相关论文: Bacterial evolution and the Bak-Sneppen model

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…

The idea of this review is to connect the different models of evolution to those of biological ageing through Darwin's theory. We start with the Eigen model of quasispecies for microevolution, then introduce the Bak-Sneppen model for…

Antibiotic resistance is a growing public health problem. To gain a fundamental understanding of resistance evolution, a combination of systematic experimental and theoretical approaches is required. Evolution experiments combined with…

We present a statistical model of bacterial evolution based on the coupling between codon usage and tRNA abundance. Such a model interprets this aspect of the evolutionary process as a balance between the codon homogenization effect due to…

We study the dynamics of the Bak-Sneppen model on small-world networks. For each site in the network, we define a ``connectance,'' which measures the distance to all other sites. We find radically different patterns of activity for…

Cooperation and self-organized criticality are two main keywords in current studies of evolution. We propose a generalized Bak-Sneppen model and provide a natural mechanism which accounts for both phenomena simultaneously. We use the…

We study here the Bak and Sneppen model, a prototype model for the study of Self-Organized Criticality. In this model several species interact and undergo extinction with a power law distribution of activity bursts. Species are defined…

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…

Levy flights in the space of mutations model time evolution of bacterial DNA. Parameters in the model are adjusted in order to fit observations coming from the Long Time Evolution Experiment with E. Coli.

The dynamics of complex systems in nature often occurs in terms of punctuations, or avalanches, rather than following a smooth, gradual path. A comprehensive theory of avalanche dynamics in models of growth, interface depinning, and…

The Bak-Sneppen model displaying punctuated equilibria in biological evolution is studied on random complex networks. By using the rate equation and the random walk approaches, we obtain the analytic solution of the fitness threshold $x_c$…

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…

The Bak Sneppen (BS) model is a very simple model that exhibits all the richness of self-organized criticality theory. At the thermodynamic limit, the BS model converges to a situation where all particles have a fitness that is uniformly…

Levy-Loewner evolution (LLE) is a generalization of the Schramm-Loewner evolution (SLE) where the branching is possible in a course of growth process. We consider a class of radial Levy-Loewner evolutions for which sets of points of the…

One of the key problems related to the Bak-Sneppen evolution model on the circle is to compute the limit distribution of the fitness at a fixed observation vertex in the stationary regime, as the size of the system tends to infinity.…

Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…

The Lenski experiment investigates the long-term evolution of bacterial populations. Its design allows the direct comparison of the reproductive fitness of an evolved strain with its founder ancestor. It was observed by Wiser et al. (2013)…

Temporal evolution of a clonal bacterial population is modelled taking into account reversible mutation and selection mechanisms. For the mutation model, an efficient algorithm is proposed to verify whether experimental data can be…

Various bacterial strains exhibit colonial branching patterns during growth on poor substrates. These patterns reflect bacterial cooperative self-organization and cybernetic processes of communication, regulation and control employed during…

This article gives a brief introduction to the mathematical modeling of large-scale biological evolution and extinction. We give three examples of simple models in this field: the coevolutionary avalanche model of Bak and Sneppen, the…