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

Large N spin quantum Hall effect

We introduce a large N version of the spin quantum Hall transition problem. It is formulated as a problem of Dirac fermions coupled to disorder, whose Hamiltonian belong to the symmetry class C. The fermions carry spin degrees of freedom valued in the algebra sp(2N), the spin quantum Hall effect corresponding to N=1. Arguments based on renormalization group transformations as well as on a sigma model formulation, valid in the large N limit, indicate the existence of a crossover as N varies. Contrary to the N=1 case, the large N models are shown to lead to localized states at zero energy. We also present a sigma model analysis for the system of Dirac fermions coupled to only sp(2N) random gauge potentials, which reproduces known exact results.Comment: 29 pages; few references added, statement about the density of states improved; published versio

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

Comparing effects of microplastic exposure, FPOM resource quality, and consumer density on the response of a freshwater particle feeder and associated ecosystem processes

Fine particulate organic matter (FPOM) is an important basal resource in stream ecosystems for deposit- and filter-feeding macroinvertebrates (collectively ‘particle feeders’). Microplastics (MP) share many characteristics with FPOM (e.g. size range, surface area to volume ratios) and are potentially consumed by particle feeders. Accordingly, MP contamination of natural FPOM pools might affect particle feeder growth and survival, particularly when background FPOM resource quality is low, or intraspecific competition is high. We conducted a microcosm experiment to evaluate how a realistic (1400 particles/kg sediment) polyethylene MP (ø = 45–53 µm) concentration interacts with FPOM (ø = 63–250 µm) resource quality (low versus high nutrient content) and consumer density (10 versus 20 individuals per microcosm) to affect growth and survival of larval Chironomus riparius (Diptera: Chironomidae), a model particle feeder. We additionally quantified community respiration, based on three hour measurements of oxygen consumption in the microcosms at the end of the experiment. MP exposure reduced larval body lengths by 26.7%, but only under the low consumer density treatment. MPs reduced community respiration by 26.2%, but only in the absence of chironomids, indicating an impact on microbial respiration. In comparison, low resource quality and high consumer density were associated with 53.5–70.2% reductions in community respiration, chironomid body length and/or body mass. These results suggest that effects of contamination of FPOM with MPs at environmentally realistic concentrations on the life histories of particle feeders such as C. riparius might be limited, especially relative to the effects of resource quality and consumer density. However, the reduction in microbial respiration when MPs were present highlights the need for further research addressing MP impacts on microbes, given their key roles in ecosystem functioning.publishedVersio

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

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

The selective phosphodiesterase 4 inhibitor roflumilast and phosphodiesterase 3/4 inhibitor pumafentrine reduce clinical score and TNF expression in experimental colitis in mice.

The specific inhibition of phosphodiesterase (PDE)4 and dual inhibition of PDE3 and PDE4 has been shown to decrease inflammation by suppression of pro-inflammatory cytokine synthesis. We examined the effect of roflumilast, a selective PDE4 inhibitor marketed for severe COPD, and the investigational compound pumafentrine, a dual PDE3/PDE4 inhibitor, in the preventive dextran sodium sulfate (DSS)-induced colitis model. The clinical score, colon length, histologic score and colon cytokine production from mice with DSS-induced colitis (3.5% DSS in drinking water for 11 days) receiving either roflumilast (1 or 5 mg/kg body weight/d p.o.) or pumafentrine (1.5 or 5 mg/kg/d p.o.) were determined and compared to vehicle treated control mice. In the pumafentrine-treated animals, splenocytes were analyzed for interferon-γ (IFNγ) production and CD69 expression. Roflumilast treatment resulted in dose-dependent improvements of clinical score (weight loss, stool consistency and bleeding), colon length, and local tumor necrosis factor-α (TNFα) production in the colonic tissue. These findings, however, were not associated with an improvement of the histologic score. Administration of pumafentrine at 5 mg/kg/d alleviated the clinical score, the colon length shortening, and local TNFα production. In vitro stimulated splenocytes after in vivo treatment with pumafentrine showed a significantly lower state of activation and production of IFNγ compared to no treatment in vivo. These series of experiments document the ameliorating effect of roflumilast and pumafentrine on the clinical score and TNF expression of experimental colitis in mice

Thermal metal in network models of a disordered two-dimensional superconductor

We study the universality class for localization which arises from models of non-interacting quasiparticles in disordered superconductors that have neither time-reversal nor spin-rotation symmetries. Two-dimensional systems in this category, which is known as class D, can display phases with three different types of quasiparticle dynamics: metallic, localized, or with a quantized (thermal) Hall conductance. Correspondingly, they can show a variety of delocalization transitions. We illustrate this behavior by investigating numerically the phase diagrams of network models with the appropriate symmetry, and for the first time show the appearance of the metallic phase.Comment: 5 pages, 3 figure

RNA secondary structure formation: a solvable model of heteropolymer folding

The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the transition between the native and molten phase of the RNA as a function of temperature. The transition is driven by a competition between the energy gained from the polymer's overlap with the native structure and the entropic gain of forming random contacts. A simplified Go-like model is proposed and solved exactly. The predicted critical behavior is verified via exact numerical enumeration of a large ensemble of similarly designed sequences.Comment: 4 pages including 2 figure

Statistical mechanics of secondary structures formed by random RNA sequences

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical studies. First, a two-replica calculation is performed. By mapping the two-replica problem to the denaturation of a single homogeneous RNA in 6-dimensional embedding space, we show that sequence disorder is perturbatively irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten phase where many secondary structures with comparable total energy coexist. A numerical study of various models at high temperature reproduces behaviors characteristic of the molten phase. On the other hand, a scaling argument based on the extremal statistics of rare regions can be constructed to show that the low temperature phase is unstable to sequence disorder. We performed a detailed numerical study of the low temperature phase using the droplet theory as a guide, and characterized the statistics of large-scale, low-energy excitations of the secondary structures from the ground state structure. We find the excitation energy to grow very slowly (i.e., logarithmically) with the length scale of the excitation, suggesting the existence of a marginal glass phase. The transition between the low temperature glass phase and the high temperature molten phase is also characterized numerically. It is revealed by a change in the coefficient of the logarithmic excitation energy, from being disorder dominated to entropy dominated.Comment: 24 pages, 16 figure