TY - JOUR A1 - Gutheil, Inge A1 - Berg, Tommy A1 - Grotendorst, Johannes T1 - Performance Analysis of Parallel Eigensolvers of two Libraries on BlueGene/P JF - Journal of Mathematics and Systems Science N2 - Many applications in computational science and engineering require the computation of eigenvalues and vectors of dense symmetric or Hermitian matrices. For example, in DFT (density functional theory) calculations on modern supercomputers 10% to 30% of the eigenvalues and eigenvectors of huge dense matrices have to be calculated. Therefore, performance and parallel scaling of the used eigensolvers is of upmost interest. In this article different routines of the linear algebra packages ScaLAPACK and Elemental for parallel solution of the symmetric eigenvalue problem are compared concerning their performance on the BlueGene/P supercomputer. Parameters for performance optimization are adjusted for the different data distribution methods used in the two libraries. It is found that for all test cases the new library Elemental which uses a two-dimensional element by element distribution of the matrices to the processors shows better performance than the old ScaLAPACK library which uses a block-cyclic distribution. KW - performance analysis KW - Elemental KW - ScaLAPACK KW - eigensolvers KW - Numerical linear algebra Y1 - 2012 U6 - https://doi.org/10.17265/2159-5291/2012.04.003 SN - 2159-5291 VL - 2 IS - 4 SP - 231 EP - 236 PB - David Publishing CY - Libertyville ER - TY - JOUR A1 - Grotendorst, Johannes T1 - IAS Winter School: Hierarchical Methods for Dynamics in Complex Molecular Systems JF - Innovatives Supercomputing in Deutschland : inSiDE. 10 (2012), H. 1 Y1 - 2012 SP - 104 PB - - ER - TY - JOUR A1 - Grinsven, Bart van A1 - Bon, Natalie vanden A1 - Strauven, Hannelore A1 - Grieten, Lars A1 - Murib, Mohammed A1 - Jiménez Monroy, Kathia L. A1 - Janssens, Stoffel D. A1 - Haenen, Ken A1 - Schöning, Michael Josef A1 - Vermeeren, Veronique A1 - Ameloot, Marcel A1 - Michiels, Luc A1 - Thoelen, Ronald A1 - Ceuninck, Ward de A1 - Wagner, Patrick T1 - Heat-Transfer Resistance at Solid-Liquid Interfaces: A Tool for The Detection of Single Nucleotide Polymorphisms in DNA. JF - ACS Nano N2 - In this article, we report on the heat-transfer resistance at interfaces as a novel, denaturation-based method to detect single-nucleotide polymorphisms in DNA. We observed that a molecular brush of double-stranded DNA grafted onto synthetic diamond surfaces does not notably affect the heat-transfer resistance at the solid-to-liquid interface. In contrast to this, molecular brushes of single-stranded DNA cause, surprisingly, a substantially higher heat-transfer resistance and behave like a thermally insulating layer. This effect can be utilized to identify ds-DNA melting temperatures via the switching from low- to high heat-transfer resistance. The melting temperatures identified with this method for different DNA duplexes (29 base pairs without and with built-in mutations) correlate nicely with data calculated by modeling. The method is fast, label-free (without the need for fluorescent or radioactive markers), allows for repetitive measurements, and can also be extended toward array formats. Reference measurements by confocal fluorescence microscopy and impedance spectroscopy confirm that the switching of heat-transfer resistance upon denaturation is indeed related to the thermal on-chip denaturation of DNA. Y1 - 2012 U6 - https://doi.org/10.1021/nn300147e SN - 1936-086X VL - 6 IS - 3 SP - 2712 EP - 2721 PB - ACS Publications CY - Washington, DC ER - TY - JOUR A1 - Grande, Marion A1 - Meffert, Elisabeth A1 - Schoenberger, Eva A1 - Jung, Stefanie A1 - Frauenrath, Tobias A1 - Huber, Walter A1 - Hussmann, Katja A1 - Moormann, Mareike A1 - Heim, Stefan T1 - From a concept to a word in a syntactically complete sentence: An fMRI study on spontaneous language production in an overt picture description task JF - NeuroImage N2 - Spontaneous language has rarely been subjected to neuroimaging studies. This study therefore introduces a newly developed method for the analysis of linguistic phenomena observed in continuous language production during fMRI. Most neuroimaging studies investigating language have so far focussed on single word or — to a smaller extent — sentence processing, mostly due to methodological considerations. Natural language production, however, is far more than the mere combination of words to larger units. Therefore, the present study aimed at relating brain activation to linguistic phenomena like word-finding difficulties or syntactic completeness in a continuous language fMRI paradigm. A picture description task with special constraints was used to provoke hesitation phenomena and speech errors. The transcribed speech sample was segmented into events of one second and each event was assigned to one category of a complex schema especially developed for this purpose. The main results were: conceptual planning engages bilateral activation of the precuneus. Successful lexical retrieval is accompanied – particularly in comparison to unsolved word-finding difficulties – by the left middle and superior temporal gyrus. Syntactic completeness is reflected in activation of the left inferior frontal gyrus (IFG) (area 44). In sum, the method has proven to be useful for investigating the neural correlates of lexical and syntactic phenomena in an overt picture description task. This opens up new prospects for the analysis of spontaneous language production during fMRI. Y1 - 2012 U6 - https://doi.org/10.1016/j.neuroimage.2012.03.087 SN - 1522-2586 VL - 61 IS - 3 SP - 702 EP - 714 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Frauenrath, Tobias A1 - Fuchs, Katharina A1 - Dieringer, Matthias A. A1 - Özerdem, Celal A1 - Patel, Nishan A1 - Renz, Wolfgang A1 - Greiser, Andreas A1 - Elgeti, Thomas A1 - Niendorf, Thoralf T1 - Detailing the use of magnetohydrodynamic effects for synchronization of MRI with the cardiac cycle: A feasibility study JF - Journal of Magnetic Resonance Imaging N2 - Purpose: To investigate the feasibility of using magnetohydrodynamic (MHD) effects for synchronization of magnetic resonance imaging (MRI) with the cardiac cycle. Materials and Methods: The MHD effect was scrutinized using a pulsatile flow phantom at B0 = 7.0 T. MHD effects were examined in vivo in healthy volunteers (n = 10) for B0 ranging from 0.05–7.0 T. Noncontrast-enhanced MR angiography (MRA) of the carotids was performed using a gated steady-state free-precession (SSFP) imaging technique in conjunction with electrocardiogram (ECG) and MHD synchronization. Results: The MHD potential correlates with flow velocities derived from phase contrast MRI. MHD voltages depend on the orientation between B0 and the flow of a conductive fluid. An increase in the interelectrode spacing along the flow increases the MHD potential. In vivo measurement of the MHD effect provides peak voltages of 1.5 mV for surface areas close to the common carotid artery at B0 = 7.0 T. Synchronization of MRI with the cardiac cycle using MHD triggering is feasible. MHD triggered MRA of the carotids at 3.0 T showed an overall image quality and richness of anatomic detail, which is comparable to ECG-triggered MRAs. Conclusion: This feasibility study demonstrates the use of MHD effects for synchronization of MR acquisitions with the cardiac cycle. J. Magn. Reson. Imaging 2012;36:364–372. © 2012 Wiley Periodicals, Inc. Y1 - 2012 U6 - https://doi.org/10.1002/jmri.23634 SN - 1522-2586 VL - 36 IS - 2 SP - 364 EP - 372 PB - Wiley-Liss CY - New York ER - TY - JOUR A1 - Fischer, Jan-Thomas A1 - Kowalski, Julia A1 - Pudasaini, Shiva P. T1 - Topographic curvature effects in applied avalanche modelling JF - Cold Regions Science and Technology N2 - This paper describes the implementation of topographic curvature effects within the RApid Mass MovementS (RAMMS) snow avalanche simulation toolbox. RAMMS is based on a model similar to shallow water equations with a Coulomb friction relation and the velocity dependent Voellmy drag. It is used for snow avalanche risk assessment in Switzerland. The snow avalanche simulation relies on back calculation of observed avalanches. The calibration of the friction parameters depends on characteristics of the avalanche track. The topographic curvature terms are not yet included in the above mentioned classical model. Here, we fundamentally improve this model by mathematically and physically including the topographic curvature effects. By decomposing the velocity dependent friction into a topography dependent term that accounts for a curvature enhancement in the Coulomb friction, and a topography independent contribution similar to the classical Voellmy drag, we construct a general curvature dependent frictional resistance, and thus propose new extended model equations. With three site-specific examples, we compare the apparent frictional resistance of the new approach, which includes topographic curvature effects, to the classical one. Our simulation results demonstrate substantial effects of the curvature on the flow dynamics e.g., the dynamic pressure distribution along the slope. The comparison of resistance coefficients between the two models demonstrates that the physically based extension presents an improvement to the classical approach. Furthermore a practical example highlights its influence on the pressure outline in the run out zone of the avalanche. Snow avalanche dynamics modeling natural terrain curvature centrifugal force friction coefficients. KW - Snow KW - Avalanche Y1 - 2012 U6 - https://doi.org/10.1016/j.coldregions.2012.01.005 SN - 1872-7441 VL - 74-75 SP - 21 EP - 30 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Ferrein, Alexander A1 - Steinbauer, Gerald A1 - Vassos, Stavros T1 - Action-Based Imperative Programming with YAGI N2 - Many tasks for autonomous agents or robots are best described by a specification of the environment and a specification of the available actions the agent or robot can perform. Combining such a specification with the possibility to imperatively program a robot or agent is what we call the actionbased imperative programming. One of the most successful such approaches is Golog. In this paper, we draft a proposal for a new robot programming language YAGI, which is based on the action-based imperative programming paradigm. Our goal is to design a small, portable stand-alone YAGI interpreter. We combine the benefits of a principled domain specification with a clean, small and simple programming language, which does not exploit any side-effects from the implementation language. We discuss general requirements of action-based programming languages and outline YAGI, our action-based language approach which particularly aims at embeddability. Y1 - 2012 N1 - Cognitive Robotics AAAI Technical Report WS-12-06 SP - 24 EP - 31 ER - TY - JOUR A1 - Ferrein, Alexander A1 - Meyer, Thomas T1 - A Brief Overview of Artificial Intelligence in South Africa JF - AI Magazine N2 - South Africa in recent years is the establishment of a number of research hubs involved in AI activities ranging from mobile robotics and computational intelligence, to knowledge representation and reasoning, and human language technologies. In this survey we take the reader through a quick tour of the research being conducted at these hubs, and touch on an initiative to maintain and extend the current level of interest in AI research in the country. Y1 - 2012 U6 - https://doi.org/10.1609/aimag.v33i1.2357 SN - 0738-4602 VL - 33 IS - 1 SP - 99 EP - 101 PB - AAAI CY - Menlo Park ER - TY - JOUR A1 - Fateri, Miranda A1 - Hötter, Jan-Steffen A1 - Gebhardt, Andreas T1 - Experimental and Theoretical Investigation of Buckling Deformation of Fabricated Objects by Selective Laser Melting JF - Physics Procedia N2 - Although Selective Laser Melting (SLM) process is an innovative manufacturing method, there are challenges such as inferior mechanical properties of fabricated objects. Regarding this, buckling deformation which is caused by thermal stress is one of the undesired mechanical properties which must be alleviated. As buckling deformation is more observable in hard to process materials, silver is selected to be studied theoretically and experimentally for this paper. Different scanning strategies are utilized and a Finite Element Method (FEM) is applied to calculate the temperature gradient in order to determine its effect on the buckling deformation of the objects from experiments. Y1 - 2012 U6 - https://doi.org/10.1016/j.phpro.2012.10.062 SN - 1875-3892 N1 - Part of special issue "Laser Assisted Net shape Engineering 7 (LANE 2012)" VL - 39 SP - 464 EP - 470 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Eilmann, Britta A1 - Rigling, Andreas ED - Abrams, Marc T1 - Tree-growth analyses to estimate tree species' drought tolerance JF - Tree Physiology N2 - Climate change is challenging forestry management and practices. Among other things, tree species with the ability to cope with more extreme climate conditions have to be identified. However, while environmental factors may severely limit tree growth or even cause tree death, assessing a tree species' potential for surviving future aggravated environmental conditions is rather demanding. The aim of this study was to find a tree-ring-based method suitable for identifying very drought-tolerant species, particularly potential substitute species for Scots pine (Pinus sylvestris L.) in Valais. In this inner-Alpine valley, Scots pine used to be the dominating species for dry forests, but today it suffers from high drought-induced mortality. We investigate the growth response of two native tree species, Scots pine and European larch (Larix decidua Mill.), and two non-native species, black pine (Pinus nigra Arnold) and Douglas fir (Pseudotsuga menziesii Mirb. var. menziesii), to drought. This involved analysing how the radial increment of these species responded to increasing water shortage (abandonment of irrigation) and to increasingly frequent drought years. Black pine and Douglas fir are able to cope with drought better than Scots pine and larch, as they show relatively high radial growth even after irrigation has been stopped and a plastic growth response to drought years. European larch does not seem to be able to cope with these dry conditions as it lacks the ability to recover from drought years. The analysis of trees' short-term response to extreme climate events seems to be the most promising and suitable method for detecting how tolerant a tree species is towards drought. However, combining all the methods used in this study provides a complete picture of how water shortage could limit species. Y1 - 2012 U6 - https://doi.org/10.1093/treephys/tps004 SN - 0829-318X (Print) SN - 1758-4469 (Online) VL - 32 IS - 2 SP - 178 EP - 187 PB - Oxford University Press CY - Oxford ER -