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Microbial populations adapt to their environment by acquiring advantageous mutations, but in the early twentieth century, questions about how these organisms acquire mutations arose. The experiment of Salvador Luria and Max Delbr\"uck that…
We study a model for the spread of an infectious disease which incorporates spatial and temporal effects. The model is a delayed multi-type branching process in which types represent geographic regions while infected individuals reproduce…
We study a continuous-time nearest-neighbor branching random walk on the $d$-dimensional $b$-ary hypercube $\{0,1,\dots,b-1\}^d$ as a model for viral quasispecies evolution under mutation and replication. Motivated by mutagenic antiviral…
Motivated as a null model for comparison with data, we study the following model for a phylogenetic tree on $n$ extant species. The origin of the clade is a random time in the past, whose (improper) distribution is uniform on $(0,\infty)$.…
Eigen's quasi-species model describes viruses as ensembles of different mutants of a high fitness "master" genotype. Mutants are assumed to have lower fitness than the master type, yet they coexist with it forming the quasi-species. When…
In this paper we consider a model based on branching process theory for the proliferation and the dissemination network of T cells in the adaptive immune response. A multi-type Galton Watson branching process is assumed as the basic…
We propose a physical theory underlying the temporal evolution of competing virus variants that relies on the existence of (quasi) fixed points capturing the large time scale invariance of the dynamics. To motivate our result we first…
The homogeneous reconstructed evolutionary process is a birth-death process without observed extinct lineages. Each species evolves independently with the same diversification rates (speciation rate $\lambda(t)$ and extinction rate…
We consider a branching random walk in a random space-time environment of disasters where each particle is killed when meeting a disaster. This extends the model of the "random walk in a disastrous random environment" introduced by [15]. We…
For supercritical multitype branching processes in continuous time, we investigate the evolution of types along those lineages that survive up to some time t. We establish almost-sure convergence theorems for both time and population…
In 2022, a group of basic and clinical virologists, bioinformaticians, and evolutionary and structural biologists met in Oxford, UK, to develop a consensus on methodologies used to classify viruses. They concluded that virus taxonomy, which…
We study solutions to the evolution equation $u_t=\Delta u-u +\sum_{k\geqslant 1}q_ku^k$, $t>0$, in $\mathbf{R}^d$. Here the coefficients $q_k\geqslant 0$ verify $ \sum_{k\geqslant 1}q_k=1< \sum_{k\geqslant 1}kq_k<\infty$. First, we deal…
Predicting the viral dynamics of an epidemic process requires the knowledge of the underlying contact network. However, the network is not known for most applications and has to be inferred from observing the viral state evolution instead.…
This paper explores a number of questions regarding optimal strategies evolved by viruses upon entry into a vertebrate host. The infected cell life cycle consists of a non-productively infected stage in which it is producing virions but not…
We discuss the evaluation of Luria-Delbrueck fluctuation experiments under Bellman-Harris models of cell proliferation. It is shown that under certain very natural assumptions concerning the life-time distributions and the offspring…
The Luria-Delbr{\"u}ck experiment is a cornerstone of evolutionary theory, demonstrating the randomness of mutations before selection. The distribution of the number of mutants in this experiment has been the subject of intense…
We explore the role of cellular life cycles for viruses and host cells in an infection process. For this purpose, we derive a generalized version of the basic model of virus dynamics (Nowak, M.A., Bangham, C.R.M., 1996. Population dynamics…
A previously established multiscale population genetics model states that fitness can be inferred from the physical properties of proteins under the physiological assumption that a loss of stability by any protein confers the lethal…
The Luria-Delbr\"uck distribution is a classical model of mutations in cell kinetics. It is obtained as a limit when the probability of mutation tends to zero and the number of divisions to infinity. It can be interpreted as a compound…
An explicit solution for a general two-type birth-death branching process with one way mutation is presented. This continuous time process mimics the evolution of resistance to treatment, or the onset of an extra driver mutation during…