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

Quantification of the differences between quenched and annealed averaging for RNA secondary structures

The analytical study of disordered system is usually difficult due to the necessity to perform a quenched average over the disorder. Thus, one may resort to the easier annealed ensemble as an approximation to the quenched system. In the study of RNA secondary structures, we explicitly quantify the deviation of this approximation from the quenched ensemble by looking at the correlations between neighboring bases. This quantified deviation then allows us to propose a constrained annealed ensemble which predicts physical quantities much closer to the results of the quenched ensemble without becoming technically intractable.Comment: 9 pages, 14 figures, submitted to Phys. Rev.

An elementary proof of the irrationality of Tschakaloff series

We present a new proof of the irrationality of values of the series $T_q(z)=\sum_{n=0}^\infty z^nq^{-n(n-1)/2}$ in both qualitative and quantitative forms. The proof is based on a hypergeometric construction of rational approximations to $T_q(z)$.Comment: 5 pages, AMSTe

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

Field Theory of the RNA Freezing Transition

Folding of RNA is subject to a competition between entropy, relevant at high temperatures, and the random, or random looking, sequence, determining the low- temperature phase. It is known from numerical simulations that for random as well as biological sequences, high- and low-temperature phases are different, e.g. the exponent rho describing the pairing probability between two bases is rho = 3/2 in the high-temperature phase, and approximatively 4/3 in the low-temperature (glass) phase. Here, we present, for random sequences, a field theory of the phase transition separating high- and low-temperature phases. We establish the existence of the latter by showing that the underlying theory is renormalizable to all orders in perturbation theory. We test this result via an explicit 2-loop calculation, which yields rho approximatively 1.36 at the transition, as well as diverse other critical exponents, including the response to an applied external force (denaturation transition).Comment: 96 pages, 188 figures. v2: minor correction

Glassy transition in a disordered model for the RNA secondary structure

We numerically study a disordered model for the RNA secondary structure and we find that it undergoes a phase transition, with a breaking of the replica symmetry in the low temperature region (like in spin glasses). Our results are based on the exact evaluation of the partition function.Comment: 4 pages, 3 figure

Griffiths effects and quantum critical points in dirty superconductors without spin-rotation invariance: One-dimensional examples

We introduce a strong-disorder renormalization group (RG) approach suitable for investigating the quasiparticle excitations of disordered superconductors in which the quasiparticle spin is not conserved. We analyze one-dimensional models with this RG and with elementary transfer matrix methods. We find that such models with broken spin rotation invariance {\it generically} lie in one of two topologically distinct localized phases. Close enough to the critical point separating the two phases, the system has a power-law divergent low-energy density of states (with a non-universal continuously varying power-law) in either phase, due to quantum Griffiths singularities. This critical point belongs to the same infinite-disorder universality class as the one dimensional particle-hole symmetric Anderson localization problem, while the Griffiths phases in the vicinity of the transition are controlled by lines of strong (but not infinite) disorder fixed points terminating in the critical point.Comment: 14 pages (two-column PRB format), 9 eps figure

Localization and delocalization in dirty superconducting wires

We present Fokker-Planck equations that describe transport of heat and spin in dirty unconventional superconducting quantum wires. Four symmetry classes are distinguished, depending on the presence or absence of time-reversal and spin rotation invariance. In the absence of spin-rotation symmetry, heat transport is anomalous in that the mean conductance decays like $1/\sqrt{L}$ instead of exponentially fast for large enough length $L$ of the wire. The Fokker-Planck equations in the presence of time-reversal symmetry are solved exactly and the mean conductance for quasiparticle transport is calculated for the crossover from the diffusive to the localized regime.Comment: 4 pages, RevTe

Ising model with periodic pinning of mobile defects

A two-dimensional Ising model with short-range interactions and mobile defects describing the formation and thermal destruction of defect stripes is studied. In particular, the effect of a local pinning of the defects at the sites of straight equidistant lines is analysed using Monte Carlo simulations and the transfer matrix method. The pinning leads to a long-range ordered magnetic phase at low temperatures. The dependence of the phase transition temperature, at which the defect stripes are destabilized, on the pinning strength is determined. The transition seems to be of first order, with and without pinning.Comment: 7 pages, 7 figure