Single-molecule fluorescence spectroscopy techniques such as Fluorescence Correlation Spectroscopy (FCS) and single-molecule Förster Resonance Energy Transfer (smFRET) not only possess an unprecedented high sensitivity but also have high temporal and spatial resolution. Therefore, they have an immense potential both in investigation of fundamental biological principles and in clinical applications. FCS analyses are based on both theoretical approximations of the beam geometry and assumptions of the underlying molecular processes. To address the accuracy of analysis, firstly the experimental conditions that should be fulfilled in order to obtain reliable physical parameters are discussed and the input parameters are carefully controlled accordingly to demonstrate the performance of FCS measurements on our home-built confocal multiparameter photon-counting microscope in several in vitro and in-vivo applications. Secondly, we performed a comprehensive FCS analysis of rhodamine family of dyes to evaluate the validity of assigning the correlation relaxation times to the time constant of conformational dynamics of biomolecules. While it is the common approach in literature our data suggests that conformational dynamics mainly appear in the correlation curve via modulation of the dark states of the fluorophores. The size and shape of the folded, unfolded and chemically-denatured states of the N-terminal Src-homology-3 of downstream of receptor kinases (DrkN SH3) were investigated by FCS and smFRET burst experiments. Based on the data, we conclude that a considerable sub-population of the denatured protein is in a closed loop state which is most likely formed by cooperative hydrogen bonds, salt bridges and nonpolar contacts. As a clinical application, we developed and characterized an ultrasensitive capillary electrophoresis method on our multiparameter confocal microscope. This allowed us to perform Direct Quantitative Analysis of Multiple microRNAs (DQAMmiR) with about 500 times better sensivity than a commercial instrument. Quite remarkably, we were able to analyze samples of cell lysate down to the contents of a single cell.

Single-molecule fluorescence spectroscopy techniques such as Fluorescence Correlation Spectroscopy (FCS) and single-molecule Förster Resonance Energy Transfer (smFRET) not only possess an unprecedented high sensitivity but also have high temporal and spatial resolution. Therefore, they have an immense potential both in investigation of fundamental biological principles and in clinical applications. FCS analyses are based on both theoretical approximations of the beam geometry and assumptions of the underlying molecular processes. To address the accuracy of analysis, firstly the experimental conditions that should be fulfilled in order to obtain reliable physical parameters are discussed and the input parameters are carefully controlled accordingly to demonstrate the performance of FCS measurements on our home-built confocal multiparameter photon-counting microscope in several in vitro and in-vivo applications. Secondly, we performed a comprehensive FCS analysis of rhodamine family of dyes to evaluate the validity of assigning the correlation relaxation times to the time constant of conformational dynamics of biomolecules. While it is the common approach in literature our data suggests that conformational dynamics mainly appear in the correlation curve via modulation of the dark states of the fluorophores. The size and shape of the folded, unfolded and chemically-denatured states of the N-terminal Src-homology-3 of downstream of receptor kinases (DrkN SH3) were investigated by FCS and smFRET burst experiments. Based on the data, we conclude that a considerable sub-population of the denatured protein is in a closed loop state which is most likely formed by cooperative hydrogen bonds, salt bridges and nonpolar contacts. As a clinical application, we developed and characterized an ultrasensitive capillary electrophoresis method on our multiparameter confocal microscope. This allowed us to perform Direct Quantitative Analysis of Multiple microRNAs (DQAMmiR) with about 500 times better sensivity than a commercial instrument. Quite remarkably, we were able to analyze samples of cell lysate down to the contents of a single cell.

Quantum optimal control theory is applied to find optimal pulses for controlling the motion of an ion and a molecule for two different applications. Those optimal pulses enable the control of the dynamics of the system by driving the atom or the molecule from an initial state to desired states.The evolution equations obtained by means of the quantum optimal control theory are resolved iteratively using a monotonic convergent algorithm. A number of simulation parameters are varied in order to get the optimal pulses including the duration of the pulses, the time step of the time grid, a penalty factor that limits the maximal intensity of the fields, and a guess pulse which is used to start the optimal control.The optimal pulses obtained for each application are analyzed by Fourier transform, and also by looking at the time evolution of the populations that they generate in the system.The first application is the preparation of specific vibrational states of acetylene that are usually not reachable from the ground state, and that would remain unpopulated by usual spectroscopy. Relevant state energies and transition dipole moments are extracted from the experimental literature and especially from the global acetylene Hamiltonian conferring an uncommon precision to the control simulation. The control starts from the ground state. The target states belongs to the polyad Ns=1, Nr=5 of acetylene which includes two vibrational dark states and one vibrational bright state. First, the simulation is performed with the Schrödinger equation and in a second step, with the Liouville--von Neumann equation, as mixed states are prepared. Indeed, the control starts from a Boltzmann distribution of population in the rotational levels of the vibrational ground state chosen in order to simulate an experimental condition. But the distribution is truncated to limit the computational effort. One of the dark states appears to be a potential target for a realistic experimental investigation because the average population of the Rabi oscillation remains high and decoherence is expected to be weak. The optimal pulses obtained have a high fidelity, have a spectrum with well-resolved peak frequencies, and their experimental feasibility seems achievable within the current abilities of experimental laboratories.The second application is to propose an experimental realization of a microscopic physical device able to simulate quantum dynamics. The idea is to use the motional states of a Cd^+ ion trapped in an anharmonic potential to realize a quantum dynamics simulator of a single-particle Schrödinger equation. In this way, the motional states store the information and the optimal pulse manipulates this information to realize operations. In the present case, the simulated dynamics was the propagation of a wave packet in a harmonic potential. Starting from an initial quantum state, the pulse acts on the system to modify the motional states of the ion in such a way that the final superposition of motional states corresponds to the results of the dynamics. This simulation is performed with the Liouville--von Neumann equation and also with the Lindblad equation as dissipation is included to test the robustness of the pulse against perturbations of the potential. The optimal pulses that are obtained have a high fidelity which shows that the ion trap system has correctly realized the quantum dynamics simulation. The optimal pulses are valid for any initial condition if the potential of the simulation or the mass of the propagated wave packet is unchanged. / La théorie du contrôle optimal quantique est utilisée pour trouver des impulsions optimales permettant de contrôler la dynamique d'un atome et d'une molécule les menant d'un état initial à un état final. Les équations d'évolution obtenues grâce au contrôle optimal limitent l'intensité maximale de l'impulsion et sont résolues itérativement grâce à l'algorithme de Zhu--Rabitz. Le contrôle optimal est utilisé pour réaliser deux objectifs. Le premier est la préparation d'états vibrationnels de l'acétylène qui sont généralement inaccessibles par transition au départ de l'état vibrationnel fondamental. Ces états, appelés états sombres, sont les états cibles de la simulation. Ils appartiennent à la polyade Ns=1, Nr=5 de l'acétylène qui en contient deux ainsi qu'un état, dit brillant, qui lui est accessible depuis l'état fondamental. Les énergies des états du système et les moments de transitions dipolaires sont déterminés à partir d'un Hamiltonien très précis qui confère une précision inhabituelle à la simulation. Un des états sombres apparaît être un candidat potentiel pour une réalisation expérimentale car la population moyenne de cet état reste élevée après l'application de l'impulsion.Les niveaux rotationnels des états vibrationnels sont également pris en compte.Les impulsions optimales obtenues ont une fidélité élevée et leur spectre en fréquence présente des pics résolus.Le deuxième objectif est de proposer la réalisation expérimentale d'un dispositif microscopique capable de simuler une dynamique quantique. Ce travail montre qu'on peut utiliser les états de mouvement d'un ion de Cd^+ piégé dans un potentiel anharmonique pour réaliser la propagation d'un paquet d'onde dans un potentiel harmonique. Ce dispositif stocke l'information de la dynamique simulée grâce aux états de mouvements et l'impulsion optimale manipule l'information pour réaliser les propagations. En effet, démarrant d'un état quantique initial, l'impulsion agit sur le système en modifiant les états de mouvements de l'ion de telle sorte que la superposition finale des états de mouvements corresponde aux résultats de la dynamique. De la dissipation est incluse pour tester la robustesse de l'impulsion face à des perturbations du potentiel anharmonique. Les impulsions optimales obtenues ont une fidélité élevée ce qui montre que le système a correctement réalisé la simulation de dynamique quantique. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Mit dem Begriff Wellenleiterquantenelektrodynamik (WQED) wird gemeinhin die Physik des quantisierten und in eindimensionalen Wellenleitern geführten Lichtes in Wechselwirkung mit einzelnen Emittern bezeichnet. In dieser Arbeit untersuche ich Effekte der WQED für einzelne Dreiniveausysteme (3NS) bzw. Paare von Zweiniveausystemen (2NS), die in den Wellenleiter eingebettet sind. Hierzu bediene ich mich hauptsächlich numerischer Methoden und betrachte die Modellsysteme im Rahmen der Drehwellennäherung. Ich untersuche die Dynamik der Streuung einzelner Photonen an einzelnen, in den Wellenleiter eingebetteten 3NS. Dabei analysiere ich den Einfluss dunkler bzw. nahezu dunkler Zustände der 3NS auf die Streuung und zeige, wie sich mit Hilfe stationärer elektrischer Treibfelder gezielt auf die Streuung einwirken lässt. Ich quantifiziere Verschränkung zwischen dem Lichtfeld im Wellenleiter und den Emittern mit Hilfe der Schmidt-Zerlegung und untersuche den Einfluss der Form der Einhüllenden eines Einzelphotonpulses auf die Ausbeute der Verschränkungserzeugung bei der Streuung des Photons an einem einzelnen Lambda-System im Wellenleiter. Hier zeigt sich, dass die Breite der Einhüllenden im k-Raum und die Emissionszeiten der beiden Übergänge des 3NS die maßgeblichen Parameter darstellen. Abschließend ergründe ich die Emissionsdynamik zweier im Abstand L in den Wellenleiter eingebetteter 2NS. Diese Dynamik wird insbesondere durch kavitätsartige und polaritonische Zustände des Systems aus Wellenleiter und Emitter ausschlaggebend beeinflusst. Bei der kollektiven Emission der 2NS treten - abhängig vom Abstand L - Sub- bzw. Superradianz auf. Dabei nimmt die Intensität dieser Effekte mit längerem Abstand L zu. Diese Eigenart lässt sich auf die Eindimensionalität des Wellenleiters zurückführen. / The field of waveguide quantum electrodynamics (WQED) deals with the physics of quantised light in one-dimensional (1D) waveguides coupled to single emitters. In this thesis, I investigate WQED effects for single three-level systems (3LS) and pairs of two-level systems (2LS), respectively, which are embedded in the waveguide. To this end, I utilise numerical techniques and consider all model systems within the rotating wave approximation. I investigate the dynamics of single-photon scattering by single, embedded 3LS. In doing so, I analyse the influence of dark and almost-dark states of the 3LS on the scattering dynamics. I also show, how stationary electrical driving fields can control the outcome of the scattering. I quantify entanglement between the waveguide''s light field and single emitters by utilising the Schmidt decomposition. I apply this formalism to a lambda-system embedded in a 1D waveguide and study the generation of entanglement by scattering single-photon pulses with different envelopes on the emitter. I show that this entanglement generation is mainly determined by the photon''s width in k-space and the 3LS''s emission times. Finally, I explore the emission dynamics of a pair of 2LS embedded by a distance L into the waveguide. These dynamics are primarily governed by bound states in the continuum and by polaritonic atom-photon bound-states. For collective emission processes of the two 2LS, sub- and superradiance appear and depend strongly on the 2LS''s distance: the effects increase for larger L. This is an exclusive property of the 1D nature of the waveguide.