Previous works have shown numerically that the response of a "stochastic resonator" is enhanced as a consequence of spatial coupling. Also, similar results have been obtained in a reaction-diffusion model by studying the phenomenon of stochastic resonance (SR) in spatially extended systems using nonequilibrium potential (NEP) techniques. The knowledge of the NEP for such systems allows us to determine the probability for the decay of the metastable extended states, and approximate expressions for the correlation function and the signal-to-noise ratio (SNR). Here, exploiting known forms of the NEP, we have investigated the role of NEP's symmetry on SR, the enhancement of the SNR due to a selectivity of the coupling or diffusion parameter, and discussed competition between local and nonlocal (excitatory) coupling. * Member of CONICET, Argentina; Electronic Address: wio@cab.cnea.gov.ar †

Variable (V) domains of immunoglobulins (Ig) and T cell receptors (TCR) are generated from genomic V gene segments (V-genes). At present, such V-genes have been annotated only within the genome of a few species. We have developed a bioinformatics tool that accelerates the task of identifying functional V-genes from genome datasets. Automated recognition is accomplished by recognizing key V-gene signatures, such as recombination signal sequences, size of the exon region, and position of amino acid motifs within the translated exon. This algorithm also classifies extracted V-genes into either TCR or Ig loci. We describe the implementation of the algorithm and validate its accuracy by comparing V-genes identified from the human and mouse genomes with known V-gene annotations documented and available in public repositories. The advantages and utility of the algorithm are illustrated by using it to identify functional V-genes in the rat genome, where V-gene annotation is still incomplete. This allowed us to perform a comparative human-rodent phylogenetic analysis based on V-genes that supports the hypothesis that distinct evolutionary pressures shape the TCRs and Igs V-gene repertoires. Our program, together with a user graphical interface, is available as open-source software, downloadable at http://code.google.com/p/vgenextract/.

Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged: one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia, and Aves. In this study, we determined the genomic variable (V) exons from whole genome shotgun sequencing (WGS) data in reptiles corresponding to the three main immunoglobulin (IG) loci and the four main T cell receptor (TR) loci. We show that Squamata lack the TRG and TRD genes, and snakes lack the IGKV genes. In representative species of Testudines and Crocodylia, the seven major IG and TR loci are maintained. As in mammals, genes of the IG loci can be grouped into well-defined IMGT clans through a multi-species phylogenetic analysis. We show that the reptilian IGHV and IGLV genes are distributed amongst the established mammalian clans, while their IGKV genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptilian and mammalian TRAV genes cluster into six common evolutionary clades (since IMGT clans have not been defined for TR). In contrast, the reptilian TRBV genes cluster into three clades, which have few mammalian members. In this locus, the V exon sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptilian clans. These sequences can be obtained in a freely available public repository (http://vgenerepertoire.org).

We study an extended system that without noise shows a monostable dynamics, but when submitted to an adequate multiplicative noise, an effective bistable dynamics arises. The stochastic resonance between the attractors of the noise-sustained dynamics is investigated theoretically in terms of a two-state approximation. The knowledge of the exact nonequilibrium potential allows us to obtain the output signal-to-noise ratio. Its maximum is predicted in the symmetric case for which both attractors have the same nonequilibrium potential value.

We study the phenomenon of system size stochastic resonance within the nonequilibrium potential's framework. We analyze three different cases of spatially extended systems, exploiting the knowledge of their nonequilibrium potential, showing that through the analysis of that potential we can obtain a clear physical interpretation of this phenomenon in wide classes of extended systems. Depending on the characteristics of the system, the phenomenon results to be associated to a breaking of the symmetry of the nonequilibrium potential or to a deepening of the potential minima yielding an effective scaling of the noise intensity with the system size.