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.

Doctor of Philosophy / Department of Physics / Vinod Kumarappan / In general, molecules in the gas phase are free to rotate, and measurements made on such samples are averaged over a randomly oriented distribution of molecules. Any orientation dependent information is lost in such measurements. The goal of the work presented here is to a) mitigate or completely do away with orientational averaging, and b) make fully resolved orientation dependent measurements. In pursuance of similar goals, over the past 50 years chemists and physicists have developed techniques to align molecules, or to measure their orientation and tag other quantities of interest with the orientation. We focus on laser induced alignment of asymmetric top molecules. The first major contribution of our work is the development of an effective method to align all molecular axes under field-free conditions. The method employs a sequence of nonresonant, impulsive laser pulses with varied ellipticities. The efficacy of the method is first demonstrated by solution of the time dependent Schr\"{o}dinger equation for iodobenzene, and then experimentally implemented to three dimensionally align 3,5 difluoroiodobenzene. Measurement from molecules aligned in this manner greatly reduces orientational averaging. The technique was developed via a thorough understanding and extensive computations of the dynamics of rotationally excited asymmetric top molecules. The second, and perhaps more important, contribution of our work is the development of a new measurement technique to extract the complete orientation dependence of a variety of molecular processes initiated by ultrashort laser pulses. The technique involves pump-probe measurements of the process of interest from a rotational wavepacket generated by impulsive excitation of asymmetric top molecules. We apply it to make the first measurement of the single ionization probability of an asymmetric top molecule in a strong field as a function of all relevant alignment angles. The measurement and associated calculations help identify the orbital from which the electron is ionized. We expect that this technique will be widely applicable to ultrafast-laser driven processes in molecules and provide unique insight into molecular physics and chemistry.

The studies presented in this thesis explore electronic energy transfer (EET) in light-harvesting antenna complexes and investigate the role of quantum coherence in EET. The dynamics of energy transfer are investigated in three distinct length scales and a different formulation of the exciton transport problem is applied at each scale. These scales include: the scale of a molecular dimer, the scale of a single protein and the scale of a molecular aggregate. The antenna protein phycoerythrin 545 (PE545) isolated from the photosynthetic cryptophyte algae Rhodomonas CS4 is specifically studied in two chapters of this thesis. It is found that formation of small aggregates delocalizes the excitation across chromophores of adjacent proteins, and that this delocalization has a dramatic effect in enhancing the rate of energy transfer between pigments. Furthermore, we investigate EET from a donor to an acceptor via an intermediate site and observe that interference of coherent pathways gives a finite correction to the transfer rate that is sensitively dependent on the nature of the vibrational interactions in the system. The statistical fluctuations of a system exhibiting EET are investigated in the final chapter. The techniques of non-equilibrium statistical mechanics are applied to investigate the steady-state of a typical system exhibiting EET that is perturbed out of equilibrium due to its interaction with a fluctuating bath.

The studies presented in this thesis explore electronic energy transfer (EET) in light-harvesting antenna complexes and investigate the role of quantum coherence in EET. The dynamics of energy transfer are investigated in three distinct length scales and a different formulation of the exciton transport problem is applied at each scale. These scales include: the scale of a molecular dimer, the scale of a single protein and the scale of a molecular aggregate. The antenna protein phycoerythrin 545 (PE545) isolated from the photosynthetic cryptophyte algae Rhodomonas CS4 is specifically studied in two chapters of this thesis. It is found that formation of small aggregates delocalizes the excitation across chromophores of adjacent proteins, and that this delocalization has a dramatic effect in enhancing the rate of energy transfer between pigments. Furthermore, we investigate EET from a donor to an acceptor via an intermediate site and observe that interference of coherent pathways gives a finite correction to the transfer rate that is sensitively dependent on the nature of the vibrational interactions in the system. The statistical fluctuations of a system exhibiting EET are investigated in the final chapter. The techniques of non-equilibrium statistical mechanics are applied to investigate the steady-state of a typical system exhibiting EET that is perturbed out of equilibrium due to its interaction with a fluctuating bath.

Lfc is a guanine nucleotide exchange factor (GEF) that activates the small GTPase RhoA, and its GEF activity is tightly regulated through protein-protein interactions, phosphorylation, and cellular localization. Lfc is anchored to microtubules through its interaction with the dynein light chain Tctex-1, which results in inhibition of Lfc's GEF activity. Here we present a crystallographic structure of Tctex-1 in complex with Lfc with residues 143-155 of Lfc bound at the Tctex-1 dimer interface. Structural alignment of our structure with Tctex-1 in complex with the dynein intermediate chain (DIC) shows the binding site of the DIC peptide and Lfc substantially overlap. Biochemical evidence, NMR perturbations assays and intrinsic fluorescence provide structural validation and support an extension of the Lfc binding site to the α-helices that may accommodate additional contact points with Tctex-1. We postulate a potential mechanism for Lfc’s recruitment to the microtubules through a tripartite complex with Tctex-1 and DIC.

Lfc is a guanine nucleotide exchange factor (GEF) that activates the small GTPase RhoA, and its GEF activity is tightly regulated through protein-protein interactions, phosphorylation, and cellular localization. Lfc is anchored to microtubules through its interaction with the dynein light chain Tctex-1, which results in inhibition of Lfc's GEF activity. Here we present a crystallographic structure of Tctex-1 in complex with Lfc with residues 143-155 of Lfc bound at the Tctex-1 dimer interface. Structural alignment of our structure with Tctex-1 in complex with the dynein intermediate chain (DIC) shows the binding site of the DIC peptide and Lfc substantially overlap. Biochemical evidence, NMR perturbations assays and intrinsic fluorescence provide structural validation and support an extension of the Lfc binding site to the α-helices that may accommodate additional contact points with Tctex-1. We postulate a potential mechanism for Lfc’s recruitment to the microtubules through a tripartite complex with Tctex-1 and DIC.

Doctor of Philosophy / Department of Physics / Itzhak Ben-Itzhak / Lasers are being used widely for the study and manipulation of the dynamics of atomic and molecular targets, and advances in laser technology makes it possible to explore new areas of research — for example attosecond physics. In order to probe the fragmentation dynamics of molecular ions, we have developed a coincidence three-dimensional momentum imaging method that allows the kinematically complete study of all fragments except electrons. Recent upgrades to this method allow the measurement of slow dissociation fragments, down to nearly zero velocity, in intense ultrafast laser fields. Evidences for the low energy breakup are presented using the benchmark molecules diatomic H[subscript]2[superscript]+ and polyatomic H[subscript]3[superscript]+ . The low energy fragments in H[subscript]2[superscript]+ dissociation are due to the intriguing zero-photon dissociation phenomenon. This first experimental evidence for the zero-photon dissociation is further supported by sophisticated theoretical treatment. We have explored the laser pulse length, intensity, wavelength, and chirp dependence of zero-photon dissociation of H[subscript]2[superscript]+, and the results are well described by a two-photon process based on stimulated Raman scattering. Similar studies of the slow dissociation of H[subscript]3[superscript]+ reveal that two-body dissociation is dominant over three-body dissociation. The most likely pathways leading to low-energy breakup into H[superscript]++H[subscript]2, in contradiction to the assessments of the channels in at least one previous study, are explored by varying the laser pulse duration and the wavelength. In addition, we have investigated the dissociation and single ionization of N[subscript]2[superscript]+ , and an interesting high energy feature in addition to the low energy has been observed at higher intensities. Such high energy results from the breakup of molecules in excited states are accessible at higher intensities where their potential energy is changing rapidly with the internuclear distance. We have extended the intense field ionization studies to other molecular ions N[subscript]2[superscript]+ , CO[superscript]+, NO[superscript]+, and O[subscript]2[superscript]+ . The dissociative ionization of these molecules follow a general mechanism, a stairstep ionization mechanism. Utilizing the capability of the upgraded experimental method we have measured the non-dissociative and dissociative ionization of CO[superscript]+ using different pulse lengths. The results suggest that dissociative ionization can be manipulated by suppressing some ionization paths.

Master of Science / Department of Physics / Brett D. Esry / In the last 20 years, advancements in laser technology have allowed for the production of intense laser pulses with durations in the femtosecond (10⁻¹⁵ second) regime, giving scientists the ability to probe nuclear dynamics on their natural time scale. Study of the dissociated fragments created by these intense fields can be used to learn about the molecular structure and dynamics. The work presented in this thesis focuses on controlling this light–molecule interaction in such a way that we can preferentially dissociate the molecule to a desired final product. The hydrogen molecular ion, HD⁺, as well as LiF serve as simple systems that can be studied theoretically for a broad range of laser parameters. Our goal in using these relatively simple systems is to capture the essential physics of the light–molecule interaction and develop general methods to describe these interactions in more complex systems.

Master of Science / Physics / Vinod Kumarappan / This report includes the experimental details and results of two experiments. The first experiment addresses carrier envelope phase (CEP) effects in higher order harmonic generation (HHG), and the second experiment is a pump-probe experiment on CO₂ molecules using ultrashort laser pulses. Ultrashort laser pulses that are only a few optical cycles long are of interest for studying different atomic and molecular processes. The CEP of such a pulse is an important parameter that can affect the experimental results. Because the laser pulses we used in the HHG experiment have random CEP, we tagged a given harmonic spectrum with the CEP of the fundamental laser pulse that generated it by measuring both shot-by-shot. The first chapter of this report is about the experimental details and the results we got from our CEP-tagged HHG experiment that enabled us to observe the interference of different quantum pathways. In the second experiment, discussed in the second chapter of this report, we tried to study the structure of the CO₂⁺ ion created by strong field ionization in a pump-probe experiment. For this experiment, we used an ultrashort laser pulse to ionize CO₂ molecules, and after various time delays we probed the ionic wave packet by ionizing CO₂⁺ with another ultrashort laser pulse. By performing Fourier analysis on the delay-dependent CO₂⁺⁺ yield, we were able to identify the populated states of CO₂⁺.

Doctor of Philosophy / Department of Physics / Igor V. Litvinyuk / The goal of this dissertation project was to study the dynamics of nuclear motion in diatomic (H[subscript]2, N[subscript]2, O[subscript]2, CO) and triatomic (CO[subscript]2) molecules initiated by the ionization and/or excitation of these molecules with near-IR few-cycle laser pulses. This dynamics includes vibrational and rotational motion on the electronic potential surfaces of the molecules and their molecular ions. The experimental techniques used included the pump-probe approach, laser Coulomb explosion imaging and the COLTRIMS technique. The results are presented in four chapters. A study of rotational and vibrational nuclear dynamics in H[subscript]2 and D[subscript]2 molecules and ions initiated by 8 fs near-IR pulses is presented in Chapter 4. Transient alignment of the neutral molecules was observed and simulated; rotational frequency components contributing to the rotational wavepacket dynamics were recovered. Chapter 5 is dedicated to revealing the contribution of excited dissociative states of D[subscript]2[superscript]+ ions to the process of fragmentation by electron recollision. It was shown that it is possible to isolate the process of resonant excitation and estimate the individual contributions of the [superscript]2sigma[subscript]u[superscript]+ and [superscript]2pi[subscript]u states. In Chapter 6 the subject of investigation is the nuclear dynamics of N[subscript]2, O[subscript]2 and CO molecules initiated by ionization of a neutral molecule by a short intense laser pulse. It was shown that the kinetic energy release of the Coulomb explosion fragments, measured as a function of the delay time between pump and probe pulses, reveals the behavior of nuclear wave packet evolution on electronic states of the molecular ions. It was shown that information on the dissociation and excitation pathways can be extracted from the experimental spectra and the relative contributions of particular electronic states can be estimated. Chapter 7 is focused on studying the fragmentation of CO[subscript]2 following the interaction of this molecule with the laser field. The most important result of this study was that it presented direct experimental evidence of charge-resonant enhanced ionization (CREI), a phenomenon well-studied for diatomic molecules and predicted theoretically for triatomic molecules. The critical internuclear distance, the relevant ionic charge state and a pair of charge-resonant states responsible for the CREI were also found.