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

A rural agricultural-sustainable energy community model and its application to Felton Valley, Australia

Energy and food security require a delicate balance which should not threaten or undermine community prosperity. Where it is proposed to derive energy from conventional fossil fuel resources (such as coal, shale oil, natural gas, coal seam gas) located in established rural areas, and particularly where these areas are used for productive agricultural purposes, there are often both intense community concern as well as broader questions regarding the relative social, economic and environmental costs and benefits of different land uses and, increasingly, different energy sources. The advent of mainstream renewable energy technologies means that alternative energy options may provide a viable alternative, allowing energy demand to be met without compromising existing land uses. We demonstrate how such a Sustainable Energy Rural Model can be designed to achieve a balance between the competing social goals of energy supply, agricultural production, environmental integrity and social well-being, and apply it to the Felton Valley, a highly productive and resilient farming community in eastern Australia. Research into available wind and solar resources found that Felton Valley has a number of attributes that indicate its suitability for the development of an integrated renewable energy precinct which would complement, rather than displace, existing agricultural enterprises. Modelling results suggest a potential combined annual renewable energy output from integrated wind and solar resources of 1,287 GWh/yr from peak installed capacity of 713 MW, sufficient to supply the electrical energy needs of about 160,000 homes, in combination with total biomass food production of 31,000 tonnes per annum or 146 GWh/yr of human food energy. The portfolio of renewable energy options will not only provide energy source diversity but also ensures long-term food security and regional stability. The Felton Valley model provides an example of community-led energy transformation and has potential as a pilot project for the development of smart distributed grids that would negate the need for further expansion of coal mining and coal fired power stations

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: 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.

Ground state and glass transition of the RNA secondary structure

RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix propagation. The free energy cost for separating a chain into two equal halves offers a quantitative measure of sequence specific pairing. In the low temperature glass phase, this quantity grows quadratically with the logarithm of the chain length, but it switches to a linear behavior of entropic origin in the high temperature molten phase. Transition between the two phases is continuous, with characteristics that resemble those of a disordered elastic manifold in two dimensions. For designed sequences, however, a power-law distribution of pairing energies on a coarse-grained level may be more appropriate. Extreme value statistics arguments then predict a power-law growth of the free energy cost to break a chain, in agreement with numerical simulations. Interestingly, the distribution of pairing distances in the ground state secondary structure follows a remarkable power-law with an exponent -4/3, independent of the specific assumptions for the base pairing energies

Analytical description of finite size effects for RNA secondary structures

The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on thermodynamic parameters. For realistic choices of parameters this length can be much longer than natural RNA molecules. This has to be taken into account when applying asymptotic theory to interpret experiments or numerical results.Comment: 10 pages, 13 figures, published in Phys. Rev.

Quasiparticle density of states in dirty high-T_c superconductors

We study the density of quasiparticle states of dirty d-wave superconductors. We show the existence of singular corrections to the density of states due to quantum interference effects. We then argue that the density of states actually vanishes in the localized phase as $|E|$ or $E^2$ depending on whether time reversal is a good symmetry or not. We verify this result for systems without time reversal symmetry in one dimension using supersymmetry techniques. This simple, instructive calculation also provides the exact universal scaling function for the density of states for the crossover from ballistic to localized behaviour in one dimension. Above two dimensions, we argue that in contrast to the conventional Anderson localization transition, the density of states has critical singularities which we calculate in a $2+\epsilon$ expansion. We discuss consequences of our results for various experiments on dirty high-$T_c$ materials

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