Emergence of spike correlations in periodically forced excitable systems

In sensory neurons the presence of noise can facilitate the detection of weak information-carrying signals, which are encoded and transmitted via correlated sequences of spikes. Here we investigate relative temporal order in spike sequences induced by a subthreshold periodic input, in the presence of white Gaussian noise. To simulate the spikes, we use the FitzHugh-Nagumo model, and to investigate the output sequence of inter-spike intervals (ISIs), we use the symbolic method of ordinal analysis. We find different types of relative temporal order, in the form of preferred ordinal patterns which depend on both, the strength of the noise and the period of the input signal. We also demonstrate a resonance-like behavior, as certain periods and noise levels enhance temporal ordering in the ISI sequence, maximizing the probability of the preferred patterns. Our findings could be relevant for understanding the mechanisms underlying temporal coding, by which single sensory neurons represent in spike sequences the information about weak periodic stimuli

Analysis of noise-induced temporal correlations in neuronal spike sequences

This is a copy of the author 's final draft version of an article published in the journal European physical journal. Special topics. The final publication is available at Springer via http://dx.doi.org/10.1140/epjst/e2016-60024-6We investigate temporal correlations in sequences of noise-induced neuronal spikes, using a symbolic method of time-series analysis. We focus on the sequence of time-intervals between consecutive spikes (inter-spike-intervals, ISIs). The analysis method, known as ordinal analysis, transforms the ISI sequence into a sequence of ordinal patterns (OPs), which are defined in terms of the relative ordering of consecutive ISIs. The ISI sequences are obtained from extensive simulations of two neuron models (FitzHugh-Nagumo, FHN, and integrate-and-fire, IF), with correlated noise. We find that, as the noise strength increases, temporal order gradually emerges, revealed by the existence of more frequent ordinal patterns in the ISI sequence. While in the FHN model the most frequent OP depends on the noise strength, in the IF model it is independent of the noise strength. In both models, the correlation time of the noise affects the OP probabilities but does not modify the most probable pattern.Peer ReviewedPostprint (author's final draft

Enhancements to the GW space-time method

We describe the following new features which significantly enhance the power of the recently developed real-space imaginary-time GW scheme (Rieger et al., Comp. Phys. Commun. 117, 211 (1999)) for the calculation of self-energies and related quantities of solids: (i) to fit the smoothly decaying time/energy tails of the dynamically screened Coulomb interaction and other quantities to model functions, treating only the remaining time/energy region close to zero numerically and performing the Fourier transformation from time to energy and vice versa by a combination of analytic integration of the tails and Gauss-Legendre quadrature of the remaining part and (ii) to accelerate the convergence of the band sum in the calculation of the Green's function by replacing higher unoccupied eigenstates by free electron states (plane waves). These improvements make the calculation of larger systems (surfaces, clusters, defects etc.) accessible.Comment: 10 pages, 6 figure

Satellites in the prokaryote world

Background Satellites or tandem repeats are very abundant in many eukaryotic genomes. Occasionally they have been reported to be present in some prokaryotes, but to our knowledge there is no general comparative study on their occurrence. For this reason we present here an overview of the distribution and properties of satellites in a set of representative species. Our results provide novel insights into the evolutionary relationship between eukaryotes, Archaea and Bacteria. Results We have searched all possible satellites present in the NCBI reference group of genomes in Archaea (142 species) and in Bacteria (119 species), detecting 2735 satellites in Archaea and 1067 in Bacteria. We have found that the distribution of satellites is very variable in different organisms. The archaeal Methanosarcina class stands out for the large amount of satellites in their genomes. Satellites from a few species have similar characteristics to those in eukaryotes, but most species have very few satellites: only 21 species in Archaea and 18 in Bacteria have more than 4 satellites/Mb. The distribution of satellites in these species is reminiscent of what is found in eukaryotes, but we find two significant differences: most satellites have a short length and many of them correspond to segments of genes coding for amino acid repeats. Transposition of non-coding satellites throughout the genome occurs rarely: only in the bacteria Leptospira interrogans and the archaea Methanocella conradii we have detected satellite families of transposed satellites with long repeats. Conclusions Our results demonstrate that the presence of satellites in the genome is not an exclusive feature of eukaryotes. We have described a few prokaryotes which do contain satellites. We present a discussion on their eventual evolutionary significance.Peer ReviewedPostprint (published version

Unique features of satellite DNA transcription in different tissues of Caenorhabditis elegans

A large part of the genome is known to be transcribed as non-coding DNA including some tandem repeats (satellites) such as telomeric/centromeric satellites in different species. However, there has been no detailed study on the eventual transcription of the interspersed satellites found in many species. In the present paper, we studied the transcription of the abundant DNA satellites in the nematode Caenorhabditis elegans using available RNA-Seq results. We found that many of them have been transcribed, but usually in an irregular manner; different regions of a satellite have been transcribed with variable efficiency. Satellites with a similar repeat sequence also have a different transcription pattern depending on their position in the genome. We also describe the peculiar features of satellites associated with Helitron transposons in C. elegans. Our demonstration that some satellite RNAs are transcribed adds a new family of non-coding RNAs, a new element in the world of RNA interference, with new paths for the control of mRNA translation. This is a field that requires further investigation and will provide a deeper understanding of gene expression and control.This work was supported by grant PID2021-122830OB-C43, funded by MCIN/AEI/10.13039/501100011033 and by “ERDF: A way of making Europe”.Peer ReviewedPostprint (published version

Dna satellites are transcribed as part of the non-coding genome in eukaryotes and bacteria

It has been shown in recent years that many repeated sequences in the genome are expressed as RNA transcripts, although the role of such RNAs is poorly understood. Some isolated and tandem repeats (satellites) have been found to be transcribed, such as mammalian Alu sequences and telomeric/centromeric satellites in different species. However, there is no detailed study on the eventual transcription of the interspersed satellites found in many species. Therefore, we decided to study for the first time the transcription of the abundant DNA satellites in the bacterium Bacillus coagulans and in the nematode Caenorhabditis elegans. We have updated the data for C. elegans satellites using the latest version of the genome. We analyzed the transcription of satellites in both species in available RNA-seq results and found that they are widely transcribed. Our demonstration that satellite RNAs are transcribed adds a new family of non-coding RNAs. This is a field that requires further investigation and will provide a deeper understanding of gene expression and control.This work was supported by Ministerio de Ciencia e Innovación, Spain [Project RTI2018-094403-B-C33 funded by MCIN/ AEI 10.13039/501100011033/ FEDER].Peer ReviewedPostprint (published version

Zero-lag long-range synchronization via dynamical relaying

We show that simultaneous synchronization between two delay-coupled oscillators can be achieved by relaying the dynamics via a third mediating element, which surprisingly lags behind the synchronized outer elements. The zero-lag synchronization thus obtained is robust over a considerable parameter range. We substantiate our claims with experimental and numerical evidence of these synchronization solutions in a chain of three coupled semiconductor lasers with long inter-element coupling delays. The generality of the mechanism is validated in a neuronal model with the same coupling architecture. Thus, our results show that synchronized dynamical states can occur over long distances through relaying, without restriction by the amount of delay.Comment: 10 pages, 4 figure

Double-negative acoustic metamaterials based on quasi-two-dimensional fluid-like shells

A structured cylindrical scatterer with low-frequency resonances in both the effective bulk modulus and the dynamical mass density is designed and characterized. The proposed scattering unit is made of a rigid cylinder surrounded by a fluid-like shell embedded in a two-dimensional waveguide of height less than the length of the cylindrical scatterer. It is demonstrated that the acoustic metamaterials based on this building unit have negative acoustic parameters in a broad range of frequencies. It is also shown that double-negative behavior can be tailored by adjusting the dimensions and properties of the materials forming the structured scattering unit.This work was partially supported by the Spanish Ministerio de Ciencia e Innovacion (MICINN) under contracts TEC2010-19751 and CSD2008-66 (the CONSOLIDER program) and by the US Office of Naval Research. The authors acknowledge Victor M Garcia-Chocano for useful discussions and Kimee Moore for proofreading the paper.Graciá Salgado, R.; Torrent Martí, D.; Sánchez-Dehesa Moreno-Cid, J. (2012). Double-negative acoustic metamaterials based on quasi-two-dimensional fluid-like shells. New Journal of Physics. 14. https://doi.org/10.1088/1367-2630/14/10/103052S1