Related papers: Bifurcation in cellular evolution
We explain how hierarchical organization of biological systems emerges naturally during evolution, through a transition in the units of individuality. We will show how these transitions are the result of competing selective forces operating…
The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…
We analyze evolutionary dynamics in a confluent, branching cellular population, such as in a growing duct, vasculature, or in a branching microbial colony. We focus on the coarse-grained features of the evolution and build a statistical…
Directed and heterogeneous hypergraphs capture directional higher-order interactions with intrinsically asymmetric functional dependencies among nodes. As a result, damage to certain nodes can suppress entire hyperedges, whereas failure of…
From transportation networks to complex infrastructures, and to social and communication networks, a large variety of systems can be described in terms of multiplexes formed by a set of nodes interacting through different networks (layers).…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which…
Percolation is perhaps the simplest example of a process exhibiting a phase transition and one of the most studied phenomena in statistical physics. The percolation transition is continuous if sites/bonds are occupied independently with the…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that 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…
We discuss the transition paths in a coupled bistable system consisting of interacting multiple identical bistable motifs. We propose a simple model of coupled bistable gene circuits as an example, and show that its transition paths are…
We present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…
The representation of a biochemical network as a graph is the coarsest level of description in cellular biochemistry. By studying the network structure one can draw conclusions on the large scale organisation of the biochemical processes.…
Transition out of a topological phase is typically characterized by discontinuous changes in topological invariants along with bulk gap closings. However, as a clean system is geometrically punctured, it is natural to ask the fate of an…
Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting…
This article is addressing a recurrent problem in biology: mining newly built large scale networks. Our approach consists in comparing these new networks to well known ones. The visual backbone of this comparative analysis is provided by a…
Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
A large number of studies have shown the existence of metabolic covalent modifications in different molecular structures, able to store biochemical information that is not encoded by the DNA. Some of these covalent mark patterns can be…