Related papers: Semiconservative Replication in the Quasispecies M…
In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary…
Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Evolutionary dynamics in an uncorrelated rugged fitness landscape is studied in the framework of Eigen's molecular quasispecies model. We consider the case of strong selection, which is analogous to the zero temperature limit in the…
A quasispecies evolving on a fitness landscape with a single peak of fluctuating height is studied. In the approximation that back mutations can be ignored, the rate equations can be solved analytically. It is shown that the error threshold…
Life uses non-equilibrium mechanisms to create ordered structures not attainable at equilibrium; the resulting order is assumed to provide functional benefits that outweigh costs of time and energy needed by these mechanisms. Here, we show…
Gutzwiller's trace formula for the semiclassical density of states diverges at the bifurcation points of periodic orbits and has to be replaced with uniform semiclassical approximations. We present a method to derive these expressions from…
We consider the convexity properties of distortion functionals, particularly the linear distortion, defined for homeomorphisms of domains in Euclidean $n$-spaces, $n\geq 3$. The inner and outer distortion functionals are lower…
Consider a mathematical model of evolutionary adaptation of fitness landscape and mutation matrix as a reaction to population changes. As a basis, we use an open quasispecies model, which is modified to include explicit death flow. We…
Choosing the right selection rate is a long standing issue in evolutionary computation. In the continuous unconstrained case, we prove mathematically that a single parent $\mu=1$ leads to a sub-optimal simple regret in the case of the…
A fundamental property of DNA is that the reverse complement (RC) of a sequence often carries identical biological meaning. However, state-of-the-art DNA language models frequently fail to capture this symmetry, producing inconsistent…
In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A$, $\overline{A}=T$, $\overline{C}=G$, and $\overline{G}=C$. Given an integer $m\ge 2$, a secondary structure in a DNA sequence refers to the existence of two…
We express the Crow-Kimura and Eigen models of quasispecies theory in a functional integral representation. We formulate the spin coherent state functional integrals using the Schwinger Boson method. In this formulation, we are able to…
We introduce a family of averaged meta-Fibonacci recursions $$ Q_{\alpha,m}(n) = 1+ \left\lfloor \alpha \frac1m \sum_{j=1}^m Q_{\alpha,m}(n-Q_{\alpha,m}(n-j)) \right\rfloor , $$ with initial conditions $$…
The analysis of competing risks data is often complicated by misclassification of the cause of failure. This issue can lead to seriously biased estimates and invalid conclusions. One way to deal with such misclassification is to use a…
This paper extends and clarifies results of Steinsaltz and Evans [Trans. Amer. Math. Soc. 359 (2007) 1285-1234], which found conditions for convergence of a killed one-dimensional diffusion conditioned on survival, to a quasistationary…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
Unlike primates, training artificial neural networks on changing data distributions leads to a rapid decrease in performance on old tasks. This phenomenon is commonly referred to as catastrophic forgetting. In this paper, we investigate the…
Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic…
This work addresses the problem of (global) maximal regularity for quasilinear evolution equations with sublinear gradient growth and right-hand side in Lebesgue spaces, complemented with Neumann boundary conditions. The proof relies on a…