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Tetsuhiro S. Hatakeyama

Publications and source records attributed to Tetsuhiro S. Hatakeyama.

17 recordsLinked to original sources

Anomalous First Passage in Evolution: Edge-KPZ Theory

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 mean time for the first individual to reach a prescribed phenotypic distance scales approximately as $(σ^2)^{-3/2}$ with mutation variance $σ^2$. Two crossovers bound this regime, with inverse-variance scaling on either side. Combining coalescent theory with Kardar-Parisi-Zhang (KPZ) fluctuations at the dilute population edge, we develop an edge-KPZ theory of all three regimes. The anomaly persists under weak selection.

q-bio.PE↗

Global geometry of the genotype-phenotype map illuminates a trade-off between penetrance and mutational adaptability

Evolution in changing environments requires both reliable expression of the currently favored phenotype, as quantified by penetrance, and the capacity to reach alternative phenotypes through mutation. Previous studies suggest that high penetrance may restrict such mutational access. However, because these studies focus on evolved genotypes and local mutational neighborhoods, they cannot determine whether this local constraint limits mutational adaptability under environmental change. Such adaptability depends on a genotype's position relative to high-fitness regions for other environments. Addressing this question requires reconstructing the full probability distribution over phenotypes for every genotype and the resulting environment-specific fitness landscapes across genotype space. Such reconstruction is generally infeasible because genotype and phenotype spaces grow combinatorially. Here, an abstract model of stochastic genotype-phenotype mapping, inspired by interacting spins in statistical physics, permits exhaustive reconstruction of the map. We find that high-penetrance genotypes tend to occupy the interior of environment-specific high-fitness regions and are mutationally robust, whereas lower-penetrance genotypes tend to lie near their boundaries and have greater mutational access to high-fitness regions for alternative environments. This global geometry generates a trade-off between penetrance and mutational adaptability. In evolutionary simulations, stronger phenotypic noise in a fixed environment increases the selective advantage of reliable expression, thereby favoring high penetrance and mutational robustness. Frequent environmental change instead favors mutational accessibility at the expense of penetrance. Thus, penetrance and adaptability are opposing consequences of the same global geometry, with environmental conditions determining their evolutionary balance.

q-bio.PE↗

Evolutionary Le Chatelier's Principle: Phenotypic Plasticity and Genetic Assimilation via Timescale Separation in the Price Equation

Phenotypic plasticity and genetic assimilation play key roles in adaptive evolution, yet their underlying mechanism has lacked a unified physical description. A major theoretical difficulty lies in the fundamental difference in timescales, as phenotypic plasticity occurs rapidly within a generation whereas genetic changes accumulate slowly across generations. Here, we formalize these processes by bridging the continuous-time Price equation, a foundational equation of evolutionary dynamics, with the physical concept of timescale separation. A sudden environmental change induces a fast plastic displacement of the phenotype relative to the slow genotypic variable. Through genotype--phenotype coupling, this displacement generates an internal genetic stress. We demonstrate that genetic assimilation is a dynamical relaxation process in which the genotype evolves to resolve this self-generated stress. These evolutionary dynamics mathematically realize Le Chatelier's principle, where the slow genetic response naturally amplifies the initial plastic shift in the same direction. The theory predicts that a weaker restoring force, which can manifest as larger clonal phenotypic fluctuations, requires a longer evolutionary timescale for assimilation. In the ideal limit of cost-free, perfectly adaptive plasticity, the relaxation time diverges, so assimilation effectively stalls. This formulation provides a macroscopic physical mechanism for genetic assimilation, offering a universal response law for evolutionary systems in which rapid phenotypic responses precede slower genetic change.

q-bio.PE↗

Thermodynamic cost-controllability tradeoff in metabolic currency coupling

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-energy) states to mediate energy transfer. While distinct currency metabolites are associated with different metabolic functions, their charged and uncharged forms are generally interchangeable via biochemical reactions such as ${\rm ATP{\,+\,}GDP{\,\rightleftharpoons\,}ADP{\,+\,}GTP}$ and $\rm NADP^+{\,+\,}NADH{\,\rightleftharpoons\,}NADPH{\,+\,}NAD^+ $. Thus, their energetic states are generally coupled and influence each other, which would hinder the independent regulation of different currency metabolites. Despite the extensive knowledge of the molecular biology of individual currency metabolites, it remains poorly understood how the coordination of various coupled currency metabolites shapes metabolic regulation, efficiency, and ultimately the evolution of organisms. Here, we present a minimal theoretical model of metabolic currency coupling and reveal a fundamental tradeoff relationship between metabolic controllability and thermodynamic cost: increasing the capacity to independently regulate multiple currency metabolites generally requires comparable abundances of those metabolites, which in turn incurs a higher entropy production rate. The tradeoff suggests that in complex environments, organisms evolutionarily favor an equal abundance of currency metabolites to enhance metabolic controllability at the expense of a higher thermodynamic cost; conversely, in simple environments, organisms evolve to have imbalanced amounts of them to reduce heat dissipation. These considerations also offer a hypothesis regarding evolutionary trends in nucleotide-pool balance and genomic GC content.

physics.bio-ph↗

Anti-aligning Self-propelled Model of Two Species: Emergence of Self-organized Heterogeneous Aligned and Clustered Order

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 and interact through aligning interactions between different species, a global polar order can emerge through the formation of elongated clusters with alternating domains of each species. By developing a mean-field theory, we reveal the conditions for cluster formation and characterize the resulting patterns. Our findings highlight the critical role of inter-species interactions in the emergence of complex ordered states.

cond-mat.soft↗

Enzyme as Maxwell's Demon: Steady-state Deviation from Chemical Equilibrium by Enhanced Enzyme Diffusion

Enhanced enzyme diffusion (EED), in which the diffusion coefficient of an enzyme transiently increases during catalysis, has been extensively reported experimentally. We numerically and analytically demonstrate that such enzymes can act as Maxwell's demons. They use their enhanced diffusion as a memory of the previous catalytic reaction, to gain information and drive steady-state chemical concentrations away from chemical equilibrium. Our theoretical analysis identifies the conditions for this process, highlighting the functional role of EED and its relevance to cellular systems.

physics.bio-ph↗

Global Constraint Principle for Microbial Growth Law

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 often considered to be locally constrained by a single reaction. In contrast, this paper shows that a global constraint principle of resource allocation to metabolic processes can well describe the nature of cell growth. This concept is a generalization of Liebig's law, a growth law for higher organisms, and explains the dependence of microbial growth on the availability of multiple nutrients, in contrast to Monod's law.

q-bio.CB↗

Enzymatic Mpemba Effect: Slowing of biochemical reactions by increasing enzyme concentration

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 enzymatic reaction. We consider a simple allosteric protein with multiple modification sites, catalyzed by two enzymes with the same catalytic activity, but slightly different affinities. We show that increasing the concentration of one enzyme can slow the relaxation to the equilibrium state. The mechanism for this slowing is similar the Markovian Mpemba effect, and we name this phenomenon as the Enzymatic Mpemba effect.

physics.chem-ph↗

Evolutionary Innovation by Polyploidy

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 role of polyploidy in the evolution of novel traits. There are two hypotheses regarding the effects of polyploidy on evolution: Polyploidy reduces the effect of a single mutation and slows evolution. In contrast, the gene redundancy introduced by polyploidy will promote neofunctionalization and accelerate evolution. Does polyploidy speed up or slow down evolution? In this study, we proposed a simple model of polyploid cells and showed that the evolutionary rate of polyploids is similar to or much slower than that of haploids under neutral selection or during gradual evolution. However, on a fitness landscape where cells should jump over a lethal valley to increase their fitness, the probability of evolution in polyploidy could be drastically increased, and the optimal number of chromosomes was identified. We theoretically discussed the existence of this optimal chromosome number from the large deviation theory. Furthermore, we proposed that the optimization for achieving evolutionary innovation could determine the range of chromosome numbers in polyploid bacteria.

q-bio.PE↗

Linear Response Theory of Evolved Metabolic Systems

Predicting cellular metabolic states is a central problem in biophysics. Conventional approaches, however, sensitively depend on the microscopic details of individual metabolic systems. In this Letter, we derived a universal linear relationship between the metabolic responses against nutrient conditions and metabolic inhibition, with the aid of a microeconomic theory. The relationship holds in arbitrary metabolic systems as long as the law of mass conservation stands, as supported by extensive numerical calculations. It offers quantitative predictions without prior knowledge of systems.

q-bio.MN↗

Active thermodynamic force driven mitochondrial alignment

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 constant ATP concentration, but little is known about the mechanism. In this letter, we show theoretically that ATP production and ATP-dependent non-directional movement of mitochondria are sufficient for alignment, even in the absence of an explicit repulsive force between them. This is similar to thermodynamic forces driven by thermal fluctuations, even generated by non-equilibrium processes, and demonstrates the diversity of mechanisms governing the motion of biological matter.

physics.bio-ph↗

Dynamical-systems theory of cellular reprogramming

In cellular reprogramming, almost all epigenetic memories of differentiated cells are erased by the overexpression of few genes, regaining pluripotency, potentiality for differentiation. Considering the interplay between oscillatory gene expression and slower epigenetic modifications, such reprogramming is perceived as an unintuitive, global attraction to the unstable manifold of a saddle, which represents pluripotency. The universality of this scheme is confirmed by the repressilator model, and by gene regulatory networks randomly generated and those extracted from embryonic stem cells.

physics.bio-ph↗

A Linear Reciprocal Relationship Between Robustness and Plasticity in Homeostatic Biological Networks

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 networks so that the expression of target genes (partial system) is insensitive to environmental changes. Then, we found the expression levels of the remaining genes autonomously increase as a plastic response. Negative proportionality was observed between the average changes in target and remnant genes, reflecting reciprocity between the macroscopic robustness of homeostatic genes and plasticity of regulator genes. This reciprocity follows the lever principle, which was satisfied throughout the evolutionary course, imposing an evolutionary constraint.

physics.bio-ph↗

Transition in relaxation paths in allosteric molecules: enzymatic kinetically constrained model

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 a statistical physics model of interacting spins that also incorporates enzymatic reactions to extend the classic model for allosteric regulation. Through Monte Carlo simulations, we found that the relaxation dynamics are much slower than the elementary reactions and are logarithmic in time with several plateaus, as is commonly observed for glasses. This is because of the kinetic constraints from the cooperativity via the competition for an enzyme, which has different affinity for molecules with different structures. Our model showed symmetry breaking in the relaxation trajectories that led to inherently kinetic transitions without any correspondence to the equilibrium state. In this paper, we discuss the relevance of these results for diverse responses in biology.

physics.bio-ph↗

Robustness of spatial patterns in buffered reaction-diffusion systems and its reciprocity with phase plasticity

Robustness of spatial pattern against perturbations is an indispensable property of developmental processes for organisms, which need to adapt to changing environments. Although specific mechanisms for this robustness have been extensively investigated, little is known about a general mechanism for achieving robustness in reaction-diffusion systems. Here, we propose a buffered reaction-diffusion system, in which active states of chemicals mediated by buffer molecules contribute to reactions, and demonstrate that robustness of the pattern wavelength is achieved by the dynamics of the buffer molecule. This robustness is analytically explained as a result of the scaling properties of the buffered system, which also lead to a reciprocal relationship between the wavelength's robustness and the plasticity of the spatial phase upon external perturbations. Finally, we explore the relevance of this reciprocity to biological systems.

nlin.AO↗

Reciprocity Between Robustness of Period and Plasticity of Phase in Biological Clocks

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 unclear how both are simultaneously achieved. By investigating distinct models of circadian clocks, we demonstrate reci- procity between robustness and plasticity: higher robustness in the period implies higher plasticity in the phase, where changes in period and in phase follow a linear relationship with a negative coef- ficient. The robustness of period is achieved by the adaptation on the limit cycle via a concentration change of a buffer molecule, whose temporal change leads to a phase shift following a shift of the limit-cycle orbit in phase space. Generality of reciprocity in clocks with the adaptation mechanism is confirmed with theoretical analysis of simple models, while biological significance is discussed.

q-bio.MN↗

Generic temperature compensation of biological clocks by autonomous regulation of catalyst concentration

Circadian clocks ubiquitous in life forms ranging bacteria to multi-cellular organisms, often exhibit intrinsic temperature compensation; the period of circadian oscillators is maintained constant over a range of physiological temperatures, despite the expected Arrhenius form for the reaction coefficient. Observations have shown that the amplitude of the oscillation depends on the temperature but the period does not---this suggests that although not every reaction step is temperature independent, the total system comprising several reactions still exhibits compensation. We present a general mechanism for such temperature compensation. Consider a system with multiple activation energy barriers for reactions, with a common enzyme shared across several reaction steps with a higher activation energy. These reaction steps rate-limit the cycle if the temperature is not high. If the total abundance of the enzyme is limited, the amount of free enzyme available to catalyze a specific reaction decreases as more substrates bind to common enzyme. We show that this change in free enzyme abundance compensate for the Arrhenius-type temperature dependence of the reaction coefficient. Taking the example of circadian clocks with cyanobacterial proteins KaiABC consisting of several phosphorylation sites, we show that this temperature compensation mechanisms is indeed valid. Specifically, if the activation energy for phosphorylation is larger than that for dephosphorylation, competition for KaiA shared among the phosphorylation reactions leads to temperature compensation. Moreover, taking a simpler model, we demonstrate the generality of the proposed compensation mechanism, suggesting relevance not only to circadian clocks but to other (bio)chemical oscillators as well.

q-bio.MN↗