Related papers: Optimality of mutation and selection in germinal c…
We consider a model of a population of fixed size $N$ undergoing selection. Each individual acquires beneficial mutations at rate $\mu_N$, and each beneficial mutation increases the individual's fitness by $s_N$. Each individual dies at…
Maintaining genetic diversity as a means to avoid premature convergence is critical in Genetic Programming. Several approaches have been proposed to achieve this, with some focusing on the mating phase from coupling dissimilar solutions to…
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such…
When beneficial mutations are relatively common, competition between multiple unfixed mutations can reduce the rate of fixation in well-mixed asexual populations. We introduce a one dimensional model with a steady accumulation of beneficial…
Investigating the emergence of a particular cell type is a recurring theme in models of growing cellular populations. The evolution of resistance to therapy is a classic example. Common questions are: when does the cell type first occur,…
In evolutionary optimization, it is important to understand how fast evolutionary algorithms converge to the optimum per generation, or their convergence rate. This paper proposes a new measure of the convergence rate, called average…
The adaptive evolution of large asexual populations is generally characterized by competition between clones carrying different beneficial mutations. This interference phenomenon slows down the adaptation speed and makes the theoretical…
How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a…
Continuous cultures of mammalian cells are complex systems displaying hallmark phenomena of nonlinear dynamics, such as multi-stability, hysteresis, as well as sharp transitions between different metabolic states. In this context…
Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…
B cells receptor (BCR) signaling in response to membrane-bound antigen increases with antigen affinity, a process known as affinity discrimination. We use computational modeling to show that B cell affinity discrimination requires that…
Biological populations are subject to fluctuating environmental conditions. Different adaptive strategies can allow them to cope with these fluctuations: specialization to one particular environmental condition, adoption of a generalist…
In proliferating cell populations, adaptive changes to biochemical reactions can change a cell's division time, which in turn can change the population size. However, biochemical reactions are subject to noise, and therefore the conditions…
Infinite population models are important tools for studying population dynamics of evolutionary algorithms. They describe how the distributions of populations change between consecutive generations. In general, infinite population models…
Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary structure, have become computationally tractable,…
We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…
This paper is concerned with the evolution of haploid organisms that reproduce asexually. In a seminal piece of work, Eigen and coauthors proposed the quasispecies model in an attempt to understand such an evolutionary process. Their work…
B cells signaling in response to antigen is proportional to antigen affinity, a process known as affinity discrimination. Recent research suggests that B cells can acquire antigen in membrane-bound form on the surface of antigen-presenting…
The outcomes of evolution are determined by which mutations occur and fix. In rapidly adapting microbial populations, this process is particularly hard to predict because lineages with different beneficial mutations often spread…
Any process in which competing solutions replicate with errors and numbers of their copies depend on their respective fitnesses is the evolutionary optimization process. As during carcinogenesis mutated genomes replicate according to their…