相关论文: Information-theoretic View of Sequence Organizatio…
We study the $k$-core of a random (multi)graph on $n$ vertices with a given degree sequence. In our previous paper [Random Structures Algorithms 30 (2007) 50--62] we used properties of empirical distributions of independent random variables…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic…
We extend a formal framework that previously derived time from the multifractal structure of biological lineages (Hudnall \& D'Souza, 2025). That work showed that time itself is multifractal -- not a universal background dimension, but an…
We consider the transmission of a state from the root of a tree towards its leaves, assuming that each transmission occurs through a noisy channel. The states at the leaves are observed, while at deeper nodes we can compute the likelihood…
Using aggregated journal-journal citation networks, the measurement of the knowledge base in empirical systems is factor-analyzed in two cases of interdisciplinary developments during the period 1995-2005: (i) the development of…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
A pattern of a sequence is a sequence of integer indices with each index describing the order of first occurrence of the respective symbol in the original sequence. In a recent paper, tight general bounds on the block entropy of patterns of…
We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate…
The spectral form factor of random matrix theory plays a key role in the description of disordered and chaotic quantum systems. While its moments are known to be approximately Gaussian, corrections subleading in the matrix dimension, $D$,…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
Correlation measure of order $k$ is an important measure of randomness in binary sequences. This measure tries to look for dependence between several shifted version of a sequence. We study the relation between the correlation measure of…
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
The information spectrum approach gives general formulae for optimal rates of codes in many areas of information theory. In this paper the quantum spectral divergence rates are defined and properties of the rates are derived. The entropic…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…
How condensed-matter simulations depend on the number of molecules being simulated ($N$) is sometimes itself a valuable piece of information. Liquid crystals provide a case in point. Light scattering and $2d$-IR experiments on…
Fluctuations and noise may alter the behavior of dynamical systems considerably. For example, oscillations may be sustained by demographic fluctuations in biological systems where a stable fixed point is found in the absence of noise. We…
Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed…
The $k$-core percolation is a fundamental structural transition in complex networks. Through the analysis of the size jump behaviors of $k$-core in the evolution process of networks, we confirm that $k$-core percolation is continuous phase…
Degree distribution, or equivalently called degree sequence, has been commonly used to be one of most significant measures for studying a large number of complex networks with which some well-known results have been obtained. By contrast,…