Cross-layer optimizations in multi-hop ad hoc networks

Unlike traditional wireless networks, characterized by the presence of last-mile, static and reliable infrastructures, Mobile ad Hoc Networks (MANETs) are dynamically formed by collections of mobile and static terminals that exchange data by enabling each other's communication. Supporting multi-hop communication in a MANET is a challenging research area because it requires cooperation between different protocol layers (MAC, routing, transport). In particular, MAC and routing protocols could be considered mutually cooperative protocol layers. When a route is established, the exposed and hidden terminal problems at MAC layer may decrease the end-to-end performance proportionally with the length of each route. Conversely, the contention at MAC layer may cause a routing protocol to respond by initiating new routes queries and routing table updates. Multi-hop communication may also benefit the presence of pseudo-centralized virtual infrastructures obtained by grouping nodes into clusters. Clustering structures may facilitate the spatial reuse of resources by increasing the system capacity: at the same time, the clustering hierarchy may be used to coordinate transmissions events inside the network and to support intra-cluster routing schemes. Again, MAC and clustering protocols could be considered mutually cooperative protocol layers: the clustering scheme could support MAC layer coordination among nodes, by shifting the distributed MAC paradigm towards a pseudo-centralized MAC paradigm. On the other hand, the system benefits of the clustering scheme could be emphasized by the pseudo-centralized MAC layer with the support for differentiated access priorities and controlled contention. In this thesis, we propose cross-layer solutions involving joint design of MAC, clustering and routing protocols in MANETs. As main contribution, we study and analyze the integration of MAC and clustering schemes to support multi-hop communication in large-scale ad hoc networks. A novel clustering protocol, named Availability Clustering (AC), is defined under general nodes' heterogeneity assumptions in terms of connectivity, available energy and relative mobility. On this basis, we design and analyze a distributed and adaptive MAC protocol, named Differentiated Distributed Coordination Function (DDCF), whose focus is to implement adaptive access differentiation based on the node roles, which have been assigned by the upper-layer's clustering scheme. We extensively simulate the proposed clustering scheme by showing its effectiveness in dominating the network dynamics, under some stressing mobility models and different mobility rates. Based on these results, we propose a possible application of the cross-layer MAC+Clustering scheme to support the fast propagation of alert messages in a vehicular environment. At the same time, we investigate the integration of MAC and routing protocols in large scale multi-hop ad-hoc networks. A novel multipath routing scheme is proposed, by extending the AOMDV protocol with a novel load-balancing approach to concurrently distribute the traffic among the multiple paths. We also study the composition effect of a IEEE 802.11-based enhanced MAC forwarding mechanism called Fast Forward (FF), used to reduce the effects of self-contention among frames at the MAC layer. The protocol framework is modelled and extensively simulated for a large set of metrics and scenarios. For both the schemes, the simulation results reveal the benefits of the cross-layer MAC+routing and MAC+clustering approaches over single-layer solutions.

Enabling computationally intensive bioinformatics applications on the Grid platform

Bioinformatics is a recent and emerging discipline which aims at studying biological problems through computational approaches. Most branches of bioinformatics such as Genomics, Proteomics and Molecular Dynamics are particularly computationally intensive, requiring huge amount of computational resources for running algorithms of everincreasing complexity over data of everincreasing size. In the search for computational power, the EGEE Grid platform, world's largest community of interconnected clusters load balanced as a whole, seems particularly promising and is considered the new hope for satisfying the everincreasing computational requirements of bioinformatics, as well as physics and other computational sciences. The EGEE platform, however, is rather new and not yet free of problems. In addition, specific requirements of bioinformatics need to be addressed in order to use this new platform effectively for bioinformatics tasks. In my three years' Ph.D. work I addressed numerous aspects of this Grid platform, with particular attention to those needed by the bioinformatics domain. I hence created three major frameworks, Vnas, GridDBManager and SETest, plus an additional smaller standalone solution, to enhance the support for bioinformatics applications in the Grid environment and to reduce the effort needed to create new applications, additionally addressing numerous existing Grid issues and performing a series of optimizations. The Vnas framework is an advanced system for the submission and monitoring of Grid jobs that provides an abstraction with reliability over the Grid platform. In addition, Vnas greatly simplifies the development of new Grid applications by providing a callback system to simplify the creation of arbitrarily complex multistage computational pipelines and provides an abstracted virtual sandbox which bypasses Grid limitations. Vnas also reduces the usage of Grid bandwidth and storage resources by transparently detecting equality of virtual sandbox files based on content, across different submissions, even when performed by different users. BGBlast, evolution of the earlier project GridBlast, now provides a Grid Database Manager (GridDBManager) component for managing and automatically updating biological flatfile databases in the Grid environment. GridDBManager sports very novel features such as an adaptive replication algorithm that constantly optimizes the number of replicas of the managed databases in the Grid environment, balancing between response times (performances) and storage costs according to a programmed cost formula. GridDBManager also provides a very optimized automated management for older versions of the databases based on reverse delta files, which reduces the storage costs required to keep such older versions available in the Grid environment by two orders of magnitude. The SETest framework provides a way to the user to test and regressiontest Python applications completely scattered with side effects (this is a common case with Grid computational pipelines), which could not easily be tested using the more standard methods of unit testing or test cases. The technique is based on a new concept of datasets containing invocations and results of filtered calls. The framework hence significantly accelerates the development of new applications and computational pipelines for the Grid environment, and the efforts required for maintenance. An analysis of the impact of these solutions will be provided in this thesis. This Ph.D. work originated various publications in journals and conference proceedings as reported in the Appendix. Also, I orally presented my work at numerous international conferences related to Grid and bioinformatics.

Wind ensamble forecasting using an adaptive mass-consistent model

[EN]Ensemble forecasting [1] is a methodology to deal with uncertainties in the numerical wind prediction. In this work we propose to apply ensemble methods to the adaptive wind forecasting model presented in [2]. The wind _eld forecasting is based on a mass-consistent model and a log-linear wind pro_le using as input data the resulting forecast wind from Harmonie [3], a Non-Hydrostatic Dynamic model. The mass-consistent model parameters are estimated by using genetic algorithms [4]. The mesh is generated using the meccano method [5] and adapted to the geometry. The main source of uncertainties in this model is the parameter estimation and the in- trinsic uncertainties of the Harmonie Model…

Tetrahedral mesh optimization combining boundary and inner node relocation and adaptive local refinement

[EN]This work introduces a new technique for tetrahedral mesh optimization. The procedure relocates boundary and inner nodes without changing the mesh topology. In order to maintain the boundary approximation while boundary nodes are moved, a local refinement of tetrahedra with faces on the solid boundary is necessary in some cases. New nodes are projected on the boundary by using a surface parameterization. In this work, the proposed method is applied to tetrahedral meshes of genus-zero solids that are generated by the meccano method. In this case, the solid boundary is automatically decomposed into six surface patches which are parameterized into the six faces of a cube with the Floater parameterization...

Adaptive Finite Element Method with a local element parametrization nested meses

[EN]This work presents a novel approach to solve a two dimensional problem by using an adaptive finite element approach. The most common strategy to deal with nested adaptivity is to generate a mesh that represents the geometry and the input parameters correctly, and to refine this mesh locally to obtain the most accurate solution. As opposed to this approach, the authors propose a technique using independent meshes : geometry, input data and the unknowns. Each particular mesh is obtained by a local nested refinement of the same coarse mesh at the parametric space…

A molecular dynamics study of the influence of chain branching on the properties of polymer systems

Die vorliegende Arbeit beschäftigt sich mit dem Einfluß von Kettenverzweigungen unterschiedlicher Topologien auf die statischen Eigenschaften von Polymeren. Diese Untersuchungen werden mit Hilfe von Monte-Carlo- und Molekular-Dynamik-Simulationen durchgeführt.Zunächst werden einige theoretische Konzepte und Modelle eingeführt, welche die Beschreibung von Polymerketten auf mesoskopischen Längenskalen gestatten. Es werden wichtige Bestimmungsgrößen eingeführt und erläutert, welche zur quantitativen Charakterisierung von Verzweigungsstrukturen bei Polymeren geeignet sind. Es wird ebenso auf die verwendeten Optimierungstechniken eingegangen, die bei der Implementierung des Computerprogrammes Verwendung fanden. Untersucht werden neben linearen Polymerketten unterschiedliche Topolgien -Sternpolymere mit variabler Armzahl, Übergang von Sternpolymeren zu linearen Polymeren, Ketten mit variabler Zahl von Seitenketten, reguläre Dendrimere und hyperverzweigte Strukturen - in Abhängigkeit von der Lösungsmittelqualität. Es wird zunächst eine gründliche Analyse des verwendeten Simulationsmodells an sehr langen linearen Einzelketten vorgenommen. Die Skalierungseigenschaften der linearen Ketten werden untersucht in dem gesamten Lösungsmittelbereich vom guten Lösungsmittel bis hin zu weitgehend kollabierten Ketten im schlechten Lösungsmittel. Ein wichtiges Ergebnis dieser Arbeit ist die Bestätigung der Korrekturen zum Skalenverhalten des hydrodynamischen Radius Rh. Dieses Ergebnis war möglich aufgrund der großen gewählten Kettenlängen und der hohen Qualität der erhaltenen Daten in dieser Arbeit, insbesondere bei den linearen ketten, und es steht im Widerspruch zu vielen bisherigen Simulations-Studien und experimentellen Arbeiten. Diese Korrekturen zum Skalenverhalten wurden nicht nur für die linearen Ketten, sondern auch für Sternpolymere mit unterchiedlicher Armzahl gezeigt. Für lineare Ketten wird der Einfluß von Polydispersität untersucht.Es wird gezeigt, daß eine eindeutige Abbildung von Längenskalen zwischen Simulationsmodell und Experiment nicht möglich ist, da die zu diesem Zweck verwendete dimensionslose Größe eine zu schwache Abhängigkeit von der Polymerisation der Ketten besitzt. Ein Vergleich von Simulationsdaten mit industriellem Low-Density-Polyäthylen(LDPE) zeigt, daß LDPE in Form von stark verzweigten Ketten vorliegt.Für reguläre Dendrimere konnte ein hochgradiges Zurückfalten der Arme in die innere Kernregion nachgewiesen werden.

Tris(trimethylsilyl)silyl stabilized phosphorus and lead clusters

Die Hypersilylgruppe (Me3Si)3Si stellt einen sehr sperrigen, Elektronen liefernden Substituenten dar und kann zur Stabilisierung niedriger Oxidationsstufen sowie ungewöhnlicher Strukturelemente dienen. Durch Reaktionen der base-freien Hypersilanide der Alkalimetalle sowie des Dihypersilylplumbandiyls mit unterschiedlichsten phosphorhaltigen Reagenzien konnten eine Reihe hypersilyl-stabilisierter Phosphor- und Bleicluster-Verbindungen erhalten werden. Kaliumhypersilanid reagiert in Toluol glatt mit weißem Phosphor bei Raumtemperatur in Toluol unter quantitativer Bildung von rotem Kalium-bis(hypersilyl)tetraphosphenid [(Me3Si)3Si]2P4K2 (1), einem Kaliumsalz des Tetraphosphens (Me3Si)3Si-PH-P=P-PH-Si(SiMe3)3. In Benzol oder Toluol steht 1 im Gleichgewicht mit dem dimeren Octaphosphanid [(Me3Si)3Si]4P8K4 (2). Bei längerem Stehen der toluolischen Lösungen zerfällt 1 langsam vermutlich in Folge einer Protolyse zum gelben Pentaphosphanid [(Me3Si)3Si]3P5K2 (4). Aus benzolischer Lösung konnte hingegen ein weiteres Oktaphosphanid, [(Me3Si)3Si]3P8K3 (5), isoliert werden. Führt man die Reaktion Kaliumhypersilanid mit P4 in stärker koordinierenden Lösungsmitteln wie Diethylether durch, so entstehen neben 1 größere Mengen des Triphosphenids [(Me3Si)3Si]2P3K (3); dieses enthält ein Triphosphaallyl-Anion mit partieller P-P-Doppelbindung. Setzt man Lithiumhypersilanid mit weißem Phosphor um, so beobachtet man eine vollständig andere Produktpallette. Als Hauptprodukte lassen Polyphosphane wie beispielsweise [(Me3Si)3Si]2P4 (6) nachweisen, das zu 1 analoge [(Me3Si)3Si]2P4Li2 (7) entsteht nur in vergleichsweise kleinen Mengen. In der Gegenwart von Hexahydro-1,3,5-trimethyl-S-triazin, entsteht aus Lithiumhypersilanid und P4 hingegen im wesentlichen [(Me3Si)3Si]2P3Li (8) neben beträchtlichen Mengen von (Me3Si)4Si. Dessen Bildung erfordert eine Si-Si-Bindungsspaltung im Verlauf der Reaktion. Die Reaktion von Natriumhypersilanid mit P4 verläuft sehr unübersichtlich, das Pentaphosphanid [(Me3Si)3Si]3P5Na2 (9) ist das einzige isolierbare Produkt. Setzt man 1 mit [(Me3Si)2Si]2Sn um, so bilden sich überraschenderweise, je nach verwendetem Solvens [(Me3Si)3Si]3P4SnK (10) oder [(Me3Si)3Si]2[(Me3Si)2N]P4SnK (11). Alle neuen Verbindungen wurden NMR-spektroskopisch charakterisiert, die Phosphenide 1, 7, 8 sowie die Phosphanide 2, 4, 5, 9, 10 darüber hinaus durch Kristallstrukturanalysen. Dihypersilylplumbandiyl und -stannandiyl reagieren bei tiefer Temperatur mit P4, MPH2 (M=Li, K), PMe3, and PH3 zu formalen Lewis-Säure-Base-Addukten. Die Addukte {[(Me3Si)3Si]2PbPH2}M [M = Li (15), K (18)], {{[(Me3Si)3Si]2Pb}2PH2}M [M = Li (19), K (20)], und [(Me3Si)3Si]2EPMe3 [E = Pb (21), Sn (22)] wurden als kristalline Feststoffe erhalten und konnten vollständig charakterisiert werden. Die metastabilen Addukte {[(Me3Si)3Si]2E}4P4 (E = Pb, Sn) und [(Me3Si)3Si]2PbPH3 konnten lediglich NMR-spektroskopisch nachgewiesen werden. Bei Raumtemperatur entstehen in Folge von Ligandenaustausch-Prozessen die kristallographisch charakterisierten Heterokubane [(Me3Si)3Si]4P4E4 [E = Pb (12), Sn (14)], das Diphosphen (Me3Si)3SiP=PSi(SiMe3)3 (13) sowie der Pb2P2-Heterocyclus [(Me3Si)3SiPbP(H)Si(SiMe3)3]2 (17). Bei tiefer Temperatur wird aus einer sehr langsamen Reaktion von Dihypersilylplumbandiyl und PH3 in sehr kleinen Ausbeuten ein weiteres, völlig unerwartetes Produkt gebildet: der Bleicluster [(Me3Si)3Si]6Pb12 (23). Er weist ein verzerrt ikosaedrisches, zentrosymmetrisches Pb12-Gerüst auf. Nach jetzigen Erkenntnissen läuft seine Bildung über das nicht fassbare Hydridoplumbandiyl HPbSi(SiMe3)3, das intermediär durch Substituentenaustausch zwischen Pb[Si(SiMe3)3]2 and PH3 entsteht. Der Ersatz des Phosphans durch andere Hydridquellen wie (Ph3PCuH)6, (iBu)2AlH, and Me3NAlH3 führt ebenfalls zur Bildung von Bleiclustern, allerdings ist jetzt der Cluster [(Me3Si)3Si]6Pb10 (24) das Hauptprodukt. Beide Cluster, 23 und 24, gehorchen den Wade-Regeln.

Quantum effects and dynamics in hydrogen-bonded systems: a first-principles approach to spectroscopic experiments

Computer simulations have become an important tool in physics. Especially systems in the solid state have been investigated extensively with the help of modern computational methods. This thesis focuses on the simulation of hydrogen-bonded systems, using quantum chemical methods combined with molecular dynamics (MD) simulations. MD simulations are carried out for investigating the energetics and structure of a system under conditions that include physical parameters such as temperature and pressure. Ab initio quantum chemical methods have proven to be capable of predicting spectroscopic quantities. The combination of these two features still represents a methodological challenge. Furthermore, conventional MD simulations consider the nuclei as classical particles. Not only motional effects, but also the quantum nature of the nuclei are expected to influence the properties of a molecular system. This work aims at a more realistic description of properties that are accessible via NMR experiments. With the help of the path integral formalism the quantum nature of the nuclei has been incorporated and its influence on the NMR parameters explored. The effect on both the NMR chemical shift and the Nuclear Quadrupole Coupling Constants (NQCC) is presented for intra- and intermolecular hydrogen bonds. The second part of this thesis presents the computation of electric field gradients within the Gaussian and Augmented Plane Waves (GAPW) framework, that allows for all-electron calculations in periodic systems. This recent development improves the accuracy of many calculations compared to the pseudopotential approximation, which treats the core electrons as part of an effective potential. In combination with MD simulations of water, the NMR longitudinal relaxation times for 17O and 2H have been obtained. The results show a considerable agreement with the experiment. Finally, an implementation of the calculation of the stress tensor into the quantum chemical program suite CP2K is presented. This enables MD simulations under constant pressure conditions, which is demonstrated with a series of liquid water simulations, that sheds light on the influence of the exchange-correlation functional used on the density of the simulated liquid.

Thermodynamic concepts in adaptive resolution simulations

This thesis work is devoted to the conceptual and technical development of the Adaptive Resolution Scheme (AdResS), a molecular dynamics method that allows the simulation of a system with different levels of resolution simultaneously. The simulation domain is divided into high and low resolution zones and a transition region that links them, through which molecules can freely diffuse.rnThe first issue of this work regards the thermodynamic consistency of the method, which is tested and verified in a model liquid of tetrahedral molecules. The results allow the introduction of the concept of the Thermodynamic Force, an external field able to correct spurious density fluctuations present in the transition region in usual AdResS simulations.rnThe AdResS is also applied to a system where two different representations with the same degree of resolution are confronted. This simple test extends the method from an Adaptive Resolution Scheme to an Adaptive Representation Scheme, providing a way of coupling different force fields based on thermodynamic consistency arguments. The Thermodynamic Force is successfully applied to the example described in this work as well.rnAn alternative approach of deducing the Thermodynamic Force from pressure consistency considerations allows the interpretation of AdResS as a first step towards a molecular dynamics simulation in the Grand Canonical ensemble. Additionally, such a definition leads to a practical way of determining the Thermodynamic Force, tested in the well studied tetrahedral liquid. The effects of AdResS and this correction on the atomistic domain are analyzed by inspecting the local distribution of velocities, radial distribution functions, pressure and particle number fluctuation. Their comparison with analogous results coming from purely atomistic simulations shows good agreement, which is greatly improved under the effect of the external field.rnA further step in the development of AdResS, necessary for several applications in biophysics and material science, consists of its application to multicomponent systems. To this aim, the high-resolution representation of a model binary mixture is confronted with its coarse-grained representation systematically parametrized. The Thermodynamic Force, whose development requires a more delicate treatment, also gives satisfactory results.rnFinally, AdResS is tested in systems including two-body bonded forces, through the simulation of a model polymer allowed to adaptively change its representation. It is shown that the distribution functions that characterize the polymer structure are in practice not affected by the change of resolution.rnThe technical details of the implementation of AdResS in the ESPResSo package conclude this thesis work.

Coarse-graining and quantum-classical adaptive coupling in soft matter

Die vorliegende Arbeit untersucht den Zusammenhang zwischen Skalen in Systemen weicher Materie, der für Multiskalen-Simulationen eine wichtige Rolle spielt. Zu diesem Zweck wurde eine Methode entwickelt, die die Approximation der Separierbarkeit von Variablen für die Molekulardynamik und ähnliche Anwendungen bewertet. Der zweite und größere Teil dieser Arbeit beschäftigt sich mit der konzeptionellen und technischen Erweiterung des Adaptive Resolution Scheme'' (AdResS), einer Methode zur gleichzeitigen Simulation von Systemen mit mehreren Auflösungsebenen. Diese Methode wurde auf Systeme erweitert, in denen klassische und quantenmechanische Effekte eine Rolle spielen.rnrnDie oben genannte erste Methode benötigt nur die analytische Form der Potentiale, wie sie die meisten Molekulardynamik-Programme zur Verfügung stellen. Die Anwendung der Methode auf ein spezielles Problem gibt bei erfolgreichem Ausgang einen numerischen Hinweis auf die Gültigkeit der Variablenseparation. Bei nicht erfolgreichem Ausgang garantiert sie, dass keine Separation der Variablen möglich ist. Die Methode wird exemplarisch auf ein zweiatomiges Molekül auf einer Oberfläche und für die zweidimensionale Version des Rotational Isomer State (RIS) Modells einer Polymerkette angewandt.rnrnDer zweite Teil der Arbeit behandelt die Entwicklung eines Algorithmus zur adaptiven Simulation von Systemen, in denen Quanteneffekte berücksichtigt werden. Die Quantennatur von Atomen wird dabei in der Pfadintegral-Methode durch einen klassischen Polymerring repräsentiert. Die adaptive Pfadintegral-Methode wird zunächst für einatomige Flüssigkeiten und tetraedrische Moleküle unter normalen thermodynamischen Bedingungen getestet. Schließlich wird die Stabilität der Methode durch ihre Anwendung auf flüssigen para-Wasserstoff bei niedrigen Temperaturen geprüft.

Constraining mass and shape of galaxy clusters through large scale structures

The mass estimation of galaxy clusters is a crucial point for modern cosmology, and can be obtained by several different techniques. In this work we discuss a new method to measure the mass of galaxy clusters connecting the gravitational potential of the cluster with the kinematical properties of its surroundings. We explore the dynamics of the structures located in the region outside virialized cluster, We identify groups of galaxies, as sheets or filaments, in the cluster outer region, and model how the cluster gravitational potential perturbs the motion of these structures from the Hubble fow. This identification is done in the redshift space where we look for overdensities with a filamentary shape. Then we use a radial mean velocity profile that has been found as a quite universal trend in simulations, and we fit the radial infall velocity profile of the overdensities found. The method has been tested on several cluster-size haloes from cosmological N-body simulations giving results in very good agreement with the true values of virial masses of the haloes and orientation of the sheets. We then applied the method to the Coma cluster and even in this case we found a good correspondence with previous. It is possible to notice a mass discrepancy between sheets with different alignments respect to the center of the cluster. This difference can be used to reproduce the shape of the cluster, and to demonstrate that the spherical symmetry is not always a valid assumption. In fact, if the cluster is not spherical, sheets oriented along different axes should feel a slightly different gravitational potential, and so give different masses as result of the analysis described before. Even this estimation has been tested on cosmological simulations and then applied to Coma, showing the actual non-sphericity of this cluster.

OpenMP task scheduling strategies to mitigate hardware variability in tightly-coupled shared memory clusters

In questa tesi sono stati apportati due importanti contributi nel campo degli acceleratori embedded many-core. Abbiamo implementato un runtime OpenMP ottimizzato per la gestione del tasking model per sistemi a processori strettamente accoppiati in cluster e poi interconnessi attraverso una network on chip. Ci siamo focalizzati sulla loro scalabilità e sul supporto di task di granularità fine, come è tipico nelle applicazioni embedded. Il secondo contributo di questa tesi è stata proporre una estensione del runtime di OpenMP che cerca di prevedere la manifestazione di errori dati da fenomeni di variability tramite una schedulazione efficiente del carico di lavoro.

Sensing applications of biofunctionalised plasmonic gold nanoparticles

Plasmonische Metallnanopartikel bündeln, verstärken und beeinflussen Licht auf nanoskopischer Ebene. Diese grundlegende Eigenschaft kommt von koheränten, kollektiven Schwingungen der Leitungsbandelektronen, die von einfallendem Licht resonant angeregt und lokalisierte Oberflächenplasmonenresonanz (LSPR) oder ‚Partikelplasmonen‘ genannt werden. Plasmonen in Metallnanopartikeln wurden bisher z.B. zur Erkennen von pathogenen Biomolekülen, bei der photothermischen Therapie und zur Verbesserung der Effizienz von Solarzellen verwendet. In dieser Arbeit werde ich meinen Fokus auf die Synthese und Funktionalisierung von Goldnanopartikeln zur Anwendung als Sensoren legen.rnrnKürzliche Verbesserungen in der nasschemischen Synthese haben zur Herstellung von Goldnanopartikel mit unterschiedlichen Formen und Größen geführt, die sich in ihren Sensoreigenschaften unterscheiden. Unter den unterschiedlichen Sensorgeometrien sind Goldnanostäbchen die bevorzugte Form zur Biomolekül-Sensorik durch LSPR. Nanostäbchen werden durch eine positiv geladene CTAB-Schicht stabilisiert, die Proteine bei neutralem pH-Wert anziehen kann. Die Adsorption und Desorption von Proteinen an der Nanopartikeloberfläche und damit die Bindungskinetiken von Proteinen kann auf Einzelmolekülebene erforscht werden. Ich zeige hier eine Studie mit hoher örtlicher und zeitlicher Auflösung um einzelne Bindungsereignisse von Fibronectin auf Goldnanostäbchen darzustellen.rnrnGoldnanostäbchen müssen mit spezifischen biologischen Erkennungselementen funktionalisiert werden um eine Analyterkennung oder Proteinwechselwirkung zu erreichen. Ich funktionalisiere Goldnanostäbchen mit kurzen DNA-Sequenzen (Aptamer-Sequenzen und NTA konjugierten Polihymidinen) und habe anhand diese unterschiedlich sensitiven Partikel eine Studie mit verschiedenen Analyten (oder Protein-Protein Wechselwirkungen) erfolgreich durchgeführt.rn rnPlasmonen von Nanopartikel-Clustern koppeln miteinander, was ihre Resonanzenergie ändert. Der kontrollierte Zusammenbau von Nanopartikeln zu Dimeren oder höher geordneten Strukturen wie ‚Core-Satellites‘ können dazu dienen ihre Sensitivität zu erhöhen. Diese Cluster bieten eine hohe Sensitivität auf Grund der Anwesenheit von plasmonischen Hotspots in der Lücke zwischen zwei Partikeln. Die Plasmonkopplung ist ein Phänomen, das abhängig vom Abstand zweier Partikel zueinander ist und bildet somit die Basis von sogenannten Plasmon-Linealen. Ich habe eine Strategie entwickelt um Dimere aus Hsp90 funktionalisierten Goldnanosphären zu bilden. Diese Technik wird nicht durch Ausbleichen oder das Blinken von Farbstoffen limitiert und ich zeige zum ersten Mal wie man dadurch dynamische Proteinkonformationen untersuchen kann.rn

A study of extended radio galaxies in the Shapley concentration core

Extended cluster radio galaxies show different morphologies com- pared to those found isolated in the field. Indeed, symmetric double radio galaxies are only a small percentage of the total content of ra- dio loud cluster galaxies, which show mainly tailed morphologies (e.g. O’Dea & Owen, 1985). Moreover, cluster mergers can deeply affect the statistical properties of their radio activity. In order to better understand the morphological and radio activity differences of the radio galaxies in major mergeing and non/tidal-merging clusters, we performed a multifrequency study of extended radio galax- ies inside two cluster complexes, A3528 and A3558. They belong to the innermost region of the Shapley Concentration, the most massive con- centration of galaxy clusters (termed supercluster) in the local Universe, at average redshift z ≈ 0.043. We analysed low frequency radio data performed at 235 and 610 MHz with Giant Metrewave Radio Telescope (GMRT) and we combined them with proprietary and literature observations, in order to have a wide frequency range (150 MHz to 8.4 GHz) to perform the spectral analysis. The low frequency images allowed us to carry out a detailed study of the radio tails and diffuse emission found in some cases. The results in the radio band were also qualitatively compared with the X-ray information coming from XMM-Newton observations, in order to test the interaction between radio galaxies and cluster weather. We found that the brightest central galaxies (BCGs) in the A3528 cluster complex are powerful and present substantial emission from old relativistic plasma characterized by a steep spectrum (α > 2). In the light of observational pieces of evidence, we suggest they are possible re-started radio galaxies. On the other hand, the tailed radio galaxies trace the host galaxy motion with respect to the ICM, and our find- ings is consistent with the dynamical interpretation of a tidal interaction (Gastaldello et al. 2003). On the contrary, the BCGs in the A3558 clus- ter complex are either quiet or very faint radio galaxies, supporting the hypothesis that clusters mergers quench the radio emission from AGN.

Rapid parallel adaptive radiations from a single hybridogenic ancestral population

The Alpine lake whitefish (Coregonus lavaretus) species complex is a classic example of a recent radiation, associated with colonization of the Alpine lakes following the glacial retreat (less than 15 kyr BP). They have formed a unique array of endemic lake flocks, each with one to six described sympatric species differing in morphology, diet and reproductive ecology. Here, we present a genomic investigation of the relationships between and within the lake flocks. Comparing the signal between over 1000 AFLP loci and mitochondrial control region sequence data, we use phylogenetic tree-based and population genetic methods to reconstruct the phylogenetic history of the group and to delineate the principal centres of genetic diversity within the radiation. We find significant cytonuclear discordance showing that the genomically monophyletic Alpine whitefish clade arose from a hybrid swarm of at least two glacial refugial lineages. Within this radiation, we find seven extant genetic clusters centred on seven lake systems. Most interestingly, we find evidence of sympatric speciation within and parallel evolution of equivalent phenotypes among these lake systems. However, we also find the genetic signature of human-mediated gene flow and diversity loss within many lakes, highlighting the fragility of recent radiations.