Related papers: Semiconservative Replication in the Quasispecies M…
An equation describing the evolution of phenotypic distribution is derived using methods developed in statistical physics. The equation is solved by using the singular perturbation method, and assuming that the number of bases in the…
Viruses present an amazing genetic variability. An ensemble of infecting viruses, also called a viral quasispecies, is a cloud of mutants centered around a specific genotype. The simplest model of evolution, whose equilibrium state is…
The quasi-species equation describes the evolution of the probability that a random individual in a population carries a given genome. Here we map the quasi-species equation for individuals of a self-reproducing population to an ensemble of…
Error estimates are rigorously derived for a semi-discrete version of a conservative spectral method for approximating the space-homogeneous Fokker-Planck-Landau (FPL) equation associated to hard potentials. The analysis included shows that…
In the theoretical biology framework one fundamental problem is the so-called error catastrophe in Darwinian evolution models. We reexamine Eigen's fundamental equations by mapping them into a polymer depinning transition problem in a…
In Soda'06, Chaudhuri, Chen, Mihaescu and Rao study algorithmic properties of the tandem duplication - random loss model of genome rearrangement, well-known in evolutionary biology. In their model, the cost of one step of duplication-loss…
Using an exactly solvable model of the Wigner-Weisskopf atom it is shown that an unstable quantum state cannot be recovered completely by the procedure involving detection of the decay products followed by creation of the time reversed…
We address the question as to why, in the semiclassical limit, classically chaotic systems generically exhibit universal quantum spectral statistics coincident with those of Random Matrix Theory. To do so, we use a semiclassical resummation…
In this work, we prove rigorous convergence properties for a semi-discrete, moment-based approximation of a model kinetic equation in one dimension. This approximation is equivalent to a standard spectral method in the velocity variable of…
Semiclassical approximation based on extracting a c-number classical component from quantum field is widely used in the quantum field theory. Semiclassical states are considered then as Gaussian wave packets in the functional Schrodinger…
We introduce a model of molecular evolution in which the fitness of an individual depends both on its own and on the parent's genotype. The model can be solved by means of a nonlinear mapping onto the standard quasispecies model. The…
A new estimation method for the two-component mixture model introduced in \cite{Van13} is proposed. This model consists of a two-component mixture of linear regressions in which one component is entirely known while the proportion, the…
We study Eigen's quasispecies model in the asymptotic regime where the length of the genotypes goes to infinity and the mutation probability goes to 0. A limiting infinite system of differential equations is obtained. We prove the…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
Detecting and counting copies of permutation patterns are fundamental algorithmic problems, with applications in the analysis of rankings, nonparametric statistics, and property testing tasks such as independence and quasirandomness…
A quasispecies is a set of interrelated genotypes that have reached a situation of equilibrium while evolving according to the usual Darwinian principles of selection and mutation. Quasispecies studies invariably assume that it is possible…
We review the major progress in the rigorous analysis of the classical quasispecies model that usually comes in two related but different forms: the Eigen model and the Crow--Kimura model. The model itself was formulated almost 50 years…
New insight into the correspondence between Quantum Chaos and Random Matrix Theory is gained by developing a semiclassical theory for the autocorrelation function of spectral determinants. We study in particular the unitary operators which…
We study codes that can correct backtracking errors during nanopore sequencing. In this channel, a sequence of length $n$ over an alphabet of size $q$ is being read by a sliding window of length $\ell$, where from each window we obtain only…
The semiclassical trace formula provides the basic construction from which one derives the semiclassical approximation for the spectrum of quantum systems which are chaotic in the classical limit. When the dimensionality of the system…