Related papers: Quantifying Local Randomness in Human DNA and RNA …
Consider the subgraph of the discrete $d$-dimensional torus of size length $N$, $d\ge3$, induced by the range of the simple random walk on the torus run until the time $uN^d$. We prove that for all $d\ge 3$ and $u>0$, the mixing time for…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
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…
We consider random walks that start and are absorbed on the leaves of random networks and study the length of such walks. For the networks we investigate, Erdos-Renyi random graphs and Barabasi-Albert scale free networks, these walks are…
We investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously derived cost function and the error minimization percentage…
In physics, biology and engineering, network systems abound. How does the connectivity of a network system combine with the behavior of its individual components to determine its collective function? We approach this question for networks…
In this article, we first give a comprehensive description of random walk (RW) problem focusing on self-similarity, dynamic scaling and its connection to diffusion phenomena. One of the main goals of our work is to check how robust the RW…
Sood and Grassberger studied in [Phys. Rev. Lett. 99, 098701 (2007)] random walks on random graphs that are biased towards a fixed target point. They put forward a critical bias strength b_c such that a random walker on an infinite graph…
Simple heuristics often show a remarkable performance in practice for optimization problems. Worst-case analysis often falls short of explaining this performance. Because of this, "beyond worst-case analysis" of algorithms has recently…
We study the evolution of a random walker on a conservative dynamic random environment composed of independent particles performing simple symmetric random walks, generalizing results of [16] to higher dimensions and more general transition…
Motivated by average-case trace reconstruction and coding for portable DNA-based storage systems, we initiate the study of \emph{coded trace reconstruction}, the design and analysis of high-rate efficiently encodable codes that can be…
Replication of genetic material is an important process for all living organisms. Origins of replication initiate the copying of DNA at many points on a chromosome, and it is the distribution of these points that is relevant here, as it…
Record numbers are basic statistics in random walks, whose deviation principles are not very clear so far. In this paper, the asymptotic probabilities of large and moderate deviations for numbers of weak records in right continuous or left…
A simple strategy to explore a network is to use a random-walk where the walker jumps from one node to an adjacent node at random. It is known that biasing the random jump, the walker can explore every walk of the same length with equal…
Random walks are a series of up, down, and level steps that enumerate distinct paths from $(0,0)$ to $(2n,0)$, where $n$ is the semi-length of the path. We used these paths to analyze Catalan, Schr\"{o}der, and Motzkin number sequences…
We show the existence of regular combinatorial objects which previously were not known to exist. Specifically, for a wide range of the underlying parameters, we show the existence of non-trivial orthogonal arrays, t-designs, and t-wise…
Motivated by storage applications, we study the following data structure problem: An encoder wishes to store a collection of jointly-distributed files $\overline{X}:=(X_1,X_2,\ldots, X_n) \sim \mu$ which are \emph{correlated}…
We model long range correlations of nucleotides in the human DNA sequence using the long range one dimensional Ising model. We show that for distances between $10^3$ and $10^6$ bp the correlations show an universal behaviour and may be…
It is known that Tardos's collusion-secure probabilistic fingerprinting code (Tardos code; STOC'03) has length of theoretically minimal order with respect to the number of colluding users. However, Tardos code uses certain continuous…
We consider a sparse Erd\H{o}s--R\'{e}nyi graph $\mathcal{G}(n,\lambda/n)$ where each edge is independently assigned a random signed weight. For two uniformly chosen vertices, we study the joint distribution of the total weights and…