253 citations · 3k across the 163 of their papers we have counts for
15 papers · 1 filter
Dynamical-systems theory of cellular reprogramming
Yuuki Matsushita, Tetsuhiro S. Hatakeyama, Kunihiko Kaneko
In cellular reprogramming, almost all epigenetic memories of differentiated cells are erased by the overexpression of few genes, regaining pluripotency, potentiality for differenti…
Error Catastrophe Can Be Avoided by Proofreading Innate to Template-Directed Polymerization
Yoshiya J. Matsubara, Nobuto Takeuchi, Kunihiko Kaneko
An important issue for the origins of life is ensuring the accurate maintenance of information in replicating polymers in the face of inevitable errors. Here, we investigated how t…
A Linear Reciprocal Relationship Between Robustness and Plasticity in Homeostatic Biological Networks
Tetsuhiro S. Hatakeyama, Kunihiko Kaneko
In physics of living systems, a search for relationships of a few macroscopic variables that emerge from many microscopic elements is a central issue. We evolved gene regulatory ne…
Dimensional reduction in evolving spin-glass model: correlation of phenotypic responses to environmental and mutational changes
Ayaka Sakata, Kunihiko Kaneko
The evolution of high-dimensional phenotypes is investigated using a statistical physics model consists of interacting spins, in which genotypes, phenotypes, and environments are r…
Transition in relaxation paths in allosteric molecules: enzymatic kinetically constrained model
Tetsuhiro S. Hatakeyama, Kunihiko Kaneko
A hierarchy of timescales is ubiquitous in biological systems, where enzymatic reactions play an important role because they can hasten the relaxation to equilibrium. We introduced…
Kinetic Selection of Template Polymer with Complex Sequences
Yoshiya J. Matsubara, Kunihiko Kaneko
Emergence and maintenance of polymers with complex sequences is a major question in the study of origins of life. To answer this, we studied a model polymerization reaction, where…
Theory for transitions between log and stationary phases: universal laws for lag time
Yusuke Himeoka, Kunihiko Kaneko
Quantitative characterization of bacterial growth has gathered substantial attention since Monod's pioneering study. Theoretical and experimental work has uncovered several laws fo…
Enzyme oscillation can enhance the thermodynamic efficiency of cellular metabolism: Consequence of anti-phase coupling between reaction flux and affinity
Yusuke Himeoka, Kunihiko Kaneko
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essen…
Weber's Law in Autocatalytic Reaction Networks
Masayo Inoue, Kunihiko Kaneko
Biological responses often obey Weber's law, according to which the magnitude of the response depends only on the fold change in the external input. In this study, we demonstrate t…
A thermodynamic force generated by chemical gradient and adsorption reaction
Takeshi Sugawara, Kunihiko Kaneko
Biological units such as macromolecules, organelles, and cells are directed to a proper location under gradients of relevant chemicals. By considering a macroscopic element that ha…
Dynamics of Coupled Adaptive Elements : Bursting and Intermittent Oscillations Generated by Frustration in Networks
Masayo Inoue, Kunihiko Kaneko
Adaptation to environmental change is a common property of biological systems. Cells initially respond to external changes in the environment, but after some time, they regain thei…
On the Distribution of State Values of Reproducing Cells: the General Evolution Equation and its Applications
Katsuhiko Sato, Kunihiko Kaneko
Fluctuations of cell state, e.g., abundances of some proteins, have attracted much attention both theoretically and experimentally. The distribution of such state over cells, howev…
Zipf's Law in Gene Expression
Chikara Furusawa, Kunihiko Kaneko
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…
Alteration of Chemical Concentrations through Discreteness-Induced Transitions in Small Autocatalytic Systems
Yuichi Togashi, Kunihiko Kaneko
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…
Transitions Induced by the Discreteness of Molecules in a Small Autocatalytic System
Yuichi Togashi, Kunihiko Kaneko
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 molec…