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.

Qualification Tests of 474 Photomultiplier Tubes for the Inner Detector of the Double Chooz Experiment

The hemispherical 10" photomultiplier tube (PMT) R7081 from Hamamatsu Photonics K.K. (HPK) is used in various experiments in particle and astroparticle physics. We describe the test and calibration of 474 PMTs for the reactor antineutrino experiment Double Chooz. The unique test setup at Max-Planck-Institut f\"ur Kernphysik Heidelberg (MPIK) allows one to calibrate 30 PMTs simultaneously and to characterize the single photo electron response, transit time spread, linear behaviour and saturation effects, photon detection efficiency and high voltage calibration

Qualification Tests of 474 Photomultiplier Tubes for the Inner Detector of the Double Chooz Experiment

The hemispherical 10" photomultiplier tube (PMT) R7081 from Hamamatsu Photonics K.K. (HPK) is used in various experiments in particle and astroparticle physics. We describe the test and calibration of 474 PMTs for the reactor antineutrino experiment Double Chooz. The unique test setup at Max-Planck-Institut f\"ur Kernphysik Heidelberg (MPIK) allows one to calibrate 30 PMTs simultaneously and to characterize the single photo electron response, transit time spread, linear behaviour and saturation effects, photon detection efficiency and high voltage calibration

Qualification Tests of 474 Photomultiplier Tubes for the Inner Detector of the Double Chooz Experiment

The hemispherical 10" photomultiplier tube (PMT) R7081 from Hamamatsu Photonics K.K. (HPK) is used in various experiments in particle and astroparticle physics. We describe the test and calibration of 474 PMTs for the reactor antineutrino experiment Double Chooz. The unique test setup at Max-Planck-Institut f\"ur Kernphysik Heidelberg (MPIK) allows one to calibrate 30 PMTs simultaneously and to characterize the single photo electron response, transit time spread, linear behaviour and saturation effects, photon detection efficiency and high voltage calibration

GIOVE, a shallow laboratory Ge-spectrometer with 100 μBq/kg sensitivity

A new germanium gamma spectrometer called GIOVE ( G ermanium spectrometer with I nner and O uter V eto) has been set up at the underground/shallow laboratory (15 m w.e.) of MPI-K. Its double plastic scintillator veto system and neutron moderation interlayer lower the background by more than one order of magnitude compared to the other existing spectrometer at this facility. The integral (40-2700 keV) background rate of about 290 counts (day kg)−1 is just a factor 4 to 8 above that of the GeMPI spectrometers operated at LNGS (3800 m w.e.) and thus proves that even under shallow overburden sub mBq/kg sensitivities are achievable. Extended material screening and neutron attenuation studies preceded the final design of the spectrometer. The technical realization of the spectrometer is described in detail with special emphasis on the inner veto system. For its optimisation a simulation model was developed for light collection on small low activity PMT’s under various geometrical conditions. Radon suppression is accomplished by employing a gas tight sample container and a nitrogen flushed glove-box system with an airlock. The active volume of the crystal was modelled by absorption scanning measurements and Monte Carlo simulations. The complete shield is implemented in a Geant4 based simulation framework

Controlled non uniform random generation of decomposable structures

Consider a class of decomposable combinatorial structures, using different types of atoms \Atoms = \{\At_1,\ldots ,\At_{|{\Atoms}|}\}. We address the random generation of such structures with respect to a size $n$ and a targeted distribution in $k$ of its \emph{distinguished} atoms. We consider two variations on this problem. In the first alternative, the targeted distribution is given by $k$ real numbers \TargFreq_1, \ldots, \TargFreq_k such that 0 < \TargFreq_i < 1 for all $i$ and \TargFreq_1+\cdots+\TargFreq_k \leq 1. We aim to generate random structures among the whole set of structures of a given size $n$, in such a way that the {\em expected} frequency of any distinguished atom \At_i equals \TargFreq_i. We address this problem by weighting the atoms with a $k$-tuple \Weights of real-valued weights, inducing a weighted distribution over the set of structures of size $n$. We first adapt the classical recursive random generation scheme into an algorithm taking \bigO{n^{1+o(1)}+mn\log{n}} arithmetic operations to draw $m$ structures from the \Weights-weighted distribution. Secondly, we address the analytical computation of weights such that the targeted frequencies are achieved asymptotically, i. e. for large values of $n$. We derive systems of functional equations whose resolution gives an explicit relationship between \Weights and \TargFreq_1, \ldots, \TargFreq_k. Lastly, we give an algorithm in \bigO{k n^4} for the inverse problem, {\it i.e.} computing the frequencies associated with a given $k$-tuple \Weights of weights, and an optimized version in \bigO{k n^2} in the case of context-free languages. This allows for a heuristic resolution of the weights/frequencies relationship suitable for complex specifications. In the second alternative, the targeted distribution is given by a $k$ natural numbers $n_1, \ldots, n_k$ such that $n_1+\cdots+n_k+r=n$ where $r \geq 0$ is the number of undistinguished atoms. The structures must be generated uniformly among the set of structures of size $n$ that contain {\em exactly} $n_i$ atoms \At_i ($1 \leq i \leq k$). We give a \bigO{r^2\prod_{i=1}^k n_i^2 +m n k \log n} algorithm for generating $m$ structures, which simplifies into a \bigO{r\prod_{i=1}^k n_i +m n} for regular specifications

RNA denaturation: excluded volume, pseudoknots and transition scenarios

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.Comment: 4 pages 3 figure

R-chie: a web server and R package for visualizing RNA secondary structures

Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R-chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems

RNAmute: RNA secondary structure mutation analysis tool

BACKGROUND: RNAMute is an interactive Java application that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their similarity with respect to the wild type predicted structure. The secondary structure predictions are performed using the Vienna RNA package. Several alternatives are used for the categorization of single point mutations: Vienna's RNAdistance based on dot-bracket representation, as well as tree edit distance and second eigenvalue of the Laplacian matrix based on Shapiro's coarse grain tree graph representation. RESULTS: Selecting a category in each one of the processed tables lists all single point mutations belonging to that category. Selecting a mutation displays a graphical drawing of the single point mutation and the wild type, and includes basic information such as associated energies, representations and distances. RNAMute can be used successfully with very little previous experience and without choosing any parameter value alongside the initial RNA sequence. The package runs under LINUX operating system. CONCLUSION: RNAMute is a user friendly tool that can be used to predict single point mutations leading to conformational rearrangements in the secondary structure of RNAs. In several cases of substantial interest, notably in virology, a point mutation may lead to a loss of important functionality such as the RNA virus replication and translation initiation because of a conformational rearrangement in the secondary structure

RNAalifold: improved consensus structure prediction for RNA alignments

<p>Abstract</p> <p>Background</p> <p>The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a set of aligned sequences, is one of the oldest and most widely used tools for this task. In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach.</p> <p>Results</p> <p>We show that the accuracy of RNAalifold predictions can be improved substantially by introducing a different, more rational handling of alignment gaps, and by replacing the rather simplistic model of covariance scoring with more sophisticated RIBOSUM-like scoring matrices. These improvements are achieved without compromising the computational efficiency of the algorithm. We show here that the new version of RNAalifold not only outperforms the old one, but also several other tools recently developed, on different datasets.</p> <p>Conclusion</p> <p>The new version of RNAalifold not only can replace the old one for almost any application but it is also competitive with other approaches including those based on SCFGs, maximum expected accuracy, or hierarchical nearest neighbor classifiers.</p