Related papers: Phase transitions in microbial lineage trees
Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. Signatures of regime shifts in gene…
Proliferation and motility are ubiquitous drivers of activity in biological systems. Here, we study a dense binary mixture of motile and proliferating particles with exclusively repulsive interactions, where homeostasis in the proliferating…
Compact stars above a critical stellar mass develop large scalar fields in some scalar-tensor theories. This scenario, called spontaneous scalarization, has been an intense topic of study since it passes weak-field gravity tests naturally…
The Topological Hypothesis states that phase transitions should be related to changes in the topology of configuration space. The necessity of such changes has already been demonstrated. We characterize exactly the topology of the…
Stability is a desirable property of complex ecosystems. If a community of interacting species is at a stable equilibrium point then it is able to withstand small perturbations to component species' abundances without suffering adverse…
This paper explores the connection between dynamical system properties and statistical physics of ensembles of such systems. Simple models are used to give novel phase transitions; particularly for finite N particle systems with many…
We investigate the evolutionary dynamics of a population structured in phenotype, subjected to trait dependent selection with a linearly moving optimum and an asexual mode of reproduction. Our model consists of a non-local and non-linear…
A variety of genome transformations can occur as a microbial population adapts to a large environmental change. In particular, genomic surveys indicate that, following the transition to an obligate, host-dependent symbiont, the density of…
In this work we employ a simple pairing interaction model in order to study and classify an eventual pairing phase transition in finite fermionic systems. We show that systems with as few as 10-16 fermions can exhibit clear features…
Plasmids are major players in Horizontal Gene Transfer mechanisms, hence they are highly variable in their gene content and length. We propose a model for the fitness of a plasmid as a function of its length, which predicts diminishing…
Motivated by recent findings, we discuss the existence of a direct and robust mechanism providing discontinuous absorbing transitions in short range systems with single species, with no extra symmetries or conservation laws. We consider…
We experimentally study the emergence of collective bacterial swimming, a phenomenon often referred to as bacterial turbulence. A phase diagram of the flow of 3D E. coli suspensions spanned by bacterial concentration, the swimming speed of…
It has been recently shown that the exponential growth rate of a population of bacterial cells starting from a single cell shows transient oscillations due to early synchronized bursts of division. These oscillations are enhanced by cell…
State transitions are fundamental in biological systems but challenging to observe directly. Here, we present the first single-cell observation of state transitions in a synthetic bacterial genetic circuit. Using a mother machine, we…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
We study the evolution of sexual and asexual populations in general fitness landscapes. We find deep relations between the mathematics of biological evolution and the formalism of quantum mechanics. We give the general structure of the…
We study a class of evolution models, where the breeding process involves an arbitrary exchangeable process, allowing for mutations to appear. The population size $n$ is fixed, hence after breeding, selection is applied. Individuals are…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
Microbiology is the science of microbes, particularly bacteria. Many bacteria are motile: they are capable of self-propulsion. Among these, a significant class execute so-called run-and-tumble motion: they follow a fairly straight path for…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…