Related papers: Conspiracy in bacterial genomes
The presence of slipknots in configurations of proteins and DNA has been shown to affect their functionality, or alter it entirely. Historically, polymers are modeled as polygonal chains in space. As an alternative to space curves, we…
We investigate cascades in networks consisting of strategic agents with interdependent security. We assume that the strategic agents have choices between i) investing in protecting themselves, ii) purchasing insurance to transfer (some)…
A new family of compound Poisson distribution functions from statistical linguistic is used to study the n-tuples and nucleotide composition features of DNA sequences. The relative frequency distribution of the 6-tuples and 7- tuples…
Counts in cells are used to analyse the higher order properties of the statistics of the EDSGC survey. The probability distribution is obtained from an equal area projection source catalog with infinite oversampling over the range…
In modeling DNA chains, the number of alternations between Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs can be considered as a measure of the heterogeneity of the chain, which in turn could affect its dynamics. A probability…
The unconstrained genomic DNA of bacteria forms a coil, which volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to…
As an application of generalised statistical mechanics, it is studied a possible route toward a consistent generalised information theory in terms of a family of non-extensive, non-parametric entropies $H^\pm_D(P)$. Unlike other proposals…
Percolation theory can be used to describe the structural properties of complex networks using the generating function formulation. This mapping assumes that the network is locally tree-like and does not contain short-range loops between…
In this article we consider the cycle structure of compositions of pairs of involutions in the symmetric group S_n chosen uniformly at random. These can be modeled as modified 2-regular graphs, giving rise to exponential generating…
Contagion processes are strongly linked to the network structures on which they propagate, and learning these structures is essential for understanding and intervention on complex network processes such as epidemics and (mis)information…
There is a rich history of models for the interaction of a biological contagion like influenza with the spread of related information such as an influenza vaccination campaign. Recent work on the spread of interacting contagions on networks…
Shannon entropy is widely used to quantify the uncertainty of discrete random variables. But when normalized to the unit interval, as is often done in practice, it no longer conveys the alphabet sizes of the random variables being studied.…
We calculate and analyze various entropy measures and their properties for selected probability distributions. The entropies considered include Shannon, R\'enyi, generalized R\'enyi, Tsallis, Sharma-Mittal, and modified Shannon entropy,…
The scattering amplitude in simple quantum graphs is a well-known process which may be highly complex. In this work, motivated by the Shannon entropy, we propose a methodology that associates to a graph a scattering entropy, which we call…
Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…
Accurately determining dependency structure is critical to discovering a system's causal organization. We recently showed that the transfer entropy fails in a key aspect of this---measuring information flow---due to its conflation of dyadic…
We study how the Shannon entropy of sequences produced by an information source converges to the source's entropy rate. We synthesize several phenomenological approaches to applying information theoretic measures of randomness and memory to…
The average redundancy of the Shannon code, $R_n$, as a function of the block length $n$, is known to exhibit two very different types of behavior, depending on the rationality or irrationality of certain parameters of the source: It either…
The identification of motifs--subgraphs that appear significantly more often in a particular network than in an ensemble of randomized networks--has become a ubiquitous method for uncovering potentially important subunits within networks…
The uneven distribution of digits in numerical data, known as Benford's law, was discovered in 1881. Since then, this law has been shown to be correct in copious numerical data relating to economics, physics and even prime numbers. Although…