The Synthetic Biology of N2-Fixing Cyanobacteria for Photosynthetic Terpenoid Production

In the last few decades, concerns over global climate change, energy security, and environmental pollution have been rising. To overcome these challenges, the concept of “-nth generation” biofuels has emerged as a strategy to convert solar radiation into fuels and bulk industrial chemicals for societal use, while decreasing our consumption of nonrenewable energy sources. Nitrogen-fixing cyanobacteria hold a distinct advantage in biofuel production over plants, given their ability to convert sunlight, air (CO2 and N2), and mineralized water to energy-dense carbon molecules, as well as fix atmospheric nitrogen gas into ammonia for metabolism. Engineered cyanobacteria with re-wired metabolic pathways have recently been designed through synthetic biology, and they possess the ability to synthesize new chemicals and biofuels, which are secreted from their cells. Terpenoids constitute one of the largest classes of organic molecules on Earth, and are attractive candidates as a fourth generation biofuel and industrial chemical. In cyanobacteria, the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway is responsible for building essential metabolites involved in photosynthesis, as well as precursors for terpenoid biosynthesis. This dissertation encompasses research focused on redirecting MEP flux in the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120 to engineered terpenoid sinks, namely, linalool (C10H18O) and farnesene (C15H24). Chapter 1 is a review of literature in the field of biofuels and cyanobacteria, and chapter 2 is an introduction/list of objectives for the research in this dissertation. In chapter 3, we present the genetic engineering of Anabaena to synthesize farnesene by expressing a plant farnesene synthase. In chapter 4, we present the genetic engineering of Anabaena to synthesize linalool during N2-fixation, and increased linalool production is accomplished by the over-expression of three ratelimiting enzymes in the MEP pathway. In chapter 5, we examine the feasibility of a blocking a native carbon reservoir in the cyanobacterium to increase metabolite and energy availability for terpenoid synthesis, as well as physiological aspects of glycogendeficiency in the cyanobacterium during diazotrophic growth. In chapter 6, we focus on introducing a synthetic photorespiratory bypass to reduce photorespiration and increase carbon partitioning towards linalool synthesis

Preparation of nondegenerate coherent superpositions in a three-state ladder system assisted by Stark Shifts

We propose a technique to prepare coherent superpositions of two nondegenerate quantum states in a three-state ladder system, driven by two simultaneous fields near resonance with an intermediate state. The technique, of potential application to enhancement of nonlinear processes, uses adiabatic passage assisted by dynamic Stark shifts induced by a third laser field. The method offers significant advantages over alternative techniques: (\i) it does not require laser pulses of specific shape and duration and (\ii) it requires less intense fields than schemes based on two-photon excitation with non-resonant intermediate states. We discuss possible experimental implementation for enhancement of frequency conversion in mercury atoms.Comment: 22 pages, 8 figures, 1 table, submitted to PHys. Rev.

Photoionization Suppression by Continuum Coherence: Experiment and Theory

We present experimental and theoretical results of a detailed study of laser-induced continuum structures (LICS) in the photoionization continuum of helium out of the metastable state 2s $^1S_0$. The continuum dressing with a 1064 nm laser, couples the same region of the continuum to the {4s $^1S_0$} state. The experimental data, presented for a range of intensities, show pronounced ionization suppression (by as much as 70% with respect to the far-from-resonance value) as well as enhancement, in a Beutler-Fano resonance profile. This ionization suppression is a clear indication of population trapping mediated by coupling to a contiuum. We present experimental results demonstrating the effect of pulse delay upon the LICS, and for the behavior of LICS for both weak and strong probe pulses. Simulations based upon numerical solution of the Schr\"{o}dinger equation model the experimental results. The atomic parameters (Rabi frequencies and Stark shifts) are calculated using a simple model-potential method for the computation of the needed wavefunctions. The simulations of the LICS profiles are in excellent agreement with experiment. We also present an analytic formulation of pulsed LICS. We show that in the case of a probe pulse shorter than the dressing one the LICS profile is the convolution of the power spectra of the probe pulse with the usual Fano profile of stationary LICS. We discuss some consequences of deviation from steady-state theory.Comment: 29 pages, 17 figures, accepted to PR

Correction of Arbitrary Errors in Population Inversion of Quantum Systems by Universal Composite Pulses

We introduce universal broadband composite pulse sequences for robust high-fidelity population inversion in two-state quantum systems, which compensate deviations in any experimental parameter (e.g. pulse amplitude, pulse duration, detuning from resonance, Stark shifts, unwanted frequency chirp, etc.) and are applicable with any pulse shape. We demonstrate the efficiency and universality of these composite pulses by experimental data on rephasing of atomic coherences in a $\text{Pr}^{3+}\text{:}\text{Y}_2\text{SiO}_5$ crystal

Experimental demonstration of composite stimulated Raman adiabatic passage

We experimentally demonstrate composite stimulated Raman adiabatic passage (CSTIRAP), which combines the concepts of composite pulse sequences and adiabatic passage. The technique is applied for population transfer in a rare-earth doped solid. We compare the performance of CSTIRAP with conventional single and repeated STIRAP, either in the resonant or the highly detuned regime. In the latter case, CSTIRAP improves the peak transfer efficiency and robustness, boosting the transfer efficiency substantially compared to repeated STIRAP. We also propose and demonstrate a universal version of CSTIRAP, which shows improved performance compared to the originally proposed composite version. Our findings pave the way towards new STIRAP applications, which require repeated excitation cycles, e.g., for momentum transfer in atom optics, or dynamical decoupling to invert arbitrary superposition states in quantum memories.Comment: 11 pages, 5 figure

Rephasing efficiency of sequences of phased pulses in spin-echo and light-storage experiments

We investigate the rephasing efficiency of sequences of phased pulses for spin echoes and light storage by electromagnetically induced transparency (EIT). We derive a simple theoretical model and show that the rephasing efficiency is very sensitive to the phases of the imperfect rephasing pulses. The obtained efficiency differs substantially for spin echoes and EIT light storage, which is due to the spatially retarded coherence phases after EIT light storage. Similar behavior is also expected for other light-storage protocols with spatial retardation or for rephasing of collective quantum states with an unknown or undefined phase, e.g., as relevant in single-photon storage. We confirm the predictions of our theoretical model by experiments in a Pr$^{3+}$:Y$_{2}$SiO$_{5}$ crystal

Two-Photon Excitation of Low-Lying Electronic Quadrupole States in Atomic Clusters

A simple scheme of population and detection of low-lying electronic quadrupole modes in free small deformed metal clusters is proposed. The scheme is analyzed in terms of the TDLDA (time-dependent local density approximation) calculations. As test case, the deformed cluster $Na^+_{11}$ is considered. Long-living quadrupole oscillations are generated via resonant two-photon (two-dipole) excitation and then detected through the appearance of satellites in the photoelectron spectra generated by a probe pulse. Femtosecond pump and probe pulses with intensities $I = 2\cdot 10^{10} - 2\cdot 10^{11} W/cm^2$ and pulse duration $T = 200 - 500$ fs are found to be optimal. The modes of interest are dominated by a single electron-hole pair and so their energies, being combined with the photoelectron data for hole states, allow to gather new information about mean-field spectra of valence electrons in the HOMO-LUMO region. Besides, the scheme allows to estimate the lifetime of electron-hole pairs and hence the relaxation time of electronic energy into ionic heat.Comment: 4 pages, 4 figure

Universal Composite Pulses for Efficient Population Inversion with an Arbitrary Excitation Profile

We introduce a method to rotate arbitrarily the excitation profile of universal broadband composite pulse sequences for robust high-fidelity population inversion. These pulses compensate deviations in any experimental parameter (e.g. pulse amplitude, pulse duration, detuning from resonance, Stark shifts, unwanted frequency chirp, etc.) and are applicable with any pulse shape. The rotation allows to achieve higher order robustness to any combination of pulse area and detuning errors at no additional cost. The latter can be particularly useful, e.g., when detuning errors are due to Stark shifts that are correlated with the power of the applied field. We demonstrate the efficiency and universality of these composite pulses by experimental implementation for rephasing of atomic coherences in a $\text{Pr}^{3+}\text{:}\text{Y}_2\text{SiO}_5\:$ crystal.Comment: arXiv admin note: text overlap with arXiv:1403.120

Theory of bright-state stimulated Raman adiabatic passage

We describe analytically and numerically the process of population transfer by stimulated Raman adiabatic passage through a bright state when the pulses propagate in a medium. Limitations of the adiabaticity are analyzed and interpreted in terms of reshaping of the pulses. We find parameters for the pulses for which the population transfer is nearly complete over long distances.Comment: 9 pages, 9 figure