相关论文: Bacterial evolution and the Bak-Sneppen model
We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations. The simplicity of the…
A variational lattice model is proposed to define an evolution of sets from a single point (nucleation) following a criterion of "maximization" of the perimeter. At a discrete level, the evolution has a "checkerboard" structure and its…
In this article, we analyze a system modeling bacteriophage treatments for infections in a noisy context. In the small noise regime, we show that after a reasonable amount of time the system is close to a sane equilibrium (which is a…
We present a model for the dynamics of a population of bacteria with a continuum of traits, who compete for resources and exchange horizontally (transfer) an otherwise vertically inherited trait with possible mutations. Competition…
Bacterial populations in natural conditions are expected to experience stochastic environmental fluctuations, and in addition, environments are affected by bacterial activities since they consume substrates and excrete various chemicals. We…
We investigate a model of evolving random network, introduced by us previously {[}{\it Phys. Rev. Lett.} {\bf 83}, 5587 (1999){]} . The model is a generalization of the Bak-Sneppen model of biological evolution, with the modification that…
The purpose of this note is to provide proofs for some facts about the NK model of evolution proposed by Kauffman and Levin. In the case of normally distributed fitness summands, some of these facts have been previously conjectured and…
The Red Queen Hypothesis, which suggests that continual evolution can result from solely biotic interactions, has been studied in macroevolutionary and microevolutionary contexts. While the latter has been effective in describing examples…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
We introduce a set-valued solution concept, M equilibrium, to capture empirical regularities from over half a century of game-theory experiments. We show M equilibrium serves as a meta theory for various models that hitherto were considered…
We show, that the specific distribution of gene's length, which is observed in natural genomes, might be a result of a growth process, in which a single length scale $L(t)$ develops that grows with time as $t^{1/3}$. This length scale could…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
This brief discusses evolutionary game theory as a powerful and unified mathematical tool to study evolution of collective behaviours. It summarises some of my recent research directions using evolutionary game theory methods, which include…
With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
The spread of an epidemic disease and the population's collective behavioural response are deeply intertwined, influencing each other's evolution. Such a co-evolution typically has been overlooked in mathematical models, limiting their…
Due to the conventional distinction between ecological (rapid) and evolutionary (slow)timescales, ecological and population models to date have typically ignored the effects of evolution. Yet the potential for rapid evolutionary change has…
Technical analysis (TA) has been used for a long time before the availability of more sophisticated instruments for financial forecasting in order to suggest decisions on the basis of the occurrence of data patterns. Many mathematical and…
Randomly moving active particles can be herded into directed motion by asymmetric geometric structures. Although such a rectification process has been extensively studied due to its fundamental, biological, and technological relevance, a…
The study of transcription remains one of the centerpieces of modern biology with implications in settings from development to metabolism to evolution to disease. Precision measurements using a host of different techniques including…