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

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

CentroidFold: a web server for RNA secondary structure prediction

The CentroidFold web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine. The server accepts two kinds of sequence data: a single RNA sequence and a multiple alignment of RNA sequences. It responses with a prediction result shown as a popular base-pair notation and a graph representation. PDF version of the graph representation is also available. For a multiple alignment sequence, the server predicts a common secondary structure. Usage of the server is quite simple. You can paste a single RNA sequence (FASTA or plain sequence text) or a multiple alignment (CLUSTAL-W format) into the textarea then click on the ‘execute CentroidFold’ button. The server quickly responses with a prediction result. The major advantage of this server is that it employs our original CentroidFold software as its prediction engine which scores the best accuracy in our benchmark results. Our web server is freely available with no login requirement

Quality analysis of fresh and dried mangoes

[EN] Organic acids, sugar and colour define the quality and the taste of mangoes. The quality deteriorates during drying on a single-layer-dryer. Quality losses can be reduced by using drying parameters that influence the quality less. In this research, the contents of ascorbic acid, organic acids and sugar as well as colour changes and shrinkage are analysed. Analyses are carried out at different temperatures, dew point temperatures and air velocities using HPLC, IC and UV/Vis- spectrometry. The quality criteria showed the lowest changes at a temperature of 60°C, dew point temperature of 20°C and an air velocity of 0.9 m/s.The underlying RELOAD-Project for this report is funded by the German Federal Ministry of Education and Research, grant number 031A247C. The responsibility for the content of this publication lies with the author.Arendt, S.; Jodicke, K.; Hofacker, W.; Speckle, W. (2018). Quality analysis of fresh and dried mangoes. En IDS 2018. 21st International Drying Symposium Proceedings. Editorial Universitat Politècnica de València. 1591-1598. https://doi.org/10.4995/IDS2018.2018.7526OCS1591159

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

Structural parameters affecting the kinetics of RNA hairpin formation

There is little experimental knowledge on the sequence dependent rate of hairpin formation in RNA. We have therefore designed RNA sequences that can fold into either of two mutually exclusive hairpins and have determined the ratio of folding of the two conformations, using structure probing. This folding ratio reflects their respective folding rates. Changing one of the two loop sequences from a purine- to a pyrimidine-rich loop did increase its folding rate, which corresponds well with similar observations in DNA hairpins. However, neither changing one of the loops from a regular non-GNRA tetra-loop into a stable GNRA tetra-loop, nor increasing the loop size from 4 to 6 nt did affect the folding rate. The folding kinetics of these RNAs have also been simulated with the program ‘Kinfold’. These simulations were in agreement with the experimental results if the additional stabilization energies for stable tetra-loops were not taken into account. Despite the high stability of the stable tetra-loops, they apparently do not affect folding kinetics of these RNA hairpins. These results show that it is possible to experimentally determine relative folding rates of hairpins and to use these data to improve the computer-assisted simulation of the folding kinetics of stem–loop structures