805 research outputs found
Issues associated with telerobotic systems in space
Research issues in using telerobotics in space are discussed. Included is a review of previous research in space telerobotics and the results of several telerobotics experiments
The Vienna RNA Websuite
The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides a web interface to the most commonly used programs of the Vienna RNA package. Among them, we find folding of single and aligned sequences, prediction of RNA–RNA interactions, and design of sequences with a given structure. Additionally, we provide analysis of folding landscapes using the barriers program and structural RNA alignments using LocARNA. The web server together with software packages for download is freely accessible at http://rna.tbi.univie.ac.at/
Telerobotic Space Station Applications
This paper presents telerobotic space station applications, important issues in telerobotics and work at the University of Alabama in Huntsville in the area of telerobotics
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.
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 and a targeted
distribution in of its \emph{distinguished} atoms. We consider two
variations on this problem. In the first alternative, the targeted distribution
is given by real numbers \TargFreq_1, \ldots, \TargFreq_k such that 0 <
\TargFreq_i < 1 for all and \TargFreq_1+\cdots+\TargFreq_k \leq 1. We
aim to generate random structures among the whole set of structures of a given
size , 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 -tuple \Weights of real-valued weights, inducing a weighted
distribution over the set of structures of size . 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 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 . 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 -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 natural numbers such that
where is the number of undistinguished atoms.
The structures must be generated uniformly among the set of structures of size
that contain {\em exactly} atoms \At_i (). We give
a \bigO{r^2\prod_{i=1}^k n_i^2 +m n k \log n} algorithm for generating
structures, which simplifies into a \bigO{r\prod_{i=1}^k n_i +m n} for
regular specifications
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
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
R-Coffee: a web server for accurately aligning noncoding RNA sequences
The R-Coffee web server produces highly accurate multiple alignments of noncoding RNA (ncRNA) sequences, taking into account predicted secondary structures. R-Coffee uses a novel algorithm recently incorporated in the T-Coffee package. R-Coffee works along the same lines as T-Coffee: it uses pairwise or multiple sequence alignment (MSA) methods to compute a primary library of input alignments. The program then computes an MSA highly consistent with both the alignments contained in the library and the secondary structures associated with the sequences. The secondary structures are predicted using RNAplfold. The server provides two modes. The slow/accurate mode is restricted to small datasets (less than 5 sequences less than 150 nucleotides) and combines R-Coffee with Consan, a very accurate pairwise RNA alignment method. For larger datasets a fast method can be used (RM-Coffee mode), that uses R-Coffee to combine the output of the three packages which combines the outputs from programs found to perform best on RNA (MUSCLE, MAFFT and ProbConsRNA). Our BRAliBase benchmarks indicate that the R-Coffee/Consan combination is one of the best ncRNA alignment methods for short sequences, while the RM-Coffee gives comparable results on longer sequences. The R-Coffee web server is available at http://www.tcoffee.org
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