68 citations · 117 across the 16 of their papers we have counts for
17 papers
Anomalous First Passage in Evolution: Edge-KPZ Theory
Tetsuhiro S. Hatakeyama
The pace of evolution depends on how rapidly new phenotypes arise. We show that neutral Wright-Fisher evolution exhibits anomalous first passage despite diffusive mutations. The me…
Global geometry of the genotype-phenotype map illuminates a trade-off between penetrance and mutational adaptability
Yutaro Ikeda, Kunihiko Kaneko, Tetsuhiro S. Hatakeyama
Evolution in changing environments requires both reliable expression of the currently favored phenotype, as quantified by penetrance, and the capacity to reach alternative phenotyp…
Evolutionary Le Chatelier's Principle: Phenotypic Plasticity and Genetic Assimilation via Timescale Separation in the Price Equation
Tetsuhiro S. Hatakeyama
Phenotypic plasticity and genetic assimilation play key roles in adaptive evolution, yet their underlying mechanism has lacked a unified physical description. A major theoretical d…
Thermodynamic cost-controllability tradeoff in metabolic currency coupling
Jumpei F. Yamagishi, Tetsuhiro S. Hatakeyama
Cellular metabolism is globally regulated by various currency metabolites such as ATP, GTP, and NAD(P)H. These metabolites cycle between charged (high-energy) and uncharged (low-en…
Enzyme as Maxwell's Demon: Steady-state Deviation from Chemical Equilibrium by Enhanced Enzyme Diffusion
Shunsuke Ichii, Tetsuhiro S. Hatakeyama, Kunihiko Kaneko
Enhanced enzyme diffusion (EED), in which the diffusion coefficient of an enzyme transiently increases during catalysis, has been extensively reported experimentally. We numericall…
Anti-aligning Self-propelled Model of Two Species: Emergence of Self-organized Heterogeneous Aligned and Clustered Order
Takahiro Oki, Tetsuhiro S. Hatakeyama, Seiya Nishikawa +2
Self-propelled particles with anti-aligning interactions generally do not form a polar order. However, in this Letter, we show that when multiple types of such particles coexist an…
Enzymatic Mpemba Effect: Slowing of biochemical reactions by increasing enzyme concentration
Tetsuhiro S. Hatakeyama
Increasing the enzyme concentration generally speeds up enzymatic reactions. However, in this Letter, we show that increasing the enzyme concentration can also slow down the enzyma…
Global Constraint Principle for Microbial Growth Law
Jumpei F. Yamagishi, Tetsuhiro S. Hatakeyama
Monod's law is a widely accepted phenomenology for bacterial growth. Since it has the same functional form as the Michaelis--Menten equation for enzyme kinetics, cell growth is oft…
Active thermodynamic force driven mitochondrial alignment
Masashi K. Kajita, Yoshiyuki Konishi, Tetsuhiro S. Hatakeyama
Mitochondria are critical organelles in eukaryotes that produce the energy currency ATP. In nerve axons, mitochondria are known to align at almost regular intervals to maintain a c…
Evolutionary Innovation by Polyploidy
Tetsuhiro S. Hatakeyama, Ryudo Ohbayashi
The preferred conditions for evolutionary innovation is a fundamental question, but little is known, in part because the question involves rare events. We focused on the potential…
Linear Response Theory of Evolved Metabolic Systems
Jumpei F. Yamagishi, Tetsuhiro S. Hatakeyama
Predicting cellular metabolic states is a central problem in biophysics. Conventional approaches, however, sensitively depend on the microscopic details of individual metabolic sys…
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…
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…
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…
Robustness of spatial patterns in buffered reaction-diffusion systems and its reciprocity with phase plasticity
Tetsuhiro S. Hatakeyama, Kunihiko Kaneko
Robustness of spatial pattern against perturbations is an indispensable property of developmental processes for organisms, which need to adapt to changing environments. Although sp…
Reciprocity Between Robustness of Period and Plasticity of Phase in Biological Clocks
Tetsuhiro S. Hatakeyama, Kunihiko Kaneko
Circadian clocks exhibit the robustness of period and plasticity of phase against environmental changes such as temperature and nutrient conditions. Thus far, however, it is unclea…
Generic temperature compensation of biological clocks by autonomous regulation of catalyst concentration
Tetsuhiro S. Hatakeyama, Kunihiko Kaneko
Circadian clocks ubiquitous in life forms ranging bacteria to multi-cellular organisms, often exhibit intrinsic temperature compensation; the period of circadian oscillators is mai…