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Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Coherent dynamics of coupled molecules are effectively characterized by the two-dimensional (2D) electronic coherent spectroscopy. Depending on the coupling between electronic and vibrational states, oscillating signals of purely…
Standard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting…
Identifying and characterizing mutational paths is an important issue in evolutionary biology and in bioengineering. We here introduce a generic description of mutational paths in terms of the goodness of sequences and of the mutational…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we…
We discuss a few aspects of the phase diagram of two color lattice QCD: we investigate the long distance screening analyzing the behavior of the interquark potential at large distances; we present a first set of results for vector mesons…
A sequence is a fractal sequence if it contains itself as a proper subsequence. (The self-containment property resembles that of visual fractals) A doubly fractal sequence of integers is defined by operations called upper trimming and lower…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
A simple model of 1D structure based on a Fibonacci sequence with variable atomic spacings is proposed. The model allows for observation of the continuous transition between periodic and non-periodic diffraction patterns. The diffraction…
Fractals define a new and interesting realm for a discussion of basic phenomena in quantum field theory and statistical mechanics. This interest results from specific properties of fractals, e.g., their dilatation symmetry and the…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
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…
We study regularity properties of frequency measures arising from random substitutions, which are a generalisation of (deterministic) substitutions where the substituted image of each letter is chosen independently from a fixed finite set.…
We study the statistics of quantum transmission through a one-dimensional disordered system modelled by a sequence of independent scattering units. Each unit is characterized by its length and by its action, which is proportional to the…
Many complex biological, social, and economical networks show topologies drastically differing from random graphs. But, what is a complex network, i.e.\ how can one quantify the complexity of a graph? Here the Offdiagonal Complexity (OdC),…
By analyzing the spacing of genes on chromosomes, we find that transcriptional and RNA-processing regulatory sequences outside coding regions leave footprints on the distribution of intergenic distances. Using analogies between genes on…
As high-throughput sequencing has become common practice, the cost of sequencing large amounts of genetic data has been drastically reduced, leading to much larger data sets for analysis. One important task is to identify biological…