PARSEC: A Parametrized Simulation Engine for Ultra-High Energy Cosmic Ray Protons

We present a new simulation engine for fast generation of ultra-high energy cosmic ray data based on parametrizations of common assumptions of UHECR origin and propagation. Implemented are deflections in unstructured turbulent extragalactic fields, energy losses for protons due to photo-pion production and electron-pair production, as well as effects from the expansion of the universe. Additionally, a simple model to estimate propagation effects from iron nuclei is included. Deflections in galactic magnetic fields are included using a matrix approach with precalculated lenses generated from backtracked cosmic rays. The PARSEC program is based on object oriented programming paradigms enabling users to extend the implemented models and is steerable with a graphical user interface.Comment: 10 pages, 6 figures, accepted for publication in Astroparticle Physic

A System for Continuous Underground Site Mapping and Exploration

3D mapping becomes ever more important not only in industrial mobile robotic applications for AGV and production vehicles but also for search and rescue scenarios. In this chapter we report on our work of mapping and exploring underground mines. Our contribution is two-fold: First, we present our custom-built 3D laser range platform SWAP and compare it against an architectural laser scanner. The advantages are that the mapping vehicle can scan in a continuous mode and does not have to do stop-and-go scanning. The second contribution is the mapping tool mapit which supports and automates the registration of large sets of point clouds. The idea behind mapit is to keep the raw point cloud data as a basis for any map generation and only store all operations executed on the point clouds. This way the initial data do not get lost, and improvements on low-level date (e.g. improved transforms through loop closure) will automatically improve the final maps. Finally, we also present methods for visualization and interactive exploration of such maps

CRPropa 3.0 - a Public Framework for Propagating UHE Cosmic Rays through Galactic and Extragalactic Space

The interpretation of experimental data of ultra-high energy cosmic rays (UHECRs) above 10^17 eV is still under controversial debate. The development and improvement of numerical tools to propagate UHECRs in galactic and extragalactic space is a crucial ingredient to interpret data and to draw conclusions on astrophysical parameters. In this contribution the next major release of the publicly available code CRPropa (3.0) is presented. It reflects a complete redesign of the code structure to facilitate high performance computing and comprises new physical features such as an interface for galactic propagation using lensing techniques and inclusion of cosmological effects in a three-dimensional environment. The performance is benchmarked and first applications are presented.Comment: 4 pages, 3 figures. Proceedings of the 33rd International Cosmic Ray Conference (ICRC), Rio de Janeiro, Brazil, 2-9 July 201

"What's (the) Matter?", A Show on Elementary Particle Physics with 28 Demonstration Experiments

We present the screenplay of a physics show on particle physics, by the Physikshow of Bonn University. The show is addressed at non-physicists aged 14+ and communicates basic concepts of elementary particle physics including the discovery of the Higgs boson in an entertaining fashion. It is also demonstrates a successful outreach activity heavily relying on the university physics students. This paper is addressed at anybody interested in particle physics and/or show physics. This paper is also addressed at fellow physicists working in outreach, maybe the experiments and our choice of simple explanations will be helpful. Furthermore, we are very interested in related activities elsewhere, in particular also demonstration experiments relevant to particle physics, as often little of this work is published. Our show involves 28 live demonstration experiments. These are presented in an extensive appendix, including photos and technical details. The show is set up as a quest, where 2 students from Bonn with the aid of a caretaker travel back in time to understand the fundamental nature of matter. They visit Rutherford and Geiger in Manchester around 1911, who recount their famous experiment on the nucleus and show how particle detectors work. They travel forward in time to meet Lawrence at Berkeley around 1950, teaching them about the how and why of accelerators. Next, they visit Wu at DESY, Hamburg, around 1980, who explains the strong force. They end up in the LHC tunnel at CERN, Geneva, Switzerland in 2012. Two experimentalists tell them about colliders and our heroes watch live as the Higgs boson is produced and decays. The show was presented in English at Oxford University and University College London, as well as Padua University and ICTP Trieste. It was 1st performed in German at the Deutsche Museum, Bonn (5/'14). The show has eleven speaking parts and involves in total 20 people.Comment: 113 pages, 88 figures. An up to date version of the paper with high resolution pictures can be found at http://www.th.physik.uni-bonn.de/People/dreiner/Downloads/. In v2 the acknowledgements and a citation are correcte

Def-6, a Novel Regulator of Small GTPases in Podocytes, Acts Downstream of Atypical Protein Kinase C (aPKC) λ/ι

Supplemental Data Supplemental Figure S1 Characterization of WT and aPKC-deficient podocytes. A–C: Genomic DNA isolated from deficient and control cell lines was tested for the presence of Cre recombinase (A), floxed and WT alleles of PKCλ/ι (B), or WT and knockout alleles of PKCζ (C). As controls, genomic DNA samples of tail biopsies were used. D: Differentiated deficient or control cells were stained with antibodies against synaptopodin or WT-1. All used cell lines were positive for the tested podocyte markers. Scale bars = 50 μm. Download Supplemental Figure S2 Relative mRNA and protein expression of PKCλ/ι, PKCζ, and Def-6 in deficient and control podocytes. A–C: Real-time PCR measurements and Western blot analysis of PKCλ/ι- and PKCζ-deficient cells in comparison with control cells. A: PKCλ/ι mRNA and protein are reduced in the PKCλ/ι −/− cells. B: PKCζ mRNA and protein are reduced in the PKCζ −/− cells. C: Def-6 mRNA is up-regulated in the PKCλ/ι −/− cells but not in PKCζ −/− cells. mRNA level is normalized for HPRT-1. Def-6 protein expression is not changed. ∗∗P < 0.01. Download Supplemental Table S1 Download Supplemental Table S2 Download Supplemental Table S3 Download Supplemental Table S4 Download Supplemental Table S5 Download Supplemental Table S6 Download Supplemental Table S7 Download Supplemental Table S8 Download Supplemental Data Supplemental material for this article can be found at . The atypical protein kinase C (aPKC) isotypes PKCλ/ι and PKCζ are both expressed in podocytes; however, little is known about differences in their function. Previous studies in mice have demonstrated that podocyte-specific loss of PKCλ/ι leads to a severe glomerular phenotype, whereas mice deficient in PKCζ develop no renal phenotype. We analyzed various effects caused by PKCλ/ι and PKCζ deficiency in cultured murine podocytes. In contrast to PKCζ-deficient podocytes, PKCλ/ι-deficient podocytes exhibited a severe actin cytoskeletal phenotype, reduced cell size, decreased number of focal adhesions, and increased activation of small GTPases. Comparative microarray analysis revealed that the guanine nucleotide exchange factor Def-6 was specifically up-regulated in PKCλ/ι-deficient podocytes. In vivo Def-6 expression is significantly increased in podocytes of PKCλ/ι-deficient mice. Cultured PKCλ/ι-deficient podocytes exhibited an enhanced membrane association of Def-6, indicating enhanced activation. Overexpression of aPKCλ/ι in PKCλ/ι-deficient podocytes could reduce the membrane-associated expression of Def-6 and rescue the actin phenotype. In the present study, PKCλ/ι was identified as an important factor for actin cytoskeletal regulation in podocytes and Def-6 as a specific downstream target of PKCλ/ι that regulates the activity of small GTPases and subsequently the actin cytoskeleton of podocytes

Measurement of the cosmic ray spectrum above 4×10184{\times}10^{18} eV using inclined events detected with the Pierre Auger Observatory

A measurement of the cosmic-ray spectrum for energies exceeding $4{\times}10^{18}$ eV is presented, which is based on the analysis of showers with zenith angles greater than $60^{\circ}$ detected with the Pierre Auger Observatory between 1 January 2004 and 31 December 2013. The measured spectrum confirms a flux suppression at the highest energies. Above $5.3{\times}10^{18}$ eV, the "ankle", the flux can be described by a power law $E^{-\gamma}$ with index $\gamma=2.70 \pm 0.02 \,\text{(stat)} \pm 0.1\,\text{(sys)}$ followed by a smooth suppression region. For the energy ($E_\text{s}$) at which the spectral flux has fallen to one-half of its extrapolated value in the absence of suppression, we find $E_\text{s}=(5.12\pm0.25\,\text{(stat)}^{+1.0}_{-1.2}\,\text{(sys)}){\times}10^{19}$ eV.Comment: Replaced with published version. Added journal reference and DO

Optimization of a new score function for the detection of remote homologs

The growth in protein sequence data has placed a premium on ways to infer structure and function of the newly sequenced proteins. One of the most effective ways is to identify a homologous relationship with a protein about which more is known. While close evolutionary relationships can be confidently determined with standard methods, the difficulty increases as the relationships become more distant. All of these methods rely on some score function to measure sequence similarity. The choice of score function is especially critical for these distant relationships. We describe a new method of determining a score function, optimizing the ability to discriminate between homologs and non-homologs. We find that this new score function performs better than standard score functions for the identification of distant homologies. Proteins 2000;41:498–503. © 2000 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34972/1/70_ftp.pd

The effect of the geomagnetic field on cosmic ray energy estimates and large scale anisotropy searches on data from the Pierre Auger Observatory

We present a comprehensive study of the influence of the geomagnetic field on the energy estimation of extensive air showers with a zenith angle smaller than $60^\circ$, detected at the Pierre Auger Observatory. The geomagnetic field induces an azimuthal modulation of the estimated energy of cosmic rays up to the ~2% level at large zenith angles. We present a method to account for this modulation of the reconstructed energy. We analyse the effect of the modulation on large scale anisotropy searches in the arrival direction distributions of cosmic rays. At a given energy, the geomagnetic effect is shown to induce a pseudo-dipolar pattern at the percent level in the declination distribution that needs to be accounted for.Comment: 20 pages, 14 figure