Related papers: Precise and scalable self-organization in mammalia…
In vitro primary cultures of dissociated invertebrate neurons from locust ganglia are used to experimentally investigate the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells…
Long ago, life obtained nucleotides in the course of evolution and became a vehicle for them. Before assembly with nucleotides, in the pre-RNA era, what system dominated heredity? What was the subject of survival competition? Is it still a…
Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available…
We study the behaviour of a natural measure defined on the leaves of the genealogical tree of some branching processes, namely self-similar growth-fragmentation processes. Each particle, or cell, is attributed a positive mass that evolves…
Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells.…
Growth-fragmentation processes model systems of cells that grow continuously over time and then fragment into smaller pieces. Typically, on average, the number of cells in the system exhibits asynchronous exponential growth and, upon…
The mechanism by which cells measure the dimension of the organ in which they are embedded, and slow down their growth when the final size is reached, is a long-standing problem of developmental biology. The role of mechanics in this…
Growth-fragmentation processes describe the evolution of systems of cells which grow continuously and fragment suddenly; they are used in models of cell division and protein polymerisation. Typically, we may expect that in the long run, the…
The mean size of exponentially dividing E. coli cells cultured in different nutrient conditions is known to depend on the mean growth rate only. However, the joint fluctuations relating cell size, doubling time and individual growth rate…
The emerging field of high-throughput compartmentalized in vitro evolution is a promising new approach to protein engineering. In these experiments, libraries of mutant genotypes are randomly distributed and expressed in microscopic…
Robustness to genetic or environmental disturbances is often considered as a key property of living systems. Yet, in spite of being discussed since the 1950s, how robustness emerges from the complexity of genetic architectures and how it…
We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…
Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates its own expression. The nonlinear coupling…
We study the genetic interfaces between two species of an expanding colony that consists of individual microorganisms that reproduce and undergo diffusion, both at the frontier and in the interior. Within the bulk of the colony, the genetic…
The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light of noise? To answer this question, we build a mathematical model to explore the trade-off…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Understanding cell fate patterning and morphogenesis in the mammalian embryo remains a formidable challenge. Recently, in vivo models based on embryonic stem cells (ESCs) have emerged as complementary methods to quantitatively dissect the…
We analyze the dynamical evolution of systems which obey simple growth laws, like diffusion limited aggregation or dielectric breakdown. We show that, if the developing patterns is sufficiently complex, a scale invariant noise spectrum is…
Self-organization, the ability of a system of microscopically interacting entities to shape macroscopically ordered structures, is ubiquitous in Nature. Spatio-temporal patterns are abundantly observed in a large plethora of applications,…
The aim of this paper is two-fold. First, we propose a new computational method to investigate the particularities of evolution. Second, we apply this method to a model of gene regulatory networks (GRNs) and explore the evolution of…