R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

<p>Abstract</p> <p>Background</p> <p>With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams.</p> <p>Results</p> <p>We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes.</p> <p>Conclusions</p> <p>R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at <url>http://breaker.research.yale.edu/R2R</url> and as an Additional file.</p

Information-theoretic postulates for quantum theory

Why are the laws of physics formulated in terms of complex Hilbert spaces? Are there natural and consistent modifications of quantum theory that could be tested experimentally? This book chapter gives a self-contained and accessible summary of our paper [New J. Phys. 13, 063001, 2011] addressing these questions, presenting the main ideas, but dropping many technical details. We show that the formalism of quantum theory can be reconstructed from four natural postulates, which do not refer to the mathematical formalism, but only to the information-theoretic content of the physical theory. Our starting point is to assume that there exist physical events (such as measurement outcomes) that happen probabilistically, yielding the mathematical framework of "convex state spaces". Then, quantum theory can be reconstructed by assuming that (i) global states are determined by correlations between local measurements, (ii) systems that carry the same amount of information have equivalent state spaces, (iii) reversible time evolution can map every pure state to every other, and (iv) positivity of probabilities is the only restriction on the possible measurements.Comment: 17 pages, 3 figures. v3: some typos corrected and references updated. Summarizes the argumentation and results of arXiv:1004.1483. Contribution to the book "Quantum Theory: Informational Foundations and Foils", Springer Verlag (http://www.springer.com/us/book/9789401773027), 201

Fluids in cosmology

We review the role of fluids in cosmology by first introducing them in General Relativity and then by applying them to a FRW Universe's model. We describe how relativistic and non-relativistic components evolve in the background dynamics. We also introduce scalar fields to show that they are able to yield an inflationary dynamics at very early times (inflation) and late times (quintessence). Then, we proceed to study the thermodynamical properties of the fluids and, lastly, its perturbed kinematics. We make emphasis in the constrictions of parameters by recent cosmological probes.Comment: 34 pages, 4 figures, version accepted as invited review to the book "Computational and Experimental Fluid Mechanics with Applications to Physics, Engineering and the Environment". Version 2: typos corrected and references expande

Duality Invariant Actions and Generalised Geometry

We construct the non-linear realisation of the semi-direct product of E(11) and its first fundamental representation at lowest order and appropriate to spacetime dimensions four to seven. This leads to a non-linear realisation of the duality groups and introduces fields that depend on a generalised space which possess a generalised vielbein. We focus on the part of the generalised space on which the duality groups alone act and construct an invariant action.Comment: 59 pages (typos fixed and added comments

Neutron Electric Dipole Moment Constraint on Scale of Minimal Left-Right Symmetric Model

Using an effective theory approach, we calculate the neutron electric dipole moment (nEDM) in the minimal left-right symmetric model with both explicit and spontaneous CP violations. We integrate out heavy particles to obtain flavor-neutral CP-violating effective Lagrangian. We run the Wilson coefficients from the electroweak scale to the hadronic scale using one-loop renormalization group equations. Using the state-of-the-art hadronic matrix elements, we obtain the nEDM as a function of right-handed W-boson mass and CP-violating parameters. We use the current limit on nEDM combined with the kaon-decay parameter $\epsilon$ to provide the most stringent constraint yet on the left-right symmetric scale $M_{W_R} > (10 \pm 3)$ TeV.Comment: 20 pages and 8 figure

The Overall Coefficient of the Two-loop Superstring Amplitude Using Pure Spinors

Using the results recently obtained for computing integrals over (non-minimal) pure spinor superspace, we compute the coefficient of the massless two-loop four-point amplitude from first principles. Contrasting with the mathematical difficulties in the RNS formalism where unknown normalizations of chiral determinant formulae force the two-loop coefficient to be determined only indirectly through factorization, the computation in the pure spinor formalism can be smoothly carried out.Comment: 29 pages, harvmac TeX. v2: add reference

Effective action in a higher-spin background

We consider a free massless scalar field coupled to an infinite tower of background higher-spin gauge fields via minimal coupling to the traceless conserved currents. The set of Abelian gauge transformations is deformed to the non-Abelian group of unitary operators acting on the scalar field. The gauge invariant effective action is computed perturbatively in the external fields. The structure of the various (divergent or finite) terms is determined. In particular, the quadratic part of the logarithmically divergent (or of the finite) term is expressed in terms of curvatures and related to conformal higher-spin gravity. The generalized higher-spin Weyl anomalies are also determined. The relation with the theory of interacting higher-spin gauge fields on anti de Sitter spacetime via the holographic correspondence is discussed.Comment: 40 pages, Some errors and typos corrected, Version published in JHE

Measuring our universe from galaxy redshift surveys

Galaxy redshift surveys have achieved significant progress over the last couple of decades. Those surveys tell us in the most straightforward way what our local universe looks like. While the galaxy distribution traces the bright side of the universe, detailed quantitative analyses of the data have even revealed the dark side of the universe dominated by non-baryonic dark matter as well as more mysterious dark energy (or Einstein's cosmological constant). We describe several methodologies of using galaxy redshift surveys as cosmological probes, and then summarize the recent results from the existing surveys. Finally we present our views on the future of redshift surveys in the era of Precision Cosmology.Comment: 82 pages, 31 figures, invited review article published in Living Reviews in Relativity, http://www.livingreviews.org/lrr-2004-