Related papers: Phase transitions in microbial lineage trees
A cyclically dominating three-species ecosystem, modeled within the framework of rock-paper-scissor game, is studied in presence of natural death and an effect of the environment. The environmental impact is parameterized along with the…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…
Many complex systems satisfy a set of constraints on their degrees of freedom, and at the same time, they are able to work and adapt to different conditions. Here, we describe the emergence of this ability in a simplified model in which the…
We discuss several pairing-related phenomena in nuclear systems, ranging from superfluidity in neutron stars to the gradual breaking of pairs in finite nuclei. We describe recent experimental evidence that points to a relation between…
Biological information processing manifests a huge variety in its complexity and capability among different organisms, which presumably stems from the evolutionary optimization under limited computational resources. Starting from the…
Flocks of birds and schools of fish are familiar examples of spatial patterns formed by living organisms. In contrast to the patterns on the skins of, say, zebra and giraffe, the patterns of our interest are {\it transient} although…
One of the most challenging problems in microbiology is to understand how a small fraction of microbes that resists killing by antibiotics can emerge in a population of genetically identical cells, the phenomenon known as persistence or…
The relationship between the dynamics of a community and its constituent pairwise interactions is a fundamental problem in ecology. Higher-order ecological effects beyond pairwise interactions may be key to complex ecosystems, but…
In complex ecosystems such as microbial communities, there is constant ecological and evolutionary feedback between the residing species and the environment occurring on concurrent timescales. Species respond and adapt to their surroundings…
We introduce an analytical model for population dynamics with intra-specific competition, mutation and assortative mating as basic ingredients. The set of equations that describes the time evolution of population size in a mean-field…
Phase transitions are the macroscopic manifestation of microscopic processes that drive a system towards a new state. The detailed evolution of these processes, particularly in abrupt phase transitions, are currently not fully understood.…
The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…
(abridged) In this paper, we present the issues we consider as essential as far as the statistical mechanics of finite systems is concerned. In particular, we emphasis our present understanding of phase transitions in the framework of…
Phenological timing -- i.e. the course of annually recurring development stages in nature -- is of particular interest since it can be understood as a proxy for the climate at a specific region; moreover changes in the so called…
Many intracellular processes continue to oscillate during the cell cycle. Although it is not well-understood how they are affected by discontinuities in the cellular environment, the general assumption is that oscillations remain robust…
A bit-string model for the evolution of a population of haploid organisms, subject to competition, reproduction with mutation and selection is studied, using mean field theory and Monte Carlo simulations. We show that, depending on…
Biological mixtures such as the cytosol may consist of thousands of distinct components. There is now a substantial body of evidence showing that, under physiological conditions, intracellular mixtures can phase separate into spatially…
Generative diffusion models have achieved spectacular performance in many areas of machine learning and generative modeling. While the fundamental ideas behind these models come from non-equilibrium physics, variational inference and…
We are interested in the evolving genealogy of a birth and death process with trait structure and ecological interactions. Traits are hereditarily transmitted from a parent to its offspring unless a mutation occurs. The dynamics may depend…
Interpreting partial information collected from systems subject to noise is a key problem across scientific disciplines. Theoretical frameworks often focus on the dynamics of variables that result from coarse-graining the internal states of…