Related papers: Periodic correlation structures in bacterial and a…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repetitions within a single repeat protein can be extremely variable at the sequence level. We propose a mathematical…
Rhythmic activities that alternate between coherent and incoherent phases are ubiquitous in chemical, ecological, climate, or neural systems. Despite their importance, general mechanisms for their emergence are little understood. In order…
Bifurcation theory and continuation methods are well-established tools for the analysis of nonlinear mechanical systems subject to periodic forcing. We illustrate the added value and the complementary information provided by singularity…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
The principle of similarity, or homophily, is often used to explain patterns observed in complex networks such as transitivity and the abundance of triangles (3-cycles). However, many phenomena from division of labor to protein-protein…
The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Moir\'e patterns are omnipresent. They are important for any overlapping periodic phenomenon, from vibrational and electromagnetic, to condensed matter. Here we show, both theoretically and via experimental simulations by ultracold atoms,…
The transmissivity of a one-dimensional random system that is periodic on average is studied. It is shown that the transmission coefficient for frequencies corresponding to a gap in the band structure of the average periodic system…
We study the energy structure and the transfer of an extra electron or hole along periodic polymers made of $N$ monomers, with a repetition unit made of $P$ monomers, using a Tight-Binding wire model, where a site is a monomer (e.g., in…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
A great variety of systems in nature, society and technology -- from the web of sexual contacts to the Internet, from the nervous system to power grids -- can be modeled as graphs of vertices coupled by edges. The network structure,…
The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of families of…
Novel experimental techniques reveal the simultaneous activity of larger and larger numbers of neurons. As a result there is increasing interest in the structure of cooperative -- or correlated -- activity in neural populations, and in the…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
The structural properties of additive binary hard-sphere mixtures are addressed as a follow-up of a previous paper [S. Pieprzyk et al., Phys. Rev. E 101, 012117 (2020)]. The so-called rational-function approximation method and an approach…
We study the evolution of networks through `triplets' - three-node graphlets. We develop a method to compute a transition matrix to describe the evolution of triplets in temporal networks. To identify the importance of higher-order…