Related papers: Periodic correlation structures in bacterial and a…
For more than 150 years the structure of the periodic system of the chemical elements has intensively motivated research in different areas of chemistry and physics. However, there is still no unified picture of what a periodic system is.…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…
Understanding the function of network motifs in an attempt to gain insight into how their combinations create larger reaction networks that drive cellular functions, has been a longstanding pursuit of systems biology. One specific objective…
The spectral theory of quantum graphs is related via an exact trace formula with the spectrum of the lengths of periodic orbits (cycles) on the graphs. The latter is a degenerate spectrum, and understanding its structure (i.e.,finding out…
A new numerical characterization of symbolic sequences is proposed. The partition of sequence based on Ke and Tong algorithm is a starting point. Algorithm decomposes original sequence into set of distinct subsequences - a patterns. The set…
Higher order interactions are increasingly recognised as a fundamental aspect of complex systems ranging from the brain to social contact networks. Hypergraph as well as simplicial complexes capture the higher-order interactions of complex…
Using transfer matrices up to next-nearest-neighbour (NNN) interactions, we examine the structural correlations of quasi-one-dimensional systems of hard disks confined by two parallel lines and hard spheres confined in cylinders.…
Chirality transfer from the level of molecular structure up to mesoscopic lengthscales of supramolecular morphologies is a broad and persistent theme in self-assembled soft materials, from biological to synthetic matter. Here, we analyze…
We compare two recently proposed methods for the characterization of phase transitions in small systems. The usefulness of these techniques is evaluated for the case of structural transition in alanine-based peptides.
We review data analysis techniques that can be used to study temporal correlations among conductance traces in break junction measurements. We show that temporal histograms are a simple but efficient tool to check the temporal homogeneity…
The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features of nucleotide sequences in the vicinity of promoters for the genes with expression…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
Statistical analysis of distributions of occurrence frequencies of short words in 108 microbial complete genomes reveals the existence of a set of universal "root-sequence lengths" shared by all microbial genomes. These lengths and their…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
Virtually all the emergent properties of a complex system are rooted in the non-homogeneous nature of the behaviours of its elements and of the interactions among them. However, the fact that heterogeneity and correlations can appear…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
This paper is about the tiling dynamical systems approach to the study of aperiodic order. We compare and contrast four related types of systems: ordinary (one-dimensional) symbolic systems, one-dimensional tiling systems, multidimensional…
We predict analytically that diagonal correlations of amino acid positions within protein sequences statistically enhance protein propensity for nonspecific binding. We use the term 'promiscuity' to describe such nonspecific binding.…
We employ a typical genetic circuit model to explore how noise can influence the dynamic structure. With the increase of a key interactive parameter, the model will deterministically go through two bifurcations and three dynamic structure…
We study aperiodic systems based on substitution rules by means of a transfer-matrix approach. In addition to the well-known trace map, we investigate the so-called `antitrace' map, which is the corresponding map for the difference of the…