Lineage EM algorithm for inferring latent states from cellular lineage trees.

Summary: Phenotypic variability in a population of cells can work as the bet-hedging of the cells under an unpredictably changing environment, the typical example of which is the bacterial persistence. To understand the strategy to control such phenomena, it is indispensable to identify the phenotype of each cell and its inheritance. Although recent advancements in microfluidic technology offer us useful lineage data, they are insufficient to directly identify the phenotypes of the cells.

Fitness response relation of a multitype age-structured population dynamics.

We construct a pathwise formulation for a multitype age-structured population dynamics, which involves an age-dependent cell replication and transition of gene- or phenotypes. By employing the formulation, we derive a variational representation of the stationary population growth rate; the representation comprises a tradeoff relation between growth effects and a single-cell intrinsic dynamics described by a semi-Markov process. This variational representation leads to a response relation of the stationary population growth rate, in which statistics on a retrospective history work as the response coefficients.

Stochastic and information-thermodynamic structures of population dynamics in a fluctuating environment.

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 proactive decision making, in which environmental information is sensed and exploited more actively and effectively. Understanding the fundamental relation between fitness and information is therefore crucial to clarify the limits and universal properties of adaptation.

Steady-state thermodynamics for population growth in fluctuating environments.

We report that population dynamics in fluctuating environments is characterized by a mathematically equivalent structure to steady-state thermodynamics. By employing the structure, population growth in fluctuating environments is decomposed into housekeeping and excess parts. The housekeeping part represents the integral of the stationary growth rate for each condition during a history of the environmental change.

Discreteness-induced transitions in multibody reaction systems.

A decrease in system size can induce qualitatively different behavior compared to the macroscopic behavior of the corresponding large-size system. The mechanisms of this transition, which is known as the small-size transition, can be attributed to either a relative increase in the noise intensity or to the discreteness of the state space due to the small system size. The former mechanism has been intensively investigated using several toy and realistic models.

Motif analysis for small-number effects in chemical reaction dynamics.

The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic changes in chemical-reaction dynamics and statistics compared to those observed under a macroscopic system (i.e.

Fluctuation Relations of Fitness and Information in Population Dynamics.

Phenotype switching with and without sensing environment is a common strategy of organisms to survive in a fluctuating environment. Understanding the evolutionary advantages of switching and sensing requires a quantitative evaluation of their fitness gain and its fluctuation together with the conditions for the switching and sensing strategies being adapted to a given environment. In this work, by using a pathwise formulation of the population dynamics, we show that the optimal switching strategy is characterized by a consistency condition for time-forward and backward path probabilities.

Pathwise thermodynamic structure in population dynamics.

We reveal thermodynamic structure in population dynamics with phenotype switching. Mean fitness for a population of organisms is determined by a thermodynamic variational principle described by the large deviation of phenotype-switching dynamics. Owing to this variational principle, a response relation of the mean fitness with respect to changes of environments and phenotype-switching dynamics is represented as a thermodynamic differential form.

Fluctuation theorem for the renormalized entropy change in the strongly nonlinear nonequilibrium regime.

A nonlinear relaxation process is considered for a macroscopic thermodynamic quantity, generalizing recent work by Taniguchi and Cohen [J. Stat. Phys.