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

Funnels in Energy Landscapes

Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a "folding funnel" that is concisely defined in terms of energy minima and saddle points, while at the same time conforming to a notion of a "folding funnel" as it is discussed in the protein folding literature.Comment: 6 pages, 3 figures, submitted to European Conference on Complex Systems 200

Reverse dark current in organic photodetectors and the major role of traps as source of noise

Organic photodetectors have promising applications in low-cost imaging, health monitoring and near-infrared sensing. Recent research on organic photodetectors based on donor–acceptor systems has resulted in narrow-band, flexible and biocompatible devices, of which the best reach external photovoltaic quantum efficiencies approaching 100%. However, the high noise spectral density of these devices limits their specific detectivity to around 1013 Jones in the visible and several orders of magnitude lower in the near-infrared, severely reducing performance. Here, we show that the shot noise, proportional to the dark current, dominates the noise spectral density, demanding a comprehensive understanding of the dark current. We demonstrate that, in addition to the intrinsic saturation current generated via charge-transfer states, dark current contains a major contribution from trap-assisted generated charges and decreases systematically with decreasing concentration of traps. By modeling the dark current of several donor–acceptor systems, we reveal the interplay between traps and charge-transfer states as source of dark current and show that traps dominate the generation processes, thus being the main limiting factor of organic photodetectors detectivity

ViennaRNA Package 2.0

<p>Abstract</p> <p>Background</p> <p>Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties.</p> <p>Results</p> <p>The <monospace>ViennaRNA</monospace> Package has been a widely used compilation of RNA secondary structure related computer programs for nearly two decades. Major changes in the structure of the standard energy model, the <it>Turner 2004 </it>parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic variants prompted a major technical overhaul of both the underlying <monospace>RNAlib</monospace> and the interactive user programs. New features include an expanded repertoire of tools to assess RNA-RNA interactions and restricted ensembles of structures, additional output information such as <it>centroid </it>structures and <it>maximum expected accuracy </it>structures derived from base pairing probabilities, or <it>z</it>-<it>scores </it>for locally stable secondary structures, and support for input in <monospace>fasta</monospace> format. Updates were implemented without compromising the computational efficiency of the core algorithms and ensuring compatibility with earlier versions.</p> <p>Conclusions</p> <p>The <monospace>ViennaRNA Package 2.0</monospace>, supporting concurrent computations <monospace>via OpenMP</monospace>, can be downloaded from <url>http://www.tbi.univie.ac.at/RNA</url>.</p

Understanding the errors of SHAPE-directed RNA structure modeling

Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms. Recent tests have shown that selective 2'-hydroxyl acylation by primer extension (SHAPE) can give near-zero error rates (0-2%) in modeling the helices of RNA secondary structure. Here, we benchmark the method using six molecules for which crystallographic data are available: tRNA(phe) and 5S rRNA from Escherichia coli, the P4-P6 domain of the Tetrahymena group I ribozyme, and ligand-bound domains from riboswitches for adenine, cyclic di-GMP, and glycine. SHAPE-directed modeling of these highly structured RNAs gave an overall false negative rate (FNR) of 17% and a false discovery rate (FDR) of 21%, with at least one helix prediction error in five of the six cases. Extensive variations of data processing, normalization, and modeling parameters did not significantly mitigate modeling errors. Only one varation, filtering out data collected with deoxyinosine triphosphate during primer extension, gave a modest improvement (FNR = 12%, and FDR = 14%). The residual structure modeling errors are explained by the insufficient information content of these RNAs' SHAPE data, as evaluated by a nonparametric bootstrapping analysis. Beyond these benchmark cases, bootstrapping suggests a low level of confidence (<50%) in the majority of helices in a previously proposed SHAPE-directed model for the HIV-1 RNA genome. Thus, SHAPE-directed RNA modeling is not always unambiguous, and helix-by-helix confidence estimates, as described herein, may be critical for interpreting results from this powerful methodology.Comment: Biochemistry, Article ASAP (Aug. 15, 2011

Louse (Insecta : Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable

Lice are ectoparasitic insects hosted by birds and mammals. Mitochondrial 12S rRNA sequences obtained from lice show considerable length variation and are very difficult to align. We show that the louse 12S rRNA domain III secondary structure displays considerable variation compared to other insects, in both the shape and number of stems and loops. Phylogenetic trees constructed from tree edit distances between louse 12S rRNA structures do not closely resemble trees constructed from sequence data, suggesting that at least some of this structural variation has arisen independently in different louse lineages. Taken together with previous work on mitochondrial gene order and elevated rates of substitution in louse mitochondrial sequences, the structural variation in louse 12S rRNA confirms the highly distinctive nature of molecular evolution in these insects

Statistical mechanics of secondary structures formed by random RNA sequences

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical studies. First, a two-replica calculation is performed. By mapping the two-replica problem to the denaturation of a single homogeneous RNA in 6-dimensional embedding space, we show that sequence disorder is perturbatively irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten phase where many secondary structures with comparable total energy coexist. A numerical study of various models at high temperature reproduces behaviors characteristic of the molten phase. On the other hand, a scaling argument based on the extremal statistics of rare regions can be constructed to show that the low temperature phase is unstable to sequence disorder. We performed a detailed numerical study of the low temperature phase using the droplet theory as a guide, and characterized the statistics of large-scale, low-energy excitations of the secondary structures from the ground state structure. We find the excitation energy to grow very slowly (i.e., logarithmically) with the length scale of the excitation, suggesting the existence of a marginal glass phase. The transition between the low temperature glass phase and the high temperature molten phase is also characterized numerically. It is revealed by a change in the coefficient of the logarithmic excitation energy, from being disorder dominated to entropy dominated.Comment: 24 pages, 16 figure

Phase-field models for brittle and cohesive fracture

In this paper we first recapitulate some basic notions of brittle and cohesive fracture models, as well as the phase-field approximation to fracture. Next, a critical assessment is made of the sensitivity of the phase-field approach to brittle fracture, in particular the degradation function, and the use of monolithic versus partitioned solution schemes. The last part of the paper makes extensions to a recently developed phase-field model for cohesive fracture, in particular for propagating cracks. Using some simple examples the current state of the cohesive phase-field model is shown