Related papers: Entropy concepts and DNA investigations
The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry,…
A numerical code is described for constructing Doppler maps from the orbital variation of line profiles of (mass transfering) binaries. It uses an algorithm related to Richardson-Lucy iteration, and is much faster than the standard…
The topological entropy dimension is mainly used to distinguish the zero topological entropy systems. Two types of topological entropy dimensions, the classical entropy dimension and the Pesin entropy dimension, are investigated for…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
The human brain is the substrate for human intelligence. By simulating the human brain, artificial intelligence builds computational models that have learning capabilities and perform intelligent tasks approaching the human level. Deep…
New entropy measures have been recently introduced for the quantification of the complexity of networks. Most of these entropy measures apply to static networks or to dynamical processes defined on static complex networks. In this paper we…
DNA labeling is a powerful tool in molecular biology and biotechnology that allows for the visualization, detection, and study of DNA at the molecular level. Under this paradigm, a DNA molecule is being labeled by specific k patterns and is…
The recently discovered correspondence between the distribution of rapidity gaps in electron-nucleus diffractive processes and the statistics of the height of genealogical trees in branching random walks is reviewed. In addition, a new…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth…
Many complex systems can be described in terms of networks of interacting units. Recent studies have shown that a wide class of both natural and artificial nets display a surprisingly widespread feature: the presence of highly heterogeneous…
The importance of structured, complex connectivity patterns found in several real-world systems is to a great extent related to their respective effects in constraining and even defining the respective dynamics. Yet, while complex networks…
Correlation length exponent $\nu$ for long linear DNA molecules was determined by direct measurement of the average end-to-end distance as a function of the contour length $s$ by means of atomic force microscopy (AFM). Linear DNA, up to…
The topological structure of complex networks has fascinated researchers for several decades, resulting in the discovery of many universal properties and reoccurring characteristics of different kinds of networks. However, much less is…
The topological structure of complex networks has fascinated researchers for several decades, resulting in the discovery of many universal properties and reoccurring characteristics of different kinds of networks. However, much less is…
Any physical system can be viewed from the perspective that information is implicitly represented in its state. However, the quantification of this information when it comes to complex networks has remained largely elusive. In this work, we…
Many networks are characterized by highly heterogeneous distributions of links, which are called scale-free networks and the degree distributions follow $p(k)\sim ck^{-\alpha}$. We study the robustness of scale-free networks to random…
We study the amount of reliable information that can be stored in a DNA-based storage system composed of short DNA molecules. In this regime, Shomorony and Heckel (2022) put forward a conjecture on the scaling of the number of information…