Related papers: Phase transitions in microbial lineage trees
Microbiome-based stratification of healthy individuals into compositional categories, referred to as "community types", holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types…
I give a highly selective overview of the way statistical mechanics explains the microscopic origins of the time asymmetric evolution of macroscopic systems towards equilibrium and of first order phase transitions in equilibrium. These…
Statistical fluctuations in population sizes of microbes may be quite large depending on the nature of their underlying stochastic dynamics. For example, the variance of the population size of a microbe undergoing a pure birth process with…
It has been known for many years that small fractions of persister cells resist killing in many bacterial colony-antimicrobial confrontations. These persisters are not believed to be mutants. Rather it has been hypothesized that they are…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
Although ubiquitous, interactions of groups of individuals (e.g., modern messaging applications, group meetings, or even a parliament discussion) are not yet thoroughly studied. Frequently, single-groups are modeled as critical-mass…
Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and…
Ecosystems can undergo sudden shifts to undesirable states, but recent studies with simple single species ecosystems have demonstrated that advance warning can be provided by the slowing down of population dynamics near a tipping point.…
Clonal microbes can switch between different phenotypes and recent theoretical work has shown that stochastic switching between these subpopulations can stabilize microbial communities. This phenotypic switching need not be stochastic,…
The goal of this article is to contribute towards the conceptual and quantitative understanding of the evolutionary benefits for (microbial) populations to maintain a seed bank (consisting of dormant individuals) when facing fluctuating…
Although it is well-known that some exponential family random graph model (ERGM) families exhibit phase transitions (in which small parameter changes lead to qualitative changes in graph structure), the behavior of other models is still…
Evolutionary transitions among ecological interactions are widely known, although their detailed dynamics remain absent for most population models. Adaptive dynamics has been used to illustrate how the parameters of population models might…
Recently, dynamical phase transitions have been identified based on the non-analytic behavior of the Loschmidt echo in the thermodynamic limit [Heyl et al., Phys.~Rev.~Lett.~{\bf 110}, 135704 (2013)]. By introducing conditional probability…
In the present paper, we characterize the behavior of supercritical branching processes in random environment with linear fractional offspring distributions, conditioned on having small, but positive values at some large generation. As it…
We present results on a stochastic forest fire model, where the influence of the neighbour trees is treated in a more realistic way than usual and the definition of neighbourhood can be tuned by an additional parameter. This model exhibits…
We study the evolution of artificial learning systems by means of selection. Genetic programming is used to generate a sequence of populations of algorithms which can be used by neural networks for supervised learning of a rule that…
Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such…
A general system of particles (of one or several species) on a one dimensional lattice with boundaries is considered. Two general behaviors of such systems are investigated. The stationary behavior of the system, and the dominant way of the…
We study a one parameter family of random graph models that spans a continuum between traditional random graphs of the Erd\H{o}s-R\'enyi type, where there is no underlying structure, and percolation models, where the possible edges are…
Phase transitions are fundamental features of statistical physics. While the well-studied continuous phase transitions are known to be controlled by external \textit{macroscopic} changes in the order parameter, the origin of abrupt…