Doctor of Philosophy / Department of Physics / Zenghu Chang / The observation and control of dynamics in atomic and molecular targets requires the use of laser pulses with duration less than the characteristic timescale of the process which is to be manipulated. For electron dynamics, this time scale is on the order of attoseconds where 1 attosecond = 10[superscript]-18 seconds. In order to generate pulses on this time scale, different gating methods have been proposed. The idea is to extract or “gate” a single pulse from an attosecond pulse train and switch off all the other pulses. While previous methods have had some success, they are very difficult to implement and so far very few labs have access to these unique light sources. The purpose of this work is to introduce a new method, called double optical gating (DOG), and to demonstrate its effectiveness at generating high contrast single isolated attosecond pulses from multi-cycle lasers. First, the method is described in detail and is investigated in the spectral domain. The resulting attosecond pulses produced are then temporally characterized through attosecond streaking. A second method of gating, called generalized double optical gating (GDOG), is also introduced. This method allows attosecond pulse generation directly from a carrier-envelope phase un-stabilized laser system for the first time. Next the methods of DOG and GDOG are implemented in attosecond applications like high flux pulses and extreme broadband spectrum generation. Finally, the attosecond pulses themselves are used in experiments. First, an attosecond/femtosecond cross correlation is used for characterization of spatial and temporal properties of femtosecond pulses. Then, an attosecond pump, femtosecond probe experiment is conducted to observe and control electron dynamics in helium for the first time.

Doctor of Philosophy / Department of Physics / Brett D. DePaola / In many experiments involving a magneto-optical trap (MOT) it is of great importance to know the fraction of atoms left in an excited state due to the trapping process. Generally speaking, researchers have had to use overly simplistic and untested models to estimate this fraction. In this work, the excited fraction of 87Rb atoms in a MOT is measured using a model-free approach. A simple model is fit to the fractions which were obtained for a range of MOT parameters. Using the results of this work, the excited fraction of 87Rb atoms trapped in a MOT can be accurately estimated with knowledge of only the trapping laser intensity and detuning. The results are only weakly dependent on other MOT parameters.

Doctor of Philosophy / Department of Physics / Brett D. DePaola / Many people in the science community are interested in the prospect of cold molecules for such applications as quantum computing and molecular Bose-Einstein condensates. Current methods of production fall short of the requirements for such projects. Photo association is a promising technique for forming cold molecules, but is currently facing significant obstacles. By understanding the photo association process and utilizing higher excited states, it is hoped that cold molecules can be formed from more easily produced cold atoms. Photo associative Ionization (PAI) is presented as a means to study excited state molecular dynamics at large internuclear separation, including photo association. This thesis presents a number of techniques for studying PAI in cold rubidium and a number of results obtained with the techniques. Excitation pathways for the process are explored in both narrow linewidth (MHz) and ultrafast (fs), large bandwidth (20 nm) domains.

Doctor of Philosophy / Department of Physics / Kristan L. Corwin / Current portable near-infrared optical frequency references offer modest accuracy and instability compared to laboratory references. Low pressure reference cells are necessary to realize features narrower than the Doppler broadened overtone transitions, and most setups to date have occurred in free-space. Hollow-core photonic crystal fibers offer a potential alternative to free-space setups through their small cores (~10’s of µm) and low-loss guidance. Furthermore, HC-PCF can be made into fiber cells that could be directly integrated into existing telecommunications networks. Efforts were made to fabricate these fiber cells with a low pressure of molecules trapped inside, but this has proven to be quite challenging. Therefore, investigation of these fibers is conducted by placing the ends of the fiber inside vacuum chambers loaded with acetylene (12C2H2). The linewidths of several P branch transitions (near 1.5 µm) are investigated as a function of acetylene pressure and optical pump power in three different HC-PCFs. Frequency modulation spectroscopy is then implemented on the acetylene-filled HC-PCF to generate sub-Doppler dispersion features that are useful for frequency stabilization using standard servo electronics. Instability and accuracy of this near-IR optical reference were then determined by analysis of heterodyne experiments conducted with frequency combs referenced to a GPS-disciplined rubidium oscillator. The instability and accuracy of this HC-PCF reference are within an order of magnitude of free-space experiments, as expected based on the ratio of linewidths observed in the two experiments. Therefore, HC-PCF has been shown to be suitable for potential frequency references. Further work is necessary to fabricate gas fiber cells with high optical transmission and low molecular contamination.

Doctor of Philosophy / Department of Physics / Itzhak Ben-Itzhak / Present laser technology allows for the production of ultra short (&7 fs) intense (.1016 W/cm2)pulses, which are comparable in duration and interaction strength to the vibrational period and the interaction that binds the electron in molecules, respectively. In this intense-field ultra short-pulse regime one can both measure and manipulate dynamics on the femtosecond timescale. To probe the dynamics of laser-matter interactions in this regime, we have chosen to start from the simplest possible molecule - H+ 2 , which can either dissociate into H + p or ionize into p + p + e. We have designed and employ a coincidence three-dimensional momentum imaging technique which allows us to measure ionization and dissociation of a molecular ion beam target simultaneously, while completely separating the two channels from each other. By varying the laser intensity and the pulse duration, we measure the intensity and pulse length dependent momentum distributions for laser induced fragmentation of H+ 2 at 790 nm. These dissociation measurements are in agreement with the phenomena predicted using the adiabatic Floquet picture, e.g. bond softening, in addition to more sophisticated calculations done by solving the time-dependent Schrodinger equation in the Born-Oppenheimer representation. Furthermore, the structure seen in ionization in our measurements and soon after by others is explained via a unified diabatic Floquet picture, which includes both ionization and dissociation in a single intensity and wavelength dependent picture that includes nuclear motion. Additionally, we use the same experimental techniques and apparatus to probe the laser-induced dynamics of multi-electron diatomic molecules, e.g. O+2, N+2, and ND+. The most probable dissociation and ionization pathways producing the features seen in these measurements are discerned using the angular and kinetic-energy-release distributions in conjunction with the diabatic Floquet picture. Finally, we extend these experimental techniques and interpretive models to the simplest polyatomic molecule - H+ 3 , whose fragmentation presents challenges both in our first-of-their-kind experiments and in physical interpretation.

Doctor of Philosophy / Department of Physics / Itzik Ben-Itzhak / One ultimate goal of ultrafast, strong- field laser science is to coherently control chemical reactions. Present laser technology allows for the production of intense (>10[superscript]13 W/cm[superscript]2), ultrashort ( 5 fs), carrier-envelope phase-stabilized pulses. By knowing the electric field waveform, sub-cycle resolution on the order of 100's of attoseconds (1 as=10[superscript]-18 s) can be reached -- the timescale for electron motion. Meanwhile, the laser field strengths are comparable to that which binds electrons to atoms or molecules. In this intense-field ultrashort-pulse regime one can both measure and manipulate dynamics of strong-field, quantum-mechanical processes in atoms and molecules. Despite much progress in the technology, typical durations for which lasers can be reliably locked to a specific carrier-envelope phase ranges from a few minutes to a few hours. Experiments investigating carrier-envelope phase effects that have necessarily long data acquisition times, such as those requiring coincidence between fragments originating from the same atom or molecule, are thus challenging and uncommon. Therefore, we combined the new technology for measuring the carrier-envelope phase of each and every laser shot with other single-shot coincidence three-dimensional momentum imaging techniques to alleviate the need for carrier-envelope phase stabilized laser pulses. Using phase-tagged coincidence techniques, several targets and laser-induced processes were studied. One particular highlight uses this method to study the recollision process of non-sequential double ionization of argon. By measuring the momentum of the two electrons emitted in the process, we could study their energy sharing. Furthermore, by selecting certain carrier-envelope phase values, and therefore laser pulses with a particular waveform, events with single recollision could be isolated and further analyzed. Another highlight is our studies of carrier-envelope phase effects in the dissociation of the benchmark H[subscript]2[superscript[+] ion beam. Aided by near-exact quantum mechanical calculations, we could identify interfering pathways which lead to the observed spatial asymmetry. These and other similar experiments are described in this thesis as significant steps toward their ultimate control.

Master of Science / Department of Physics / Brett D. Esry / The two-state field-aligned (1-D) model has been employed to investigate the dissociation dynamics of a hydrogen molecular ion and its isotopes under the Born-Oppenheimer approximation without rotation. The emphasis of this work was on the role of mass during the dynamical dissociation processes and on the laser-induced branching ratios between different photon pathways. Firstly, we have found that scaling the pulse duration of the laser pulse, applied to H[subscript]2+ and D[subscript]2+ , by the square root of the mass ratio of these isotopes will produce similar structure in the nuclear kinetic energy release (KER) spectra. In fact, the similarity of the spectra is enhanced by including some averaging that is necessary for comparison with experiment. For this to occur, the same broad initial vibrational distribution and a short pulse are preferred. Using this scaling idea, it is possible to produce effectively shorter laser pulses by studying heavier isotopes, like D[subscript]2+. Secondly, we have demonstrated analytically and numerically that there is a carrier-envelope phase effect in the total dissociation probability (TDP) of H[subscript]2+, and this effect grows with nuclear mass. We further show that under the same laser conditions, the CEP effect in the asymmetry between breakup channels decreases with mass. Our analytic expressions enhance the idea that CEP effects can be understood as an interference between different n-photon processes. Thirdly, the trends in the dissociation dynamics of H[subscript]2+ and D[subscript]2+ in a 800nm ultra short intense laser field were demonstrated by studying the dissociation branching ratios of multiphoton processes as a function of the laser peak intensity (from 8[times]10[superscript]9 to 10[superscript]14 W/cm[superscript]2) or pulse length (5fs-7.5fs). Based on the two-state approximation, an energy-analysis method (EAM) was employed to separate multiphoton processes. The results show that the one-photon dissociation process dominates over all other photon processes under all the laser conditions applied in the calculations and that the zero-photon process contributes to a surprisingly large fraction of the total dissociation. Two- and three- photon dissociation are weaker processes, but become more and more important as the laser peak intensity and pulse length increases. A two-state Floquet method was used to check the accuracy of the EAM, and good agreement between the two methods was found, demonstrating the reliability of the EAM. In comparison with H[subscript]2+, D[subscript]2+ displays stronger two and three photon branching ratios (above-threshold dissociation - ATD), which can be attributed to the late arrival of D[subscript]2+ to the critical distance for ATD to occur due to its heavier mass. Therefore, this "mass" effect can be used to steer the molecular dissociation pathways.

Doctor of Philosophy / Department of Physics / Brett D. Esry / The Efimov effect plays a central role in few-body systems at ultracold temperature and has thus accelerated a lot of studies on its manifestation in the collisional stability of the quantum degenerate gases. Near broad Feshbach resonances, Efimov physics has been studied both theoretically and experimentally through the zero-energy scattering observables. We have extended the theoretical studies of Efimov physics to a much broader extent. In particular, we have investigated the three-body Efimov physics near narrow Feshbach resonances and have also identified the Efimov features beyond the zero temperature limit. We have found, near a narrow Feshbach resonance, the non-trivial contribution from both of the resonance width and the short-range physics to the three-body recombination and vibrational dimer relaxation. Remarkably, the collisional stability of the Feshbach molecules are found to be opposite to that near the broad resonances: an increased stability for molecules made by bosons and a decreased stability for those made by fermions. The universal physics observed near the narrow Feshbach resonances is further found not to be limited to the zero temperature observables. We have found that the general features of Efimov physics and those pertaining to a narrow resonance are manifested in different energy ranges above zero temperature. This opens the opportunity to observe Efimov physics by changing the collisional energy while keeping the atomic interaction fixed. The landscape of the universal Efimov physics is thus delineated in both of the interaction and the energy domain. We have also investigated Efimov physics in heteronuclear four-body systems where the complexity can be reduced by approximations. In particular, we have proposed ways for controllable production of the Efimov tri-atomic molecules by three-body or four-body recombinations involving four atoms. We have also confirmed the existence of four-body Efimov effect in a system of three heavy particles and one light particle, which has resolved a decade-long controversy on this topic. Finally, we have studied the collisional properties of four identical bosons in 1D, which is important to the experiments on the quantum gases confined in the 1D optical lattices.

Le rôle des deux paires de bases universelles inverse Hoogsteen U : A ( RHUAs ) présentent chez les ARNt standards , une dans la boucle T et l'autre dans le noyau de la forme en L , a été étudiée. Pour chacun des RHUAs , un criblage génétique spécialisé in vivo chez les bactéries , le système suppresseur ambre ( pour l'étude de la RHUA dans la boucle T ) et le système d'ARNt de la sélénocystéine ( tRNASec ) ( pour l'étude de la RHUA dans le noyau ) , ont été utilisé pour générer des variants fonctionnels à partir de multiples librairies combinatoires . Ces variants ont ensuite été séquencé et soumis à une analyse systématique qui comprend la modélisation informatique et un type d'analyse phylogénétique. Les résultats du système suppresseur ambre ont montré un ensemble de variants fonctionnels qui ne nécessitent pas le motif RHUA dans la boucle T et qui ont remplacé la méthode standard de l'interaction entre les boucles D et T avec une double hélice interboucle , ILDH . D'autres études ont abouti à la détermination d'un modèle In silico de l'alternative à la norme standard de la boucle T, sous le nom de type III . Les résultats du système tRNASec ont révélé que pour cette ARNt exceptionnel, l'absence de RHUA ( dans le noyau ) assure une flexibilité accrue qui est spécifiquement nécessaire pour la fonction de tRNASec . Ainsi, les ARNt standards , à la différence de tRNASec , avec la présence universelle de RHUA dans le noyau , a été naturellement sélectionnée pour être rigide . Pris ensemble, la RHUA joue un rôle essentiel dans la stabilisation des interactions tertiaires. / The role of two universally present reverse Hoogsteen U:A base pairs (RHUAs) in the T-loop and in the core of the L-shape of standard tRNA was studied. To study each of the RHUAs, bacterial in vivo genetic screens were used including the amber suppressor system (for the study of the RHUA in the T-loop) and the selenocysteine tRNA(tRNASec) system (for the study of the RHUA in the core). These screens generated functional variants from multiple combinatorial libraries. These variants were subsequently sequenced and subjected to a systematic analysis which included computer modeling and a type of phylogenetic analysis. The results from the amber suppressor system showed a set of functional variants which did not require the RHUA motif in the T-loop, and had replaced the standard way of interaction between the D and T loops with an interloop double helix, ILDH. Further study culminated in the determination of an insilico model of the alternative to the standard T-loop known as type III. The results from the tRNASec system revealed that for this exceptional tRNA, the absence of RHUA (in the core) ensures an enhanced flexibility that is specifically required for tRNASec function. Thus standard tRNAs, unlike tRNASec, with the universal presence of RHUA in the core have been naturally selected to be rigid. Taken together, RHUA plays an essential role in the stabilization of tertiary interactions.

Les protéines sont au coeur de la vie. Ce sont d'incroyables nanomachines moléculaires spécialisées et améliorées par des millions d'années d'évolution pour des fonctions bien définies dans la cellule. La structure des protéines, c'est-à-dire l'arrangement tridimensionnel de leurs atomes, est intimement liée à leurs fonctions. L'absence apparente de structure pour certaines protéines est aussi de plus en plus reconnue comme étant tout aussi cruciale. Les protéines amyloïdes en sont un exemple marquant : elles adoptent un ensemble de structures variées difficilement observables expérimentalement qui sont associées à des maladies neurodégénératives. Cette thèse, dans un premier temps, porte sur l'étude structurelle des protéines amyloïdes bêta-amyloïde (Alzheimer) et huntingtine (Huntington) lors de leur processus de repliement et d'auto-assemblage. Les résultats obtenus permettent de décrire avec une résolution atomique les interactions des ensembles structurels de ces deux protéines. Concernant la protéine bêta-amyloïde (AB), nos résultats identifient des différences structurelles significatives entre trois de ses formes physiologiques durant ses premières étapes d'auto-assemblage en environnement aqueux. Nous avons ensuite comparé ces résultats avec ceux obtenus au cours des dernières années par d'autres groupes de recherche avec des protocoles expérimentaux et de simulations variés. Des tendances claires émergent de notre comparaison quant à l'influence de la forme physiologique de AB sur son ensemble structurel durant ses premières étapes d'auto-assemblage. L'identification des propriétés structurelles différentes rationalise l'origine de leurs propriétés d'agrégation distinctes. Par ailleurs, l'identification des propriétés structurelles communes offrent des cibles potentielles pour des agents thérapeutiques empêchant la formation des oligomères responsables de la neurotoxicité. Concernant la protéine huntingtine, nous avons élucidé l'ensemble structurel de sa région fonctionnelle située à son N-terminal en environnement aqueux et membranaire. En accord avec les données expérimentales disponibles, nos résultats sur son repliement en environnement aqueux révèlent les interactions dominantes ainsi que l'influence sur celles-ci des régions adjacentes à la région fonctionnelle. Nous avons aussi caractérisé la stabilité et la croissance de structures nanotubulaires qui sont des candidats potentiels aux chemins d'auto-assemblage de la région amyloïde de huntingtine. Par ailleurs, nous avons également élaboré, avec un groupe d'expérimentateurs, un modèle détaillé illustrant les principales interactions responsables du rôle d'ancre membranaire de la région N-terminal, qui sert à contrôler la localisation de huntingtine dans la cellule. Dans un deuxième temps, cette thèse porte sur le raffinement d'un modèle gros-grain (sOPEP) et sur le développement d'un nouveau modèle tout-atome (aaOPEP) qui sont tous deux basés sur le champ de force gros-grain OPEP, couramment utilisé pour l'étude du repliement des protéines et de l'agrégation des protéines amyloïdes. L'optimisation de ces modèles a été effectuée dans le but d'améliorer les prédictions de novo de la structure de peptides par la méthode PEP-FOLD. Par ailleurs, les modèles OPEP, sOPEP et aaOPEP ont été inclus dans un nouveau code de dynamique moléculaire très flexible afin de grandement simplifier leurs développements futurs. / Proteins are at the center of life. They are formidable molecular nanomachines specialized and optimized during million years of evolution for well-defined functions in the cell. The structure of proteins, meaning the tridimensional setting of their atoms, is closely related to their function. Absence of structure for a subset of proteins is also recognized to be as crucial. Amyloid proteins is a striking example : they fold into an ensemble of various structures hardly observable experimentally that are associated with neurodegenerative diseases. This thesis, firstly, is on the study of the structural ensemble of the amyloid proteins amyloid-beta (Alzheimer) and huntingtin (Huntington) during their folding and aggregation. Our results describe in details, with an atomic resolution, the characteristic interactions present in the structural ensemble of these two proteins. Concerning the amyloid-beta protein (AB), our results show the structural differences between three of its physiological forms during its first aggregation steps in an aqueous environment. We have then compared these results with those obtained during the past few years by several other research groups using various experimental and simulation protocols. Clear trends come out of this comparison regarding the influence of AB physiological form on its structural ensemble during its first aggregation steps. Their distinct aggregation pathways are rationalized by the identified differences. For their part, the identified similarities offer targets for therapeutical compounds disrupting the aggregation of the neurotoxic oligomers. Concerning the huntingtin protein, we identify the structural ensemble of its functional region at its N-terminal in an aqueous environment and in a phospholipid membrane. In agreement with the available experimental results on the global structure of this region in aqueous solution, our results reveal the dominant interactions, at an atomic precision, in its structural ensemble as well as the influence of its neighboring regions. We have also characterized the stability and the growth of nanotube-like structures that could occur during the aggregation of the amyloid region of huntingtin. Moreover, we have developed, in collaboration with a group of experimentalists, a precise model describing the main membrane interactions of huntingtin N-terminal, which serves as a membrane anchor that controls the localization of huntingtin in the cell. Secondly, this thesis is on the refinement of a coarse-grained model (sOPEP) and on the development of a new all-atom model (aaOPEP) that are both based on the coarse-grained OPEP force field, commonly used to study protein folding and amyloid protein aggregation. The goal behind the optimization of these models is to improve the de novo structure prediction of the PEP-FOLD method. These three models -- OPEP, sOPEP and aaOPEP -- are now also implemented in a new molecular dynamics software that we have developed specifically to greatly ease their future developments.