With the recent completion of the Human Genome Project and the announcement of the $1000 Genome Race in 2003, the interest for developing faster and cheaper sequencing technologies is continuously growing. Nanopore sequencing offers one of the most promising new ideas. This method consists in reading DNA as it passes through a small aperture perforated through a membrane; a technique similar to decoding a magnetic tape in a tape player. The process of linearly moving a flexible chain from one side of a small channel to the other is called polymer translocation. However, the physics behind this process is still not well understood. During the last ten years, theorists proposed several scaling laws in order to describe this problem and explain experimental observations. The goal of this thesis is to shed light on some of these interesting theoretical predictions. One of the most important questions addressed in this thesis is the role of the hydrodynamic interactions in the polymer translocation process. Even though the impact of such interactions have been theoretically considered, they are neglected in most simulation models. One of our aims in this thesis is to look at the implications of increasing the pore diameter in the presence of hydrodynamic interactions. We use Molecular Dynamics simulations with explicit solvent particles to generate unbiased translocation events in order to characterize the screening of the hydrodynamic interactions by the membrane and to test the hypothesis that polymer translocation is a quasi-equilibrium process. The latter question is quite fundamental since this assumption is at the origin of most theoretical approaches. Another major goal of this thesis is to clarify the nature of the transition between the two translocation regimes dominated by the pore-polymer friction and the hydrodynamic drag of the subchains outside the channel, respectively. However, such an investigation requires the ability to simulate translocation events with a very wide range of polymer lengths. We thus propose a new Monte Carlo method based on a one-dimensional random-walk representation of the translocation problem that can easily be used to study chain lengths as large as 10' monomers. This model works in conjunction with an exact calculation technique to compute the key results of the translocation events such as the probability to occur and the average time duration. It is used to validate previous and make new theoretical predictions about translocation dynamics as the polymer and channel lengths are varied. It is also applied to the study of chain heterogeneity effects.

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This thesis consists of two parts. The first part is focused on the high resolution infrared-infrared (IRIR) double resonance spectroscopy study of the Rubidium dimer triplet ground state a3Σu+. We have observed fluorescence to this state for J=30, 50 and 70 rotational quantum numbers. We have used a perturbed pair of rovibrational levels in the A1Σu+ ~ b3Πu electronic states as an intermediate excitation step to the higher lying 23Πg state to get access by fluorescence decay to the a3Σu+ state. This allowed us to calculate the term values and the potential energy curve for the triplet ground state. The second part of the thesis is a computational study of lifetimes and transition dipole moment matrix elements for the sodium dimer ion pair states of 1Σg+ symmetry. These calculated parameters will be helpful for the design of a quadruple resonance based Autler-Townes spectroscopic probe of the transition dipole moments between these states and the A1Σu+ state. The calculated lifetime values compare well with results from literature when available. This work was supported by the National Science Foundation through awards PHY 0245311, PHY 0555608 and PHY 0855502. / Physics

Master of Science / Department of Physics / Itzhak Ben-Itzhak / Collisions between simple diatomic molecular ions and target atoms have previously been limited to studying a subset of reaction channels for a given experiment, or, for cases where all reaction channels involved were measured, only the cross sections have been reported in literature. Experimentalists are faced with the challenge of improving their techniques for studying these collisions in order to gain further physical insight into the processes which occur. Our group has made progress in studying the molecular dissociation channels from the collisions via a coincidence three-dimensional momentum imaging technique. This technique allows us to measure all reaction channels involved simultaneously, while separating the channels from each other. By re-design of the experimental apparatus, i.e. changing the target from a gas cell to an open geometry jet, we have gained the ability to measure recoil ions produced in the collision in addition to the molecular fragments. Furthermore, we can also study collisions where the molecular projectile does not dissociate as long as it scatters to large angles. Results from the collision cell setup will be shown and discussed as well as first results from the jet setup. This work is a contribution to a larger project, and the emphasis for this stage will be placed on the development of the experimental technique as well as improvements for the future of the project.