TY - JOUR A1 - Murib, Mohammed S. A1 - Tran, Anh Quang A1 - Ceuninck, Ward de A1 - Schöning, Michael Josef A1 - Nesladek, Milos A1 - Serpengüzel, Ali A1 - Wagner, Patrick T1 - Analysis of an optical biosensor based on elastic light scattering from diamond-, glass-, and sapphire microspheres JF - Physica Status Solidi A N2 - Deoxyribonucleic acid (DNA) and protein recognition are now standard tools in biology. In addition, the special optical properties of microsphere resonators expressed by the high quality factor (Q-factor) of whispering gallery modes (WGMs) or morphology dependent resonances (MDRs) have attracted the attention of the biophotonic community. Microsphere-based biosensors are considered as powerful candidates to achieve label-free recognition of single molecules due to the high sensitivity of their WGMs. When the microsphere surface is modified with biomolecules, the effective refractive index and the effective size of the microsphere change resulting in a resonant wavelength shift. The transverse electric (TE) and the transverse magnetic (TM) elastic light scattering intensity of electromagnetic waves at 600 and 1400 nm are numerically calculated for DNA and unspecific binding of proteins to the microsphere surface. The effect of changing the optical properties was studied for diamond (refractive index 2.34), glass (refractive index 1.50), and sapphire (refractive index 1.75) microspheres with a 50 µm radius. The mode spacing, the linewidth of WGMs, and the shift of resonant wavelength due to the change in radius and refractive index, were analyzed by numerical simulations. Preliminary results of unspecific binding of biomolecules are presented. The calculated shift in WGMs can be used for biomolecules detection. Y1 - 2012 U6 - https://doi.org/10.1002/pssa.201100795 SN - 1862-6319 N1 - Special Issue: "Fundamentals and Applications of Diamond" VL - 209 IS - 9 SP - 1804 EP - 1810 PB - Wiley-VCH CY - Weinheim ER - TY - CHAP A1 - Logen, Steffen A1 - Höfken, Hans A1 - Schuba, Marko T1 - Simplifying RAM Forensics : A GUI and Extensions for the Volatility Framework T2 - 2012 Seventh International Conference on Availability, Reliability and Security (ARES), 20-24 August 2012, Prague, Czech Republic N2 - The Volatility Framework is a collection of tools for the analysis of computer RAM. The framework offers a multitude of analysis options and is used by many investigators worldwide. Volatility currently comes with a command line interface only, which might be a hinderer for some investigators to use the tool. In this paper we present a GUI and extensions for the Volatility Framework, which on the one hand simplify the usage of the tool and on the other hand offer additional functionality like storage of results in a database, shortcuts for long Volatility Framework command sequences, and entirely new commands based on correlation of data stored in the database. Y1 - 2012 SN - 978-1-4673-2244-7 U6 - https://doi.org/10.1109/ARES.2012.12 SP - 620 EP - 624 PB - IEEE CY - New York ER - TY - JOUR A1 - Huck, Christina A1 - Poghossian, Arshak A1 - Wagner, Patrick A1 - Schöning, Michael Josef T1 - Combined amperometric/field-effect sensor for the detection of dissolved hydrogen JF - Sensors and actuators B: Chemical N2 - Real-time and reliable monitoring of the biogas process is crucial for a stable and efficient operation of biogas production in order to avoid digester breakdowns. The concentration of dissolved hydrogen (H₂) represents one of the key parameters for biogas process control. In this work, a one-chip integrated combined amperometric/field-effect sensor for monitoring the dissolved H₂ concentration has been developed for biogas applications. The combination of two different transducer principles might allow a more accurate and reliable measurement of dissolved H₂ as an early warning indicator of digester failures. The feasibility of the approach has been demonstrated by simultaneous amperometric/field-effect measurements of dissolved H₂ concentrations in electrolyte solutions. Both, the amperometric and the field-effect transducer show a linear response behaviour in the H₂ concentration range from 0.1 to 3% (v/v) with a slope of 198.4 ± 13.7 nA/% (v/v) and 14.9 ± 0.5 mV/% (v/v), respectively. Y1 - 2012 U6 - https://doi.org/10.1016/j.snb.2012.10.050 SN - 0925-4005 N1 - Part of special issue "Selected Papers from the 14th International Meeting on Chemical Sensors" VL - 187 SP - 168 EP - 173 PB - Elsevier CY - Amsterdam ER - TY - CHAP A1 - Digel, Ilya A1 - Mansurov, Zulkhair A1 - Biisenbaev, Makhmut A1 - Savitskaya, Irina A1 - Kistaubaeva, Aida A1 - Akimbekov, Nuraly S. A1 - Zhubanova, Azhar ED - Hu, Ning T1 - Heterogeneous Composites on the Basis of Microbial Cells and Nanostructured Carbonized Sorbents T2 - Composites and Their Applications N2 - The fact that microorganisms prefer to grow on liquid/solid phase surfaces rather than in the surrounding aqueous phase was noticed long time ago [1]. Virtually any surface – animal, mineral, or vegetable – is a subject for microbial colonization and subsequent biofilm formation. It would be adequate to name just a few notorious examples on microbial colonization of contact lenses, ship hulls, petroleum pipelines, rocks in streams and all kinds of biomedical implants. The propensity of microorganisms to become surface-bound is so profound and ubiquitous that it vindicates the advantages for attached forms over their free-ranging counterparts [2]. Indeed, from ecological and evolutionary standpoints, for many microorganisms the surface-bound state means dwelling in nutritionally favorable, non-hostile environments [3]. Therefore, in most of natural and artificial ecosystems surface-associated microorganisms vastly outnumber organisms in suspension and often organize into complex communities with features that differ dramatically from those of free cells [4]. Y1 - 2012 SN - 978-953-51-0706-4 U6 - https://doi.org/10.5772/47796 SP - 249 EP - 272 PB - Intech CY - London ER - TY - JOUR A1 - Schiffer, Stefan A1 - Ferrein, Alexander A1 - Lakemeyer, Gerhard T1 - Caesar: an intelligent domestic service robot JF - Intelligent service robotics N2 - In this paper we present CAESAR, an intelligent domestic service robot. In domestic settings for service robots complex tasks have to be accomplished. Those tasks benefit from deliberation, from robust action execution and from flexible methods for human–robot interaction that account for qualitative notions used in natural language as well as human fallibility. Our robot CAESAR deploys AI techniques on several levels of its system architecture. On the low-level side, system modules for localization or navigation make, for instance, use of path-planning methods, heuristic search, and Bayesian filters. For face recognition and human–machine interaction, random trees and well-known methods from natural language processing are deployed. For deliberation, we use the robot programming and plan language READYLOG, which was developed for the high-level control of agents and robots; it allows combining programming the behaviour using planning to find a course of action. READYLOG is a variant of the robot programming language Golog. We extended READYLOG to be able to cope with qualitative notions of space frequently used by humans, such as “near” and “far”. This facilitates human–robot interaction by bridging the gap between human natural language and the numerical values needed by the robot. Further, we use READYLOG to increase the flexible interpretation of human commands with decision-theoretic planning. We give an overview of the different methods deployed in CAESAR and show the applicability of a system equipped with these AI techniques in domestic service robotics Y1 - 2012 U6 - https://doi.org/10.1007/s11370-012-0118-y SN - 1861-2776 N1 - Special Issue on Artificial Intelligence Techniques for Robotics: Sensing, Representation and Action, Part I VL - 5 IS - 4 SP - 259 EP - 276 PB - Springer CY - Berlin ER - TY - BOOK A1 - Grotendorst, Johannes T1 - Hierarchical methods for dynamics in complex molecular systems : IAS Winter School, 5 - 9 March 2012, Forschungszentrum Jülich GmbH ; lecture notes / ed. by Johannes Grotendorst, Godehard Sutmann, Gerhard Gompper, Dominik Marx Y1 - 2012 SN - 978-3-89336-768-9 N1 - (Schriften des Forschungszentrums Jülich IAS Series 10) PB - Forschungszentrum Jülich CY - Jülich ER - 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 - Nomdedeu, Mar Monsonis A1 - Willen, Christine A1 - Schieffer, Andre A1 - Arndt, Hartmut T1 - Temperature-dependent ranges of coexistence in a model of a two-prey-one-predator microbial food web JF - Marine Biology N2 - The objective of our study was to analyze the effects of temperature on the population dynamics of a three-species food web consisting of two prey bacteria (Pedobacter sp. and Acinetobacter johnsonii) and a protozoan predator (Tetrahymena pyriformis) as model organisms. We assessed the effects of temperature on the growth rates of all three species with the objective of developing a model with four differential equations based on the experimental data. The following hypotheses were tested at a theoretical level: Firstly, temperature changes can affect the dynamic behavior of a system by temperature-dependent parameters and interactions and secondly, food web response to temperature cannot be derived from the single species temperature response. The main outcome of the study is that temperature changes affect the parameter range where coexistence is possible within all three species. This has significant consequences on our ideas regarding the evaluation of effects of global warming. Y1 - 2012 U6 - https://doi.org/10.1007/s00227-012-1966-x SN - 1432-1793 VL - 159 IS - 11 SP - 2423 EP - 2430 PB - Springer CY - Berlin ER - TY - THES A1 - Schieffer, Andre T1 - Studies on diversity and coexistence in an experimental microbial community N2 - Biodiversity and the coexistence of species have puzzled and fascinated biologists since decades and is a hotspot in todays’ natural sciences. Preserving this biodiversity is a great challenge as habitats and environments underlying tremendous changes like climate change and the loss of natural habitats, which are mainly due to anthropogenic influences. The coexistence of numerous species even in homogeneous environments is a stunning feature of natural communities and has been summarized under the term ‘paradox of plankton’. Up to now, there are several mechanisms discussed, which may contribute to local and global diversity of organisms. Several interspecific trade offs have been identified maintaining the coexistence of species like their abilities regarding competition and predator avoidance, their capability to disperse in space and time, and their ability to exploit variable resources. Further, micro-evolutionary dynamics supporting the coexistence of species have been added to our knowledge, and deriving from theoretical deterministic models, non-linear dynamics which describe the temporal fluctuation of abundances of organisms. Whereas competition and predation seem to be clue structural elements within interacting organisms, the intrinsic dynamic behavior – by means of temporal changes in abundance - plays an important role regarding coexistence within a community. The present work sheds light on different factors affecting the coexistence of species using experimental microbial model systems consisting of a bacterivorous ciliate as the predator and two bacteria strains as prey organism. Additionally, another experimental setup consisting of two up to five bacteria species competing for one limiting resource was investigated. Highly controllable chemostat systems were established to exclude extrinsic disturbances. According to theoretical analyses I was able to show - experimentally and theoretically - that phenotypic plasticity of one species within a microbial one-predator-two-prey food web enlarges the range of possible coexistence of all species under different dynamic conditions, compared to a food web without phenotypic plasticity. This was accompanied by non-linear (chaotic) population dynamics within all experimental systems showing phenotypic plasticity. The experiments on the interplay of competition, predation and invasion showed that all aspects have an influence on species coexistence. Under undisturbed controlled conditions all aspects were analyzed in detail and in combination. Populations showed oscillations which were shown by quasi-chaotic attractors in phase space diagrams. Competition experiments with two up to five bacteria species competing for one limiting resource showed that all organisms were able to coexist which was mediated by species oscillations entering a regime of chaos. Besides that fact it was found, that the productivity (biomass) as well as the total cell numbers – under the same nutrition supply – increased by an increasing number of species in the experimental systems. Up to now, the occurrence of non-linear dynamics in well controlled experimental studies has been recognized several times and this phenomenon seemed to be more common in natural systems than generally assumed. N2 - Biodiversität und die Koexistenz von Arten fasziniert und verblüfft Biologen seit Jahr-zehnten und stellen einen Schwerpunkt in der heutigen Umweltforschung dar. Der Schutz und die Konservierung dieser Mannigfaltigkeit stellen eine große Herausfor-derung dar, da die natürlichen Lebensräume sowie die Umwelt enormen Verände-rungen unterworfen sind, welche meist in einem anthropogenen Ursprung wurzeln. Die Koexistenz vieler Arten, auch in relativ homogenen Habitaten ist ein faszinieren-des Charakteristikum natürlicher Lebensgemeinschaften und wird als ‚Paradox des Planktons‘ bezeichnet. Gegenwärtig werden diverse Ursachen diskutiert, welche vermutlich zur lokalen und globalen Diversität von Organismen beitragen. Einige die-ser möglichen Ursachen, die zur Aufrechterhaltung der Koexistenz der Arten beitra-gen, wurden identifiziert: Das Vermögen der Konkurrenz- und Prädationsvermeidung, die Fähigkeit räumlicher sowie zeitlicher Verteilung, sowie das Vermögen variable Ressourcen zu nutzen. Des Weiteren wurden mikro-evolutionäre Phänomene und Dynamiken identifiziert, sowie, von theoretischen deterministischen Modellen ausge-hend, nichtlineare Dynamiken, welche die zeitlichen Schwankungen der Abundanzen von Organismen beschreiben. Diese Aspekte stellen die Schlüsselkomponenten zwi-schen interagierenden Organismen dar, wobei das intrinsiche, nicht lineare dynami-sche Verhalten in Form von zeitlichen Veränderungen in Abundanzen eine zusätzli-che entscheidende Rolle bezüglich der Koexistenz von Arten spielen kann. Einige dieser Aspekte wurden in der vorliegenden Arbeit untersucht. In Anlehnung an theoretische Analysen konnte experimentell sowie theoretisch gezeigt werden, dass phänotypische Plastizität in einer Bakterienart in einem mikrobiellen Ein-Räuber-zwei-Beute-Nahrungsgewebe den Bereich der möglichen Koexistenz unter sich än-dernden experimentellen Bedingungen (Änderungen der Durchflussraten der Chemostate) – im direkten Vergleich zu einem experimentellen Nahrungsgewebe ohne phänotypische Plastizität – erweitern kann. Dies wurde begleitet durch nicht lineare Abundanzschwankungen in den Populationen aller untersuchten Versuchs-ansätze. In weiteren Untersuchungen wurde das Zusammenspiel von Konkurrenz, Prädation und Invasion in einer experimentellen mikrobiellen Gemeinschaft untersucht. Unter kontrollierten Bedingungen konnten diese Aspekte detailliert untersucht werden und es konnten Aufschlüsse darüber gewonnen werden, welche Reaktionen (Interaktionen) innerhalb der untersuchten Gemeinschaften stattfinden. Im Versuchsverlauf wurden Veränderungen in den Abundanzen sowie chaotische Schwankungen der Zellzahlen festgestellt. In Konkurrenzexperimenten von zwei bis zu fünf um eine limitierende Ressource konkurrierende Bakterienarten konnte gezeigt werden, dass alle Arten – vermittelt durch chaotische Abundanzschwankungen – nebeneinander koexistieren konnten. Begleitend dazu wurde herausgefunden, dass die Produktivität (Biomasse) sowie die Gesamtzellzahl bei gleicher Nahrungsverfügbarkeit der experimentellen Systeme mit steigender Artenzahl zunehmen. Gegenwärtig ist das Auftreten von Chaos in gut kontrollierten experimentellen Studien vereinzelt beobachtet worden, wobei dieses Phänomen jedoch häufiger in der Natur aufzutreten scheint als generell vermutet. Y1 - 2012 N1 - Köln, Univ., Diss., 2012 ER -