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In biological systems, expression dynamics that can provide fitted phenotype patterns with respect to a specific function have evolved through mutations. This has been observed in the evolution of proteins for realizing folding dynamics…
The evolution of high-dimensional phenotypes is investigated using a statistical physics model consists of interacting spins, in which genotypes, phenotypes, and environments are represented by spin configurations, interaction matrices, and…
Biological systems must be robust for stable function against perturbations, but robustness alone is not sufficient. The ability to switch between appropriate states (phenotypes) in response to different conditions is essential for…
Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness…
The relationship between genotype and phenotype plays a crucial role in determining the function and robustness of biological systems. Here the evolution progresses through the change in genotype, whereas the selection is based on the…
Phenotype of biological systems needs to be robust against mutation in order to sustain themselves between generations. On the other hand, phenotype of an individual also needs to be robust against fluctuations of both internal and external…
The characterization of plasticity, robustness, and evolvability, an important issue in biology, is studied in terms of phenotypic fluctuations. By numerically evolving gene regulatory networks, the proportionality between the phenotypic…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
Adaptation in a fluctuating environment is a process of fueling environmental information to gain fitness. Living systems have gradually developed strategies for adaptation from random and passive diversification of the phenotype to more…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
The mutation-selection mechanism of Darwinian evolution gives rise not only to adaptation to environmental conditions but also to the enhancement of robustness against mutations. When two or more phenotypes have the same fitness value, the…
We study evolutionary canalization using a spin-glass model with replica theory, where spins and their interactions are dynamic variables whose configurations correspond to phenotypes and genotypes, respectively. The spins are updated under…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
In the past years, a remarkable mapping has been found between the dynamics of a population of M individuals undergoing random mutations and selection, and that of a single system in contact with a thermal bath with temperature 1/M. This…
Many biological systems regulate phenotypic heterogeneity as a fitness-maximising strategy in uncertain and dynamic environments. Analysis of such strategies is typically confined both to a discrete set of environmental conditions, and to a…
Population dynamics on a rugged landscape is studied analytically and numerically within a simple discrete model for evolution of N individuals in one-dimensional fitness space. We reduce the set of master equations to a single Fokker-Plank…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
A macroscopic theory for describing cellular states during steady-growth is presented, which is based on the consistency between cellular growth and molecular replication, as well as the robustness of phenotypes against perturbations.…
Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…
We analyze the population dynamics of a broad class of fitness functions that exhibit epochal evolution---a dynamical behavior, commonly observed in both natural and artificial evolutionary processes, in which long periods of stasis in an…