Diego Luis Gonzalez

We study the formation and evolution of domain walls with initial inflationary fluctuations by numerical lattice calculations that, for the first time, correctly take into account correlations on superhorizon scales. We find that, contrary to the widely-held claim {over the past few tens of years}, the domain wall network exhibits remarkable stability even when the initial distribution is largely biased toward one of the minima. This is due to the fact that the domain wall network retains information about initial conditions on superhorizon scales, and that the scaling solution is not a local attractor in this sense. Our finding immediately implies that such domain walls will have a significant impact on cosmology, including the production of gravitational waves, baryogenesis, and dark matter from domain walls. Applying this result to the axion-like particle domain wall, we show that it not only explains the isotropic cosmic birefringence suggested by the recent analysis, but also predicts anisotropic cosmic birefringence that is nearly scale-invariant on large scales and can be probed by future CMB observations.

A new nonlinear circuit with frequency locking capability in the case of a generic quasi-periodic input, is presented. Due to this capability the circuit is called a Quasi-Periodic Locked Loop (Q-PLL). The locked frequency is parametrically selected from among those prescribed by the theory of resonances in dynamical systems. In particular, the locked frequency forms a three-frequency resonance with the frequencies of the quasi-periodic input. The circuit is able to lock also in case of deterministic perturbation (additional frequency components) and stochastic perturbation (wide-band noise). The circuit is closely related to the pitch perception of complex sound in humans and, as such, can be considered a bio-inspired device. From the point of view of applications, it may be considered as an extension of the Phase Locked Loop (PLL) with the additional ability of locking simultaneously to more than one frequency. Due to the dynamical and structural robustness of the locked states, the Q-PLL represents a tangible advance for the development of specific applications, for example, in medicine (hearing aids, and cochlear implants), in robotics (artificial senses), and in industrial and consumer electronics (improvement of speech intelligibility, pitch-based processing, etc.).

Circular codes represent a form of coding allowing detection/correction of frameshift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein expression levels. Strikingly, circular code marks are absent at the beginning of coding sequences, but stably occur 40 codons after the initiator codon, hinting at the translation elongation process. Finally, we use the lens of circular codes to show that codon influence on translation correlates with the strong-weak dichotomy of the first two bases of the codon. The results provide promising universal tools for sequence indicators and sequence optimization for bioinformatics and biotechnological applications, and can shed light on the molecular mechanisms behind the decoding process.

The degeneracy of amino acid coding is one of the most crucial and enigmatic aspects of the genetic code. Different theories about the origin of the genetic code have been developed. However, to date, there is no comprehensive hypothesis on the mechanism that might have generated the degeneracy as we observe it. Here, we provide a new theory that explains the origin of the degeneracy based only on symmetry principles. The approach allows one to describe exactly the degeneracy of the early code (progenitor of the genetic code of LUCA, the last universal common ancestor) which is hypothesized to have the same degeneracy as the present vertebrate mitochondrial genetic code. The theory is based upon the tessera code, that fits as the progenitor of the early code. Moreover, we describe in detail the possible evolutionary transitions implied by our theory. The approach is supported by a unified mathematical framework that accounts for the degeneracy properties of both nuclear and mitochondrial genetic codes. Our work provides a new perspective to the understanding of the origin of the genetic code and the roles of symmetry principles in the organization of genetic information.

In this article, we present a mathematical framework based on redundant (non-power) representations of integer numbers as a paradigm for the interpretation of genomic information. The core of the approach relies on modelling the degeneracy of the genetic code. The model allows one to explain many features and symmetries of the genetic code and to uncover hidden symmetries. Also, it provides us with new tools for the analysis of genomic sequences. We review briefly three main areas: (i) the Euplotid nuclear code, (ii) the vertebrate mitochondrial code, and (iii) the main coding/decoding strategies used in the three domains of life. In every case, we show how the non-power model is a natural unified framework for describing degeneracy and deriving sound biological hypotheses on protein coding. The approach is rooted on number theory and group theory; nevertheless, we have kept the technical level to a minimum by focusing on key concepts and on the biological implications.

On the one hand, biology, chemistry and also physics tell us how the process of translating the genetic information into life could possibly work, but we are still very far from a complete understanding of this process. On the other hand, mathematics and statistics give us methods to describe such natural systems—or parts of them—within a theoretical framework. Also, they provide us with hints and predictions that can be tested at the experimental level. Furthermore, there are peculiar aspects of the management of genetic information that are intimately related to information theory and communication theory. This theme issue is aimed at fostering the discussion on the problem of genetic coding and information through the presentation of different innovative points of view. The aim of the editors is to stimulate discussions and scientific exchange that will lead to new research on why and how life can exist from the point of view of the coding and decoding of genetic information. The present introduction represents the point of view of the editors on the main aspects that could be the subject of future scientific debate.