Real-time non-equilibrium dynamics of quantum glassy systems

We develop a systematic analytic approach to aging effects in quantum disordered systems in contact with an environment. Within the closed-time path-integral formalism we include dissipation by coupling the system to a set of independent harmonic oscillators that mimic a quantum thermal bath. After integrating over the bath variables and averaging over disorder we obtain an effective action that determines the real-time dynamics of the system. The classical limit yields the Martin-Siggia-Rose generating functional associated to a colored noise. We apply this general formalism to a prototype model related to the $p$ spin-glass. We show that the model has a dynamic phase transition separating the paramagnetic from the spin-glass phase and that quantum fluctuations depress the transition temperature until a quantum critical point is reached. We show that the dynamics in the paramagnetic phase is stationary but presents an interesting crossover from a region controlled by the classical critical point to another one controlled by the quantum critical point. The most characteristic property of the dynamics in a glassy phase, namely aging, survives the quantum fluctuations. In the sub-critical region the quantum fluctuation-dissipation theorem is modified in a way that is consistent with the notion of effective temperatures introduced for the classical case. We discuss these results in connection with recent experiments in dipolar quantum spin-glasses and the relevance of the effective temperatures with respect to the understanding of the low temperature dynamics.Comment: 56 pages, Revtex, 17 figures include

PCDB: a database of protein conformational diversity

PCDB (http://www.pcdb.unq.edu.ar) is a database of protein conformational diversity. For each protein, the database contains the redundant compilation of all the corresponding crystallographic structures obtained under different conditions. These structures could be considered as different instances of protein dynamism. As a measure of the conformational diversity we use the maximum RMSD obtained comparing the structures deposited for each domain. The redundant structures were extracted following CATH structural classification and cross linked with additional information. In this way it is possible to relate a given amount of conformational diversity with different levels of information, such as protein function, presence of ligands and mutations, structural classification, active site information and organism taxonomy among others. Currently the database contains 7989 domains with a total of 36581 structures from 4171 different proteins. The maximum RMSD registered is 26.7 Å and the average of different structures per domain is 4.5

Multi-Grid Monte Carlo via XYXY Embedding. II. Two-Dimensional SU(3)SU(3) Principal Chiral Model

We carry out a high-precision simulation of the two-dimensional $SU(3)$ principal chiral model at correlation lengths $\xi$ up to $\sim 4 \times 10^5$, using a multi-grid Monte Carlo (MGMC) algorithm and approximately one year of Cray C-90 CPU time. We extrapolate the finite-volume Monte Carlo data to infinite volume using finite-size-scaling theory, and we discuss carefully the systematic and statistical errors in this extrapolation. We then compare the extrapolated data to the renormalization-group predictions. The deviation from asymptotic scaling, which is $\approx 12$ at $\xi \sim 25$, decreases to $\approx 2$ at $\xi \sim 4 \times 10^5$. We also analyze the dynamic critical behavior of the MGMC algorithm using lattices up to $256 \times 256$, finding the dynamic critical exponent $z_{int,{\cal M}^2} \approx 0.45 \pm 0.02$ (subjective 68% confidence interval). Thus, for this asymptotically free model, critical slowing-down is greatly reduced compared to local algorithms, but not completely eliminated.Comment: self-unpacking archive including .tex, .sty and .ps files; 126 pages including all figure

Large-scale mapping of bioactive peptides in structural and sequence space

Health-enhancing potential bioactive peptide (BP) has driven an interest in food proteins as well as in the development of predictive methods. Research in this area has been especially active to use them as components in functional foods. Apparently, BPs do not have a given biological function in the containing proteins and they do not evolve under independent evolutionary constraints. In this work we performed a large-scale mapping of BPs in sequence and structural space. Using well curated BP deposited in BIOPEP database, we searched for exact matches in non-redundant sequences databases. Proteins containing BPs, were used in fold-recognition methods to predict the corresponding folds and BPs occurrences were mapped. We found that fold distribution of BP occurrences possibly reflects sequence relative abundance in databases. However, we also found that proteins with 5 or more than 5 BP in their sequences correspond to well populated protein folds, called superfolds. Also, we found that in well populated superfamilies, BPs tend to adopt similar locations in the protein fold, suggesting the existence of hotspots. We think that our results could contribute to the development of new bioinformatics pipeline to improve BP detection.Fil: Nardo, Agustina Estefania. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; ArgentinaFil: Añon, Maria Cristina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; ArgentinaFil: Parisi, Gustavo Daniel. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Distribution of mosquitoes in the South East of Argentina and first report on the analysis based on 18S rDNA and COI sequences

Although Mar del Plata is the most important city on the Atlantic coast of Argentina, mosquitoes inhabiting such area are almost uncharacterized. To increase our knowledge in their distribution, we sampled specimens of natural populations. After the morphological identification based on taxonomic keys, sequences of DNA from small ribosomal subunit (18S rDNA) and cytochrome c oxidase I (COI) genes were obtained from native species and the phylogenetic analysis of these sequences were done. Fourteen species from the genera Uranotaenia, Culex, Ochlerotatus and Psorophora were found and identified. Our 18S rDNA and COI-based analysis indicates the relationships among groups at the supra-species level in concordance with mosquito taxonomy. The introduction and spread of vectors and diseases carried by them are not known in Mar del Plata, but some of the species found in this study were reported as pathogen vectors

VISTA Variables in the <i>Vía Láctea</i> (VVV): Halfway Status and Results

The VISTA Variables in the Vía Láctea (VVV) survey is one of six near-infrared ESO public surveys, and is now in its fourth year of observing. Although far from being complete, the VVV survey has already delivered many results, some directly connected to the intended science goals (detection of variable stars, microlensing events, new star clusters), others concerning more exotic objects, e.g., novae. Now, at the end of the fourth observing period, and comprising roughly 50% of the proposed observations, the status of the survey, as well some of results based on the VVV data, are presented.Facultad de Ciencias Astronómicas y Geofísica

The tight-adhesion proteins TadGEF of <i>Bradyrhizobium diazoefficiens</i> USDA 110 are involved in cell adhesion and infectivity on soybean roots

Adhesion of symbiotic bacteria to host plants is an essential early step of the infection process that leads to the beneficial interaction. In the Bradyrhizobium diazoefficiens-soybean symbiosis few molecular determinants of adhesion are known. Here we identified the tight-adhesion gene products TadGEF in the open-reading frames blr3941-blr3943 of the B. diazoefficiens USDA 110 complete genomic sequence. Predicted structure of TadG indicates a transmembrane domain and two extracytosolic domains, from which the C-terminal has an integrin fold. TadE and TadF are also predicted as bearing transmembrane segments. Mutants in tadG or the small cluster tadGEF were impaired in adhesion to soybean roots, and the root infection was delayed. However, nodule histology was not compromised by the mutations, indicating that these effects were restricted to the earliest contact of the B. diazoefficiens and root surfaces. Knowledge of preinfection determinants is important for development of inoculants that are applied to soybean crops worldwide.Facultad de Ciencias ExactasInstituto de Biotecnologia y Biologia Molecula

The tight-adhesion proteins TadGEF of <i>Bradyrhizobium diazoefficiens</i> USDA 110 are involved in cell adhesion and infectivity on soybean roots

Adhesion of symbiotic bacteria to host plants is an essential early step of the infection process that leads to the beneficial interaction. In the Bradyrhizobium diazoefficiens-soybean symbiosis few molecular determinants of adhesion are known. Here we identified the tight-adhesion gene products TadGEF in the open-reading frames blr3941-blr3943 of the B. diazoefficiens USDA 110 complete genomic sequence. Predicted structure of TadG indicates a transmembrane domain and two extracytosolic domains, from which the C-terminal has an integrin fold. TadE and TadF are also predicted as bearing transmembrane segments. Mutants in tadG or the small cluster tadGEF were impaired in adhesion to soybean roots, and the root infection was delayed. However, nodule histology was not compromised by the mutations, indicating that these effects were restricted to the earliest contact of the B. diazoefficiens and root surfaces. Knowledge of preinfection determinants is important for development of inoculants that are applied to soybean crops worldwide.Facultad de Ciencias ExactasInstituto de Biotecnologia y Biologia Molecula

The tight-adhesion proteins TadGEF of <i>Bradyrhizobium diazoefficiens</i> USDA 110 are involved in cell adhesion and infectivity on soybean roots

Adhesion of symbiotic bacteria to host plants is an essential early step of the infection process that leads to the beneficial interaction. In the Bradyrhizobium diazoefficiens-soybean symbiosis few molecular determinants of adhesion are known. Here we identified the tight-adhesion gene products TadGEF in the open-reading frames blr3941-blr3943 of the B. diazoefficiens USDA 110 complete genomic sequence. Predicted structure of TadG indicates a transmembrane domain and two extracytosolic domains, from which the C-terminal has an integrin fold. TadE and TadF are also predicted as bearing transmembrane segments. Mutants in tadG or the small cluster tadGEF were impaired in adhesion to soybean roots, and the root infection was delayed. However, nodule histology was not compromised by the mutations, indicating that these effects were restricted to the earliest contact of the B. diazoefficiens and root surfaces. Knowledge of preinfection determinants is important for development of inoculants that are applied to soybean crops worldwide.Facultad de Ciencias ExactasInstituto de Biotecnologia y Biologia Molecula