Topology of RNA-RNA interaction structures

The topological filtration of interacting RNA complexes is studied and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that for two interacting RNAs, called interaction structures, there exist for fixed genus only finitely many irreducible shadows. This implies that for fixed genus there are only finitely many classes of interaction structures. In particular the simplest case of genus zero already provides the formalism for certain types of structures that occur in nature and are not covered by other filtrations. This case of genus zero interaction structures is already of practical interest, is studied here in detail and found to be expressed by a multiple context-free grammar extending the usual one for RNA secondary structures. We show that in $O(n^6)$ time and $O(n^4)$ space complexity, this grammar for genus zero interaction structures provides not only minimum free energy solutions but also the complete partition function and base pairing probabilities.Comment: 40 pages 15 figure

Computing topological invariants with one and two-matrix models

A generalization of the Kontsevich Airy-model allows one to compute the intersection numbers of the moduli space of p-spin curves. These models are deduced from averages of characteristic polynomials over Gaussian ensembles of random matrices in an external matrix source. After use of a duality, and of an appropriate tuning of the source, we obtain in a double scaling limit these intersection numbers as polynomials in p. One can then take the limit p to -1 which yields a matrix model for orbifold Euler characteristics. The generalization to a time-dependent matrix model, which is equivalent to a two-matrix model, may be treated along the same lines ; it also yields a logarithmic potential with additional vertices for general p.Comment: 30 pages, added references, changed conten

Precipitation changes in a GCM resulting from the indirect effects of anthropogenic aerosols

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94948/1/grl13844.pd

Structure and Dynamics of Metalloproteins in Live Cells

X-ray absorption spectroscopy (XAS) has emerged as one of the premier tools for investigating the structure and dynamic properties of metals in cells and in metal containing biomolecules. Utilizing the high flux and broad energy range of X-rays supplied by synchrotron light sources, one can selectively excite core electronic transitions in each metal. Spectroscopic signals from these electronic transitions can be used to dissect the chemical architecture of metals in cells, in cellular components and in biomolecules at varying degrees of structural resolution. With the development of ever-brighter X-ray sources, X-ray methods have grown into applications that can be utilized to provide both a cellular image of relative distribution of metals throughout the cell as well as a high-resolution picture of the structure of the metal. As these techniques continue to grow in their capabilities and ease of use, so to does the demand for their application by chemists and biochemists interested in studying the structure and dynamics of metals in cells, in cellular organelles and in metalloproteins

Global 2-D intercomparison of sectional and modal aerosol modules

International audienceWe present an intercomparison of several aerosol modules, sectional and modal, in a global 2-D model in order to differentiate their behavior for tropospheric and stratospheric applications. We model only binary sulfuric acid-water aerosols in this study. Three versions of the sectional model and three versions of the modal model are used to test the sensitivity of background aerosol mass and size distribution to the number of bins or modes and to the prescribed width of the largest mode. We find modest sensitivity to the number of bins (40 vs. 150) used in the sectional model. Aerosol mass is found to be reduced in a modal model if care is not taken in selecting the width of the largest lognormal mode, reflecting differences in sedimentation in the middle stratosphere. The size distributions calculated by the sectional model can be better matched by a modal model with four modes rather than three modes in most but not all situations. A simulation of aerosol decay following the 1991 eruption of Mt. Pinatubo shows that the representation of the size distribution can have a signficant impact on model-calculated aerosol decay rates in the stratosphere. Between 1991 and 1995, aerosol extinction and surface area density calculated by two versions of the modal model adequately match results from the sectional model. Calculated effective radius for the same time period shows more intermodel variability, with a 20-bin sectional model performing much better than any of the modal models

Lectures on the Asymptotic Expansion of a Hermitian Matrix Integral

In these lectures three different methods of computing the asymptotic expansion of a Hermitian matrix integral is presented. The first one is a combinatorial method using Feynman diagrams. This leads us to the generating function of the reciprocal of the order of the automorphism group of a tiling of a Riemann surface. The second method is based on the classical analysis of orthogonal polynomials. A rigorous asymptotic method is established, and a special case of the matrix integral is computed in terms of the Riemann $\zeta$-function. The third method is derived from a formula for the $\tau$-function solution to the KP equations. This method leads us to a new class of solutions of the KP equations that are \emph{transcendental}, in the sense that they cannot be obtained by the celebrated Krichever construction and its generalizations based on algebraic geometry of vector bundles on Riemann surfaces. In each case a mathematically rigorous way of dealing with asymptotic series in an infinite number of variables is established

Intersection numbers of Riemann surfaces from Gaussian matrix models

We consider a Gaussian random matrix theory in the presence of an external matrix source. This matrix model, after duality (a simple version of the closed/open string duality), yields a generalized Kontsevich model through an appropriate tuning of the external source. The n-point correlation functions of this theory are shown to provide the intersection numbers of the moduli space of curves with a p-spin structure, n marked points and top Chern class. This sheds some light on Witten's conjecture on the relationship with the pth-KdV equation

Eyes wide shut? UK consumer perceptions on aviation climate impacts and travel decisions to New Zealand

The purview of climate change concern has implicated air travel, as evidenced in a growing body of academic literature concerned with aviation CO2 emissions. This article assesses the relevance of climate change to long haul air travel decisions to New Zealand for United Kingdom consumers. Based on 15 semi-structured open-ended interviews conducted in Bournemouth, UK during June 2009, it was found that participants were unlikely to forgo potential travel decisions to New Zealand because of concern over air travel emissions. Underpinning the interviewees’ understandings and responses to air travel’s climate impact was a spectrum of awareness and attitudes to air travel and climate change. This spectrum ranged from individuals who were unaware of air travel’s climate impact to those who were beginning to consume air travel with a ‘carbon conscience’. Within this spectrum were some who were aware of the impact but not willing to change their travel behaviours at all. Rather than implicating long haul air travel, the empirical evidence instead exemplifies changing perceptions towards frequent short haul air travel and voices calls for both government and media in the UK to deliver more concrete messages on air travel’s climate impact

Topological closed-string interpretation of Chern-Simons theory

The exact free energy of SU($N$) Chern-Simons theory at level $k$ is expanded in powers of $(N+k)^{-2}.$ This expansion keeps rank-level duality manifest, and simplifies as $k$ becomes large, keeping $N$ fixed (or vice versa)---this is the weak-coupling (strong-coupling) limit. With the standard normalization, the free energy on the three-sphere in this limit is shown to be the generating function of the Euler characteristics of the moduli spaces of surfaces of genus $g,$ providing a string interpretation for the perturbative expansion. A similar expansion is found for the three-torus, with differences that shed light on contributions from different spacetime topologies in string theory.Comment: 6 pages, iassns-hep-93-30 (title change, omitted refs. added, two sign errors corrected, no significant change