells. By defining the plasticity of a cellular state, it is shown that the plasticity of cells decreases before the large extinction, from which diversity and plasticity are recovered. After this switching, decrease of plasticity again occurs, leading to the next extinction of multiple cells. This cycle is repeated. Relevance of our results to the development, evolution is briefly discussed.

nlin.AO↗

arXiv2002

Coupled map gas: structure formation and dynamics of interacting motile elements with internal dynamics

A model of interacting motile chaotic elements is proposed. The chaotic elements are distributed in space and interact with each other through interactions depending on their positions and their internal states. As the value of a governing parameter is changed, the model exhibits successive phase changes with novel pattern dynamics, including spatial clustering, fusion and fission of clusters and intermittent diffusion of elements. We explain the manner in which the interplay between internal dynamics and interaction leads to this behavior by employing certain quantities characterizing diffusion, correlation, and the information cascade of synchronization. Keywords: collective motion, coupled map system, interacting motile elements

nlin.AO↗

arXiv2002

Magic Number 7 +- 2 in Globally Coupled Dynamical Systems?

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 non-identical elements. Possible relevance to the magic number $7\pm 2$ in psychology is discussed.

nlin.CD↗

arXiv2002

A Dynamic Mechanism of Energy Conversion to a Mechanical Work

We propose a dynamic 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, irrespectively 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. The mechanism is shown to be robust and efficient. Some suggestions are given for molecular machines.

cond-mat↗

arXiv2002

Relaxation, the Boltzmann-Jeans Conjecture and Chaos

Slow (logarithmic) relaxation from a highly excited state is studied in a Hamiltonian system with many degrees of freedom. The relaxation time is shown to increase as the exponential of the square root of the energy of excitation, in agreement with the Boltzmann-Jeans conjecture, while it is found to be inversely proportional to residual Kolmogorov-Sinai entropy, introduced in this Letter. The increase of the thermodynamic entropy through this relaxation process is found to be proportional to this quantity.

cond-mat↗

arXiv2002

From Coupled Dynamical Systems to Biological Irreversibility

In the first half of the paper, some recent advances in coupled dynamical systems, in particular, a globally coupled map are surveyed. First, dominance of Milnor attractors in partially ordered phase is demonstrated. Second, chaotic itinerancy in high-dimensional dynamical systems is briefly reviewed, with discussion on a possible connection with a Milnor attractor network. Third, infinite-dimensional collective dynamics is studied, in the thermodynamic limit of the globally coupled map, where bifurcation to lower-dimensional attractors by the addition of noise is briefly reviewed. Following the study of coupled dynamical systems, a scenario for developmental process of cell society is proposed, based on numerical studies of a system with interacting units with internal dynamics and reproduction. Differentiation of cell types is found as a natural consequence of such a system. "Stem cells" that either proliferate or differentiate to different types generally appear in the system, where irreversible loss of multipotency is demonstrated. Robustness of the developmental process against microscopic and macroscopic perturbations is found and explained, while irreversibility in developmental process is analyzed in terms of the gain of stability, loss of diversity and chaotic instability. Construction of a phenomenology theory for development is discussed in comparison with the thermodynamics.

nlin.CD↗

arXiv2002

Symbiotic Sympatric Speciation: Compliance with Interaction-driven Phenotype Differentiation from a Single Genotype

A mechanism of sympatric speciation is presented based on the interaction-induced developmental plasticity of phenotypes. First, phenotypes of individuals with identical genotypes split into a few groups, according to instability in the developmental dynamics that are triggered with the competitive interaction among individuals. Then, through mutational change of genes, the phenotypic differences are fixed to genes, until the groups are completely separated in genes as well as phenotypes. It is also demonstrated that the proposed theory leads to hybrid sterility under sexual recombination, and thus speciation is completed in the sense of reproductive isolation. As a result of this post-mating isolation, the mating preference evolves later. When there are two alleles, the correlation between alleles is formed, to consolidate the speciation. When individuals are located in space, different species are later segregated spatially, implying that the speciation so far regarded to be allopatric may be a result of sympatric speciation. Relationships with previous theories, frequency-dependent selection, reinforcement, Baldwin's effect, phenotypic plasticity, and resource competition are briefly discussed. Relevance of the results to natural evolution are discussed, including punctuated equilibrium, incomplete penetrance in mutants, and the change in flexibility in genotype-phenotype correspondence. Finally, it is discussed how our theory is confirmed both in field and in laboratory (in an experiment with the use of E coli.).

nlin.AO↗

arXiv2002

Kinetic Origin of Heredity in a Replicating System with a Catalytic Network

The origin of heredity is studied as a recursive state in a replicating proto-cell consisting of many molecule species in mutually catalyzing reaction networks. Protocells divide when the number of molecules, increasing due to replication, exceeds a certain threshold. We study how the chemicals in a catalytic network can form recursive production states in the presence of errors in the replication process. Depending on the balance between the total number of molecules in a cell and the number of molecule species, we have found three phases; a phase without a recursive production state, a phase with itinerancy over a few recursive states, and a phase with fixed recursive production states. Heredity is realized in the latter two phases where molecule species that are population-wise in the minority are preserved and control the phenotype of the cell. It is shown that evolvability is realized in the itinerancy phase, where a change in the number of minority molecules controls a change of the chemical state.

nlin.AO↗

arXiv2002

Dynamical Networks in Function Dynamics

As a first step toward realizing a dynamical system that evolves while spontaneously determining its own rule for time evolution, function dynamics (FD) is analyzed. FD consists of a functional equation with a self-referential term, given as a dynamical system of a 1-dimensional map. Through the time evolution of this system, a dynamical graph (a network) emerges. This graph has three interesting properties: i) vertices appear as stable elements, ii) the terminals of directed edges change in time, and iii) some vertices determine the dynamics of edges, and edges determine the stability of the vertices, complementarily. Two aspects of FD are studied, the generation of a graph (network) structure and the dynamics of this graph (network) in the system.

nlin.AO↗

arXiv2001

Simple dynamical model with history dependence for a sandpile experiment

A lattice dynamics model is proposed for the history dependence observed in sandpile experiments. The dependence of the stress distribution on the preparation of the sandpile is explained as a dependence of certain attractors on the preparation of the system. The model has three phases, but the history dependence is shown to exist only in the phase where a perturbation is amplified selectively rather than globally when propagating in the downflow direction. The condition for this history dependence is given in terms of the spatial Lyapunov exponent.

cond-mat.soft↗