Related papers: Growing Trees and Amoebas' Replications
Trees are partial orderings where every element has a linearly ordered set of smaller elements. We define and study several natural notions of completeness of trees, extending Dedekind completeness of linear orders and Dedekind-MacNeille…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
We study Ramsey like theorems for infinite trees and similar combinatorial tools. As an application we consider the expansion problem for tree algebras.
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…
At any moment in time, evolution is faced with a formidable challenge: refining the already highly optimised design of biological species, a feat accomplished through all preceding generations. In such a scenario, the impact of random…
By unifying three foundational principles of modern biology, we develop a mathematical framework to analyze the growing tree of life. Contrary to the static case, where the analogy between phylogenetic trees and the tree that grows in soil…
One can often make inferences about a growing network from its current state alone. For example, it is generally possible to determine how a network changed over time or pick among plausible mechanisms explaining its growth. In practice,…
We show that for many models of random trees, the independence number divided by the size converges almost surely to a constant as the size grows to infinity; the trees that we consider include random recursive trees, binary and $m$-ary…
Assuming the existence of a strong cardinal $\kappa$ and a measurable cardinal above it, we force a generic extension in which $\kappa$ is a singular strong limit cardinal of any prescribed cofinality, and such that the tree property holds…
Given a set $X$ of species, a phylogenetic tree is an unrooted binary tree whose leaves are bijectively labelled by $X$. Such trees can be used to show the way species evolve over time. One way of understanding how topologically different…
We analyze a simple model for growing tree networks and find that although it never percolates, there is an anomalously large cluster at finite size. We study the growth of both the maximal cluster and the cluster containing the original…
We study the question of whether a given regular language of finite trees can be defined in first-order logic. We develop an algebraic approach to address this question and we use it to derive several necessary and sufficient conditions for…
We introduce and analyze a random tree model associated to Hoppe's urn. The tree is built successively by adding nodes to the existing tree when starting with the single root node. In each step a node is added to the tree as a child of an…
We propose a stochastic model for evolution. Births and deaths of species occur with constant probabilities. Each new species is associated with a fitness sampled from the uniform distribution on [0,1]. Every time there is a death event…
Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…
We study one specific version of the contact process on a graph. Here, we allow multiple infections carried by the nodes and include a probability of removing nodes in a graph. The removal probability is purely determined by the number of…
An infection spreads in a binary tree of height n as follows: initially, each leaf is either infected by one of k states or it is not infected at all. The infection state of each leaf is independently distributed according to a probability…
This paper, dating from May 1991, contains preliminary (and unpublishable) notes on investigations about iteration trees. They will be of interest only to the specialist. In the first two sections I define notions of support and embeddings…
Accessibility percolation is a new type of percolation problem inspired by evolutionary biology. To each vertex of a graph a random number is assigned and a path through the graph is called accessible if all numbers along the path are in…
We consider a spatial stochastic model for a pathogen population growing inside a host that attempts to eliminate the pathogens through its immune system. The pathogen population is divided into different types. A pathogen can either…