Nature of the glassy phase of RNA secondary structure

We characterize the low temperature phase of a simple model for RNA secondary structures by determining the typical energy scale E(l) of excitations involving l bases. At zero temperature, we find a scaling law E(l) \sim l^\theta with \theta \approx 0.23, and this same scaling holds at low enough temperatures. Above a critical temperature, there is a different phase characterized by a relatively flat free energy landscape resembling that of a homopolymer with a scaling exponent \theta=1. These results strengthen the evidence in favour of the existence of a glass phase at low temperatures.Comment: 7 pages, 1 figur

Statistical mechanics of RNA folding: a lattice approach

We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA consists of just one hairpin. Using exact arguments and Monte Carlo simulations we determine the phase diagram for this case. We show that the denaturation transition is first order and can either occur directly or through an intermediate molten phase.Comment: 8 pages, 9 figure

Arsenic in the Iberoamerican region. The IBEROARSEN Network and a possible economic solution for arsenic removal in isolated rural zones

In this work, a short description of the problematic of arsenic in Iberoamerica will be given, indicating the affected geographical regions and their incidence on the quality of life of the populations. In Argentina, Chile, Bolivia, Peru, Ecuador and Mexico, at least 4 million people depend on water sources with toxic concentrations of arsenic. While in these countries the problem is known since decades, in Uruguay, Brazil, Nicaragua, Honduras and El Salvador, the problem has been detected or investigated only in last years, and, in other Latinamerican countries, the studies began only recently. In Spain and Portugal the problem of As is becoming increasingly important. The presence of As in drinking waters, together with poverty and malnutrition, causes the incidence of CERHA (chronic endemic regional hydroarsenicism, HACRE in Spanish), an illness that provokes serious problems like skin lesions and even cancer. The activities of the IBEROARSEN Network of the CYTED Program, an Iberoamerican project that aims at the interconnection of groups devoted to arsenic R&D, trying to find solutions to this problem in the region, will be described. In addition, results of evaluation of the efficiency of two very simple low-cost methods for As removal in plastic bottles using solar light, one of them using heterogeneous photocatalysis with TiO2 immobilized on the walls followed by iron addition, and another one based on the use of zerovalent iron, which employs very cheap materials, are presented. The study was performed with synthetic and natural waters of rural, isolated, poor populations, not connected to the drinking water network of the provinces of Tucumán and Santiago del Estero, Argentina. For HP tests, synthetic as well as natural samples containing arsenic placed in bottles internally covered by a TiO2 layer and exposed to solar or artificial UV light followed by an addition of an iron source resulted in As concentration well below the national standards. For ZVI tests, iron wool demonstrated to be a better iron source than packing wire for As removal. Solar irradiation, in synthetic as well as in natural samples, seems to definitively improve As removal, avoiding the use of high amounts of iron. Although both HP and ZVI gave similar results, the use of the first one could be superior due to the ability of removing simultaneously As, organic matter, toxic metals and microbiological contamination

Importance of Dietary Uptake for in Situ Bioaccumulation of Systemic Fungicides Using Gammarus pulex as a Model Organism

Bioaccumulation of organic contaminants from contaminated food sources might pose an underestimated risk toward shredding invertebrates. This assumption is substantiated by monitoring studies observing discrepancies of predicted tissue concentrations determined from laboratory-based experiments compared with measured concentrations of systemic pesticides in gammarids. To elucidate the role of dietary uptake in bioaccumulation, gammarids were exposed to leaf material from trees treated with a systemic fungicide mixture (azoxystrobin, cyprodinil, fluopyram, and tebuconazole), simulating leaves entering surface waters in autumn. Leaf concentrations, spatial distribution, and leaching behavior of fungicides were characterized using liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-HRMS/MS) and matrix-assisted laser desorption ionization-mass spectrometric imaging. The contribution of leached fungicides and fungicides taken up from feeding was assessed by assembling caged (no access) and uncaged (access to leaves) gammarids. The fungicide dynamics in the test system were analyzed using LC-HRMS/MS and toxicokinetic modeling. In addition, a summer scenario was simulated where water was the initial source of contamination and leaves contaminated by sorption. The uptake, translocation, and biotransformation of systemic fungicides by trees were compound-dependent. Internal fungicide concentrations of gammarids with access to leaves were much higher than in caged gammarids of the autumn scenario, but the difference was minimal in the summer scenario. In food choice and dissectioning experiments gammarids did not avoid contaminated leaves and efficiently assimilated contaminants from leaves, indicating the relevance of this exposure pathway in the field. The present study demonstrates the potential impact of dietary uptake on in situ bioaccumulation for shredders in autumn, outside the main application period. The toxicokinetic parameters obtained facilitate modeling of environmental exposure scenarios. The uncovered significance of dietary uptake for detritivores warrants further consideration from scientific as well as regulatory perspectives. Environ Toxicol Chem 2023;00:1-14. (c) 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC

Localization-delocalization transition of disordered d-wave superconductors in class CI

A lattice model for disordered d-wave superconductors in class CI is reconsidered. Near the band-center, the lattice model can be described by Dirac fermions with several species, each of which yields WZW term for an effective action of the Goldstone mode. The WZW terms cancel out each other because of the four-fold symmetry of the model, which suggests that the quasiparticle states are localized. If the lattice model has, however, symmetry breaking terms which generate mass for any species of the Dirac fermions, remaining WZW term which avoids the cancellation can derive the system to a delocalized strong-coupling fixed point.Comment: 4 pages, revte

Statistical mechanics of RNA folding: importance of alphabet size

We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two kinds of bases, there are many alternate folding configurations, yielding thermodynamically stable ground-states only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.Comment: 7 figures; uses revtex

RNA denaturation: excluded volume, pseudoknots and transition scenarios

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.Comment: 4 pages 3 figure

Superconducting ``metals'' and ``insulators''

We propose a characterization of zero temperature phases in disordered superconductors on the basis of the nature of quasiparticle transport. In three dimensional systems, there are two distinct phases in close analogy to the distinction between normal metals and insulators: the superconducting "metal" with delocalized quasiparticle excitations and the superconducting "insulator" with localized quasiparticles. We describe experimental realizations of either phase, and study their general properties theoretically. We suggest experiments where it should be possible to tune from one superconducting phase to the other, thereby probing a novel "metal-insulator" transition inside a superconductor. We point out various implications of our results for the phase transitions where the superconductor is destroyed at zero temperature to form either a normal metal or a normal insulator.Comment: 18 page

Quantum and classical localisation, the spin quantum Hall effect and generalisations

We consider network models for localisation problems belonging to symmetry class C. This symmetry class arises in a description of the dynamics of quasiparticles for disordered spin-singlet superconductors which have a Bogoliubov - de Gennes Hamiltonian that is invariant under spin rotations but not under time-reversal. Our models include but also generalise the one studied previously in the context of the spin quantum Hall effect. For these systems we express the disorder-averaged conductance and density of states in terms of sums over certain classical random walks, which are self-avoiding and have attractive interactions. A transition between localised and extended phases of the quantum system maps in this way to a similar transition for the classical walks. In the case of the spin quantum Hall effect, the classical walks are the hulls of percolation clusters, and our approach provides an alternative derivation of a mapping first established by Gruzberg, Read and Ludwig, Phys. Rev. Lett. 82, 4254 (1999).Comment: 11 pages, 5 figure