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We suggest an enhancement to structural coding through the use of (a) causally bound codes, (b) basic constructs of graph theory and (c) statistics. As is the norm with structural coding, the codes are collected into categories. The…
The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6…
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…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
The distribution of bases spacing in human genome was investigated. An analysis of the frequency of occurrence in the human genome of different sequence lengths flanked by one type of nucleotide was carried out showing that the distribution…
A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers…
Recurrence is a fundamental property of dynamical systems, which can be exploited to characterise the system's behaviour in phase space. A powerful tool for their visualisation and analysis called recurrence plot was introduced in the late…
Trophic coherence, a measure of the extent to which the nodes of a directed network are organised in levels, has recently been shown to be closely related to many structural and dynamical aspects of complex systems, including graph…
The genetic code is considered to be universal. In order to test if some statistical properties of the coding bacterial genome were due to inherent properties of the genetic code, we compared the autocorrelation function, the scaling…
The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…
Understanding chirality transfer from the molecular to the macroscopic scale poses a significant challenge in soft and biological condensed matter physics. Many nanorods of biological origin not only have chiral molecular features but also…
Hybrid percolation transitions (HPTs) induced by cascading processes have been observed in diverse complex systems such as $k$-core percolation, breakdown on interdependent networks and cooperative epidemic spreading models. Much effort has…
Nonlinear complexity, as an important measure for assessing the randomness of sequences, is defined as the length of the shortest feedback shift registers that can generate a given sequence. In this paper, the structure of n-periodic binary…
By introducing the notions of living and dead nodes a new model of random tree evolution with continuous time parameter has been constructed. It is assumed that two random variables, the lifetime and the offspring number of living nodes…
In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…
Living cells communicate information about physiological conditions by producing signaling molecules in a specific timed manner. Different conditions can result in the same total amount of a signaling molecule, differing only in the pattern…
Datasets from several domains, such as life-sciences, semantic web, machine learning, natural language processing, etc. are naturally structured as acyclic graphs. These datasets, particularly those in bio-informatics and computational…
Periodic forcing of nonlinear oscillators leads to a large number of dynamic behaviors. The coupling of the cell-cycle to the circadian clock provides a biological realization of such forcing. Using high throughput single-cell microscopy,…
A theoretical investigation is made of acoustic wave propagation in a periodically stubbed waveguide. In general the waveguide segments and stubs are made of different materials. The acoustic wave in such a system has two independent…
The article is devoted to a matrix method of comparative analysis of long nucleotide sequences by means of a presentation of each sequence in a form of three digital binary sequences. This method uses biochemical attributes of nucleotides…