Model for Folding and Aggregation in RNA Secondary Structures

We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the secondary structure and the energy gained by pairing drives the RNA to undergo a `temperature independent' second order phase transition from a molten to an aggregated phase'. The aggregated phase thus obtained has a macroscopically large number of contacts between different RNAs. The partition function scaling exponent for this phase is \theta ~ 1/2 and the crossover exponent of the phase transition is \nu ~ 5/3. The relevance of these calculations to the aggregation of biological molecules is discussed.Comment: Revtex, 4 pages; 3 Figures; Final published versio

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

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

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

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

Quasiparticle localization in superconductors with spin-orbit scattering

We develop a theory of quasiparticle localization in superconductors in situations without spin rotation invariance. We discuss the existence, and properties of superconducting phases with localized/delocalized quasiparticle excitations in such systems in various dimensionalities. Implications for a variety of experimental systems, and to the properties of random Ising models in two dimensions, are briefly discussed.Comment: 10 page

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

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

Phase diagram of disordered fermion model on two-dimensional square lattice with π\pi-flux

A fermion model with random on-site potential defined on a two-dimensional square lattice with $\pi$-flux is studied. The continuum limit of the model near the zero energy yields Dirac fermions with random potentials specified by four independent coupling constants. The basic symmetry of the model is time-reversal invariance. Moreover, it turns out that the model has enhanced (chiral) symmetry on several surfaces in the four-dimensional space of the coupling constants. It is shown that one of the surfaces with chiral symmetry has Sp(n)$\times$Sp(n) symmety whereas others have U(2n) symmetry, both of which are broken to Sp(n), and the fluctuation around a saddle point is described, respectively, by Sp($n)_2$ WZW model and U(2n)/Sp(n) nonlinear sigma model. Based on these results, we propose a phase diagram of the model.Comment: 13 pages, 2 figure