Related papers: Interaction between directional epistasis and aver…
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…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
We consider a stochastic model of population dynamics where each individual is characterised by a trait in {0,1,...,L} and has a natural reproduction rate, a logistic death rate due to age or competition and a probability of mutation…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
This piece serves two purposes. Firstly, it aims at elucidating the role of epistasis in shaping, at a molecular level, the evolutionary paths of proteins, as well as the extent to which these epistatic effects are the outcome of an…
Evolutionary branching is analysed in a stochastic, individual-based population model under mutation and selection. In such models, the common assumption is that individual reproduction and life career are characterised by values of a…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
We are interested in modeling some two-level population dynamics, resulting from the interplay of ecological interactions and phenotypic variation of individuals (or hosts) and the evolution of cells (or parasites) of two types living in…
Ecosystems are formed by networks of species and their interactions. Traditional models of such interactions assume a constant interaction strength between a given pair of species. However, there is often significant trait variation among…
Human pathogens transmitted through environmental pathways are subject to stress and pressures outside of the host. These pressures may cause pathogen pathovars to diverge in their environmental persistence and their infectivity on an…
Seasonal variation in environmental variables, and in rates of contact among individuals, are fundamental drivers of infectious disease dynamics. Unlike most periodically-forced physical systems, for which the precise pattern of forcing is…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
This paper develops a mathematical model describing the influence that conjugation-mediated Horizontal Gene Transfer (HGT) has on the mutation-selection balance in an asexually reproducing population of unicellular, prokaryotic organisms.…
Understanding the spread of diseases through complex networks is of great interest where realistic, heterogeneous contact patterns play a crucial role in the spread. Most works have focused on mean-field behavior -- quantifying how contact…
Here we study how mutations which change physical properties of cell proteins (stability) impact population survival and growth. In our model the genotype is presented as a set of N numbers, folding free energies of cells N proteins.…
Electronic properties of DNA are believed to play a crucial role in many phenomena in living organisms, for example the location of DNA lesions by base excision repair (BER) glycosylases and the regulation of tumor-suppressor genes such as…
Potts statistical models have become a popular and promising way to analyze mutational covariation in protein Multiple Sequence Alignments (MSAs) in order to understand protein structure, function and fitness. But the statistical…
We find an advantage of recombination for a category of complex fitness landscapes. Recent studies of empirical fitness landscapes reveal complex gene interactions and multiple peaks, and recombination can be a powerful mechanism for…
We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by…
Evolution occurs in populations of reproducing individuals. It is well known that population structure can affect evolutionary dynamics. Traditionally, natural selection is studied between mutants that differ in reproductive rate, but are…