Combinatorial analysis of interacting RNA molecules

Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with two backbones drawn horizontally on top of each other such that (1) intramolecular and intermolecular bonds are noncrossing and (2) there is no "zig-zag" configuration. This paper studies joint structures with arc-length at least four in which both, interior and exterior stack-lengths are at least two (no isolated arcs). The key idea in this paper is to consider a new type of shape, based on which joint structures can be derived via symbolic enumeration. Our results imply simple asymptotic formulas for the number of joint structures with surprisingly small exponential growth rates. They are of interest in the context of designing prediction algorithms for RNA-RNA interactions.Comment: 22 pages, 15 figure

Spontaneous spatial fractal pattern formation in absorptive systems

We predict, for the first time to our knowledge, that purely-absorptive nonlinearity can support spontaneous spatial fractal pattern formation. A passive optical ring cavity with a thin slice of saturable absorber is analyzed. Linear stability analysis yields threshold curves for Turing (static) instabilities with features proposed as characteristics of potential fractal pattern formation. Numerical simulations of the fully-nonlinear dynamics, with both one and two transverse dimensions, confirm theoretical predictions

Inverse targeting -- an effective immunization strategy

We propose a new method to immunize populations or computer networks against epidemics which is more efficient than any method considered before. The novelty of our method resides in the way of determining the immunization targets. First we identify those individuals or computers that contribute the least to the disease spreading measured through their contribution to the size of the largest connected cluster in the social or a computer network. The immunization process follows the list of identified individuals or computers in inverse order, immunizing first those which are most relevant for the epidemic spreading. We have applied our immunization strategy to several model networks and two real networks, the Internet and the collaboration network of high energy physicists. We find that our new immunization strategy is in the case of model networks up to 14%, and for real networks up to 33% more efficient than immunizing dynamically the most connected nodes in a network. Our strategy is also numerically efficient and can therefore be applied to large systems

Efficient algorithm to study interconnected networks

Interconnected networks have been shown to be much more vulnerable to random and targeted failures than isolated ones, raising several interesting questions regarding the identification and mitigation of their risk. The paradigm to address these questions is the percolation model, where the resilience of the system is quantified by the dependence of the size of the largest cluster on the number of failures. Numerically, the major challenge is the identification of this cluster and the calculation of its size. Here, we propose an efficient algorithm to tackle this problem. We show that the algorithm scales as O(N log N), where N is the number of nodes in the network, a significant improvement compared to O(N^2) for a greedy algorithm, what permits studying much larger networks. Our new strategy can be applied to any network topology and distribution of interdependencies, as well as any sequence of failures.Comment: 5 pages, 6 figure

Bounds on Information Propagation in Disordered Quantum Spin Chains

We investigate the propagation of information through the disordered XY model. We find, with a probability that increases with the size of the system, that all correlations, both classical and quantum, are suppressed outside of an effective lightcone whose radius grows at most polylogarithmically with |t|.Comment: 4 pages, pdflatex, 1 pdf figure. Corrected the bound for the localised propagator and quantified the probability it bound occur

Adhesive for polyester films cures at room temperature, has high initial tack

Quick room-temperature-cure adhesive bonds polyester-insulated flat electrical cables to metal surfaces and various other substrates. The bond strength of the adhesive may be considerably increased by first applying a commercially available polyamide primer to the polyester film