Related papers: A model for mutation in bacterial populations
A model for the evolution of a finite population in a rugged fitness landscape is introduced and solved. The population is trapped in an evolutionary loop, alternating periods of stasis to periods in which it performs adaptive walks. The…
Stochastic models of sequential mutation acquisition are widely used to quantify cancer and bacterial evolution. Across manifold scenarios, recurrent research questions are: how many cells are there with $n$ alterations, and how long will…
Evolution is the process of optimal adaptation of biological populations to their living environments. This is expressed via the concept of fitness, defined as relative reproductive success. However, it has been pointed out that this…
We develop a stochastic framework for viral population dynamics at the cellular level that explicitly incorporates the replication cycle with random stage durations. The model is formulated as a structured birth-death process coupled with a…
The Darwinian paradigm of biological evolution is based on the separability of the variation and selection processes. As a result, the population thinking had always been an integral part of the Darwinian approach. I propose an alternative…
We characterize the full spatiotemporal gait of populations of swimming {\it Escherichia coli} using renewal processes to analyze the measurements of intermediate scattering functions. This allows us to demonstrate quantitatively how the…
We introduce the standard distribution width of fitness to characterize the global and individual features of a ecosystem in the Bak-Sneppen evolution model. Through tracking this quantity in evolution, a different hierarchy of avalanche…
In this paper we analyze the equilibrium properties of a large class of stochastic processes describing the fundamental biological process within bacterial cells, {\em the production process of proteins}. Stochastic models classically used…
We study the growth of a population of bacteria in a dynamical hostile environment corresponding to the immune system of the colonised organism. The immune cells evolve as subcritical open clusters of oriented percolation and are…
In this paper we introduce and discuss kinetic equations for the evolution of the probability distribution of the number of particles in a population subject to binary interactions. The microscopic binary law of interaction is assumed to be…
Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this…
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…
We analyze a variant of the Noisy $K$-Branching Random Walk, a population model that evolves according to the following procedure. At each time step, each individual produces a large number of offspring that inherit the fitness of their…
We propose a purely probabilistic model to explain the evolution path of a population maximum fitness. We show that after $n$ births in the population there are about $\ln n$ upwards jumps. This is true for any mutation probability and any…
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…
We describe the simulation method of modelling the population evolution using Monte Carlo based on the Penna model. Individuals in the populations are represented by their diploid genomes. Genes expressed after the minimum reproduction age…
We propose a model of chemostat where the bacterial population is individually-based, each bacterium is explicitly represented and has a mass evolving continuously over time. The substrate concentration is represented as a conventional…
When our immune system encounters foreign antigens (i.e., from pathogens), the B cells that produce our antibodies undergo a cyclic process of proliferation, mutation, and selection, improving their ability to bind to the specific antigen.…
We consider populations evolving according to natural selection, mutation, and recombination, and assume that the genomes of all or a representative selection of individuals are known. We pose the problem if it is possible to infer fitness…
Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity of recombining segments, several studies examined whether this could lead to the…