Related papers: Periodic correlation structures in bacterial and a…
Transfer of nucleotide strings in the Synechocystis sp. PCC6803 genome is investigated to exhibit periodic and non-periodic correlation structures by using the recurrence plot method and the phase space reconstruction technique. The…
This paper considers three kinds of length sequences of the complete genome. Detrended fluctuation analysis, spectral analysis, and the mean distance spanned within time $L$ are used to discuss the correlation property of these sequences.…
The richness of many complex systems stems from the interactions among their components. The higher-order nature of these interactions, involving many units at once, and their temporal dynamics constitute crucial properties that shape the…
Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive…
A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
We characterize the structure of the periods of a neuronal recurrence equation. Firstly, we give a characterization of k-chains in 0-1 periodic sequences. Secondly, we characterize the periods of all cycles of some neuronal recurrence…
We study a periodic vibrating string composed of a finite sequence of string segments connected periodically, with each segment characterized by a constant linear mass density. The main purpose is to provide a configuration that can mimic…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
Global transposable characteristics in the complete DNA sequence of the Saccharomyces cevevisiae yeast is determined by using the metric representation and recurrence plot methods. In the form of the correlation distance of nucleotide…
The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure.…
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…
In a series of two papers, we investigate the mechanisms by which complex oscillations are generated in a class of nonlinear dynamical systems with resets modeling the voltage and adaptation of neurons. This first paper presents…
A time series model based on the global structure of the complete genome is proposed. Three kinds of length sequences of the complete genome are considered. The correlation dimensions and Hurst exponents of the length sequences are…
In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial…
We study the resonant tunneling properties of an electron through a few types of binary periodic and aperiodic multibarrier systems. Within the framework of the effective-mass approximation, we calculate the transmission coefficients to…
Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…
The mean length and the variability of coding sequences for 48 genomes of bacteria and archaea were analyzed. It was found that the plotted data can be described by an angular area. This suggests the followings: a) The variability of a…
This work represents an in-depth study of the structural behavior of the Collatz sequences. We consider a finite arithmetic progression with a common difference is 2 and the number of terms in the sequence is equal to 2^n . After, we…
We introduce an evolving network model in which a new node attaches to a randomly selected target node and also to each of its neighbors with probability $p$. The resulting network is sparse for $p<\frac{1}{2}$ and dense (average degree…