Electron flow through cytochrome P450

The cytochromes P450 (P450s) are a remarkable class of heme enzymes that catalyze the metabolism of xenobiotics and the biosynthesis of signaling molecules. Controlled electron flow into the thiolate-ligated heme active site allows P450s to activate molecular oxygen and hydroxylate aliphatic C–H bonds via the formation of high-valent metal-oxo intermediates (compounds I and II). Due to the reactive nature and short lifetimes of these intermediates, many of the fundamental steps in catalysis have not been observed directly. The Gray group and others have developed photochemical methods, known as “flash-quench,” for triggering electron transfer (ET) and generating redox intermediates in proteins in the absence of native ET partners. Photo-triggering affords a high degree of temporal precision for the gating of an ET event; the initial ET and subsequent reactions can be monitored on the nanosecond-to-second timescale using transient absorption (TA) spectroscopies. Chapter 1 catalogues critical aspects of P450 structure and mechanism, including the native pathway for formation of compound I, and outlines the development of photochemical processes that can be used to artificially trigger ET in proteins. Chapters 2 and 3 describe the development of these photochemical methods to establish electronic communication between a photosensitizer and the buried P450 heme. Chapter 2 describes the design and characterization of a Ru-P450-BM3 conjugate containing a ruthenium photosensitizer covalently tethered to the P450 surface, and nanosecond-to-second kinetics of the photo-triggered ET event are presented. By analyzing data at multiple wavelengths, we have identified the formation of multiple ET intermediates, including the catalytically relevant compound II; this intermediate is generated by oxidation of a bound water molecule in the ferric resting state enzyme. The work in Chapter 3 probes the role of a tryptophan residue situated between the photosensitizer and heme in the aforementioned Ru-P450 BM3 conjugate. Replacement of this tryptophan with histidine does not perturb the P450 structure, yet it completely eliminates the ET reactivity described in Chapter 2. The presence of an analogous tryptophan in Ru-P450 CYP119 conjugates also is necessary for observing oxidative ET, but the yield of heme oxidation is lower. Chapter 4 offers a basic description of the theoretical underpinnings required to analyze ET. Single-step ET theory is first presented, followed by extensions to multistep ET: electron “hopping.” The generation of “hopping maps” and use of a hopping map program to analyze the rate advantage of hopping over single-step ET is described, beginning with an established rhenium-tryptophan-azurin hopping system. This ET analysis is then applied to the Ru-tryptophan-P450 systems described in Chapter 2; this strongly supports the presence of hopping in Ru-P450 conjugates. Chapter 5 explores the implementation of flash-quench and other phototriggered methods to examine the native reductive ET and gas binding events that activate molecular oxygen. In particular, TA kinetics that demonstrate heme reduction on the microsecond timescale for four Ru-P450 conjugates are presented. In addition, we implement laser flash-photolysis of P450 ferrous–CO to study the rates of CO rebinding in the thermophilic P450 CYP119 at variable temperature. Chapter 6 describes the development and implementation of air-sensitive potentiometric redox titrations to determine the solution reduction potentials of a series of P450 BM3 mutants, which were designed for non-native cyclopropanation of styrene in vivo. An important conclusion from this work is that substitution of the axial cysteine for serine shifts the wild type reduction potential positive by 130 mV, facilitating reduction by biological redox cofactors in the presence of poorly-bound substrates. While this mutation abolishes oxygenation activity, these mutants are capable of catalyzing the cyclopropanation of styrene, even within the confines of an E. coli cell. Four appendices are also provided, including photochemical heme oxidation in ruthenium-modified nitric oxide synthase (Appendix A), general protocols (Appendix B), Chapter-specific notes (Appendix C) and Matlab scripts used for data analysis (Appendix D).

The optoelectronic swept-frequency laser and its applications in ranging, three-dimensional imaging, and coherent beam combining of chirped-seed amplifiers

This thesis explores the design, construction, and applications of the optoelectronic swept-frequency laser (SFL). The optoelectronic SFL is a feedback loop designed around a swept-frequency (chirped) semiconductor laser (SCL) to control its instantaneous optical frequency, such that the chirp characteristics are determined solely by a reference electronic oscillator. The resultant system generates precisely controlled optical frequency sweeps. In particular, we focus on linear chirps because of their numerous applications. We demonstrate optoelectronic SFLs based on vertical-cavity surface-emitting lasers (VCSELs) and distributed-feedback lasers (DFBs) at wavelengths of 1550 nm and 1060 nm. We develop an iterative bias current predistortion procedure that enables SFL operation at very high chirp rates, up to 10^16 Hz/sec. We describe commercialization efforts and implementation of the predistortion algorithm in a stand-alone embedded environment, undertaken as part of our collaboration with Telaris, Inc. We demonstrate frequency-modulated continuous-wave (FMCW) ranging and three-dimensional (3-D) imaging using a 1550 nm optoelectronic SFL.

We develop the technique of multiple source FMCW (MS-FMCW) reflectometry, in which the frequency sweeps of multiple SFLs are "stitched" together in order to increase the optical bandwidth, and hence improve the axial resolution, of an FMCW ranging measurement. We demonstrate computer-aided stitching of DFB and VCSEL sweeps at 1550 nm. We also develop and demonstrate hardware stitching, which enables MS-FMCW ranging without additional signal processing. The culmination of this work is the hardware stitching of four VCSELs at 1550 nm for a total optical bandwidth of 2 THz, and a free-space axial resolution of 75 microns.

We describe our work on the tomographic imaging camera (TomICam), a 3-D imaging system based on FMCW ranging that features non-mechanical acquisition of transverse pixels. Our approach uses a combination of electronically tuned optical sources and low-cost full-field detector arrays, completely eliminating the need for moving parts traditionally employed in 3-D imaging. We describe the basic TomICam principle, and demonstrate single-pixel TomICam ranging in a proof-of-concept experiment. We also discuss the application of compressive sensing (CS) to the TomICam platform, and perform a series of numerical simulations. These simulations show that tenfold compression is feasible in CS TomICam, which effectively improves the volume acquisition speed by a factor ten.

We develop chirped-wave phase-locking techniques, and apply them to coherent beam combining (CBC) of chirped-seed amplifiers (CSAs) in a master oscillator power amplifier configuration. The precise chirp linearity of the optoelectronic SFL enables non-mechanical compensation of optical delays using acousto-optic frequency shifters, and its high chirp rate simultaneously increases the stimulated Brillouin scattering (SBS) threshold of the active fiber. We characterize a 1550 nm chirped-seed amplifier coherent-combining system. We use a chirp rate of 5*10^14 Hz/sec to increase the amplifier SBS threshold threefold, when compared to a single-frequency seed. We demonstrate efficient phase-locking and electronic beam steering of two 3 W erbium-doped fiber amplifier channels, achieving temporal phase noise levels corresponding to interferometric fringe visibilities exceeding 98%.

Experiments with a laser interferometric gravitational wave antenna

Sources and effects of astrophysical gravitational radiation are explained briefly to motivate discussion of the Caltech 40 meter antenna, which employs laser interferometry to monitor proper distances between inertial test masses. Practical considerations in construction of the apparatus are described. Redesign of test mass systems has resulted in a reduction of noise from internal mass vibrations by up to two orders of magnitude at some frequencies. A laser frequency stabilization system was developed which corrects the frequency of an argon ion laser to a residual fluctuation level bounded by the spectral density √s_v(f) ≤ 60µHz/√Hz, at fluctuation frequencies near 1.2 kHz. These and other improvements have contributed to reducing the spectral density of equivalent gravitational wave strain noise to √s_h(f)≈10^(-19)/√ Hz at these frequencies.

Finally, observations made with the antenna in February and March of 1987 are described. Kilohertz-band gravitational waves produced by the remnant of the recent supernova are shown to be theoretically unlikely at the strength required for confident detection in this antenna (then operating at poorer sensitivity than that quoted above). A search for periodic waves in the recorded data, comprising Fourier analysis of four 105-second samples of the antenna strain signal, was used to place new upper limits on periodic gravitational radiation at frequencies between 305 Hz and 5 kHz. In particular, continuous waves of any polarization are ruled out above strain amplitudes of 1.2 x 10^(-18) R.M.S. for waves emanating from the direction of the supernova, and 6.2 x 10^(-19) R.M.S. for waves emanating from the galactic center, between 1.5 and 4 kilohertz. Between 305 Hz and 5kHz no strains greater than 1.2 x 10^(-17) R.M.S. were detected from either direction. Limitations of the analysis and potential improvements are discussed, as are prospects for future searches.

Electronic and kinetic processes in the Cu/CuCl double pulse laser

Kinetic and electronic processes in a Cu/CuCl double pulsed laser were investigated by measuring discharge and laser pulse characteristics, and by computer modeling. There are two time scales inherent to the operation of the Cu/CuCl laser. The first is during the interpulse afterglow (tens to hundreds of microseconds). The second is during the pumping pulse (tens of nanoseconds). It was found that the character of the pumping pulse is largely determined by the initial conditions provided by the interpulse afterglow. By tailoring the dissociation pulse to be long and low energy, and by conditioning the afterglow, one may select the desired initial conditions and thereby significantly improve laser performance. With a low energy dissociation pulse, the fraction of metastable copper obtained from a CuCl dissociation is low. By maintaining the afterglow, contributions to the metastable state from ion recombinations are prevented, and the plasma impedance remains low thereby increasing the rate of current rise during the pumping pulse. Computer models for the dissociation pulse, afterglow, pumping pulse and laser pulse reproduced experimentally observed behavior of laser pulse energy and power as a function of time delay, pumping pulse characteristics, and buffer gas pressure. The sensitivity of laser pulse properties on collisional processes (e.g., CuCl reassociation rates) was investigated.

Combustion of CS₂/O₂ in a laminar mixing layer and processes in the CO chemical laser

The combustion of CS₂ and O₂ in a free burning laminar mixing layer at low pressure was investigated using emission spectroscopy. The temperature fields, CO vibrational distributions, and CO concentrations were measured. The data indicate that vibration ally excited CO was produced in the mixing layer flames, but that there were no vibrational population inversions. In comparison with the CS₂/O₂ premixed flames, the mixing layer flames favored greater production of COS and CO₂. Computer modeling was used to study the mechanisms responsible for the production of COS and CO₂, and to study how the branching chain mechanism responsible for production of CO affects the behavior of the mixing layer flame. The influences of the gas additives, N₂O, COS, and CNBr, were also investigated.

Aperiodic structures in optics and integrated optics and the transverse Bragg reflector laser

The first part of this work describes the uses of aperiodic structures in optics and integrated optics. In particular, devices are designed, fabricated, tested and analyzed which make use of a chirped grating corrugation on the surface of a dielectric waveguide. These structures can be used as input-output couplers, multiplexers and demultiplexers, and broad band filters.

Next, a theoretical analysis is made of the effects of a random statistical variation in the thicknesses of layers in a dielectric mirror on its reflectivity properties. Unlike the intentional aperiodicity introduced in the chirped gratings, the aperiodicity in the Bragg reflector mirrors is unintentional and is present to some extent in all devices made. The analysis involved in studying these problems relies heavily on the coupled mode formalism. The results are compared with computer experiments, as well as tests of actual mirrors.

The second part of this work describes a novel method for confining light in the transverse direction in an injection laser. These so-called transverse Bragg reflector lasers confine light normal to the junction plane in the active region, through reflection from an adjacent layered medium. Thus, in principle, it is possible to guide light in a dielectric layer whose index is lower than that of the surrounding material. The design, theory and testing of these diode lasers are discussed.

Strength of tantalum at high pressures through Richtmyer-Meshkov laser compression experiments and simulations

Strength at extreme pressures (>1 Mbar or 100 GPa) and high strain rates (106-108 s-1) of materials is not well characterized. The goal of the research outlined in this thesis is to study the strength of tantalum (Ta) at these conditions. The Omega Laser in the Laboratory for Laser Energetics in Rochester, New York is used to create such extreme conditions. Targets are designed with ripples or waves on the surface, and these samples are subjected to high pressures using Omega’s high energy laser beams. In these experiments, the observational parameter is the Richtmyer-Meshkov (RM) instability in the form of ripple growth on single-mode ripples. The experimental platform used for these experiments is the “ride-along” laser compression recovery experiments, which provide a way to recover the specimens having been subjected to high pressures. Six different experiments are performed on the Omega laser using single-mode tantalum targets at different laser energies. The energy indicates the amount of laser energy that impinges the target. For each target, values for growth factor are obtained by comparing the profile of ripples before and after the experiment. With increasing energy, the growth factor increased.

Engineering simulations are used to interpret and correlate the measurements of growth factor to a measure of strength. In order to validate the engineering constitutive model for tantalum, a series of simulations are performed using the code Eureka, based on the Optimal Transportation Meshfree (OTM) method. Two different configurations are studied in the simulations: RM instabilities in single and multimode ripples. Six different simulations are performed for the single ripple configuration of the RM instability experiment, with drives corresponding to laser energies used in the experiments. Each successive simulation is performed at higher drive energy, and it is observed that with increasing energy, the growth factor increases. Overall, there is favorable agreement between the data from the simulations and the experiments. The peak growth factors from the simulations and the experiments are within 10% agreement. For the multimode simulations, the goal is to assist in the design of the laser driven experiments using the Omega laser. A series of three-mode and four-mode patterns are simulated at various energies and the resulting growth of the RM instability is computed. Based on the results of the simulations, a configuration is selected for the multimode experiments. These simulations also serve as validation for the constitutive model and the material parameters for tantalum that are used in the simulations.

By designing samples with initial perturbations in the form of single-mode and multimode ripples and subjecting these samples to high pressures, the Richtmyer-Meshkov instability is investigated in both laser compression experiments and simulations. By correlating the growth of these ripples to measures of strength, a better understanding of the strength of tantalum at high pressures is achieved.

Rewriting Schemes for Flash Memory

Flash memory is a leading storage media with excellent features such as random access and high storage density. However, it also faces significant reliability and endurance challenges. In flash memory, the charge level in the cells can be easily increased, but removing charge requires an expensive erasure operation. In this thesis we study rewriting schemes that enable the data stored in a set of cells to be rewritten by only increasing the charge level in the cells. We consider two types of modulation scheme; a convectional modulation based on the absolute levels of the cells, and a recently-proposed scheme based on the relative cell levels, called rank modulation. The contributions of this thesis to the study of rewriting schemes for rank modulation include the following: we

•propose a new method of rewriting in rank modulation, beyond the previously proposed method of “push-to-the-top”;

•study the limits of rewriting with the newly proposed method, and derive a tight upper bound of 1 bit per cell;

•extend the rank-modulation scheme to support rankings with repetitions, in order to improve the storage density;

•derive a tight upper bound of 2 bits per cell for rewriting in rank modulation with repetitions;

•construct an efficient rewriting scheme that asymptotically approaches the upper bound of 2 bit per cell.

The next part of this thesis studies rewriting schemes for a conventional absolute-levels modulation. The considered model is called “write-once memory” (WOM). We focus on WOM schemes that achieve the capacity of the model. In recent years several capacity-achieving WOM schemes were proposed, based on polar codes and randomness extractors. The contributions of this thesis to the study of WOM scheme include the following: we

•propose a new capacity-achievingWOM scheme based on sparse-graph codes, and show its attractive properties for practical implementation;

•improve the design of polarWOMschemes to remove the reliance on shared randomness and include an error-correction capability.

The last part of the thesis studies the local rank-modulation (LRM) scheme, in which a sliding window going over a sequence of real-valued variables induces a sequence of permutations. The LRM scheme is used to simulate a single conventional multi-level flash cell. The simulated cell is realized by a Gray code traversing all the relative-value states where, physically, the transition between two adjacent states in the Gray code is achieved by using a single “push-to-the-top” operation. The main results of the last part of the thesis are two constructions of Gray codes with asymptotically-optimal rate.

Investigation of competitive antagonist binding to the nicotinic acetylcholine receptor using voltage-jump and light-flash techniques

1. The effect of 2,2’-bis-[α-(trimethylammonium)methyl]azobenzene (2BQ), a photoisomerizable competitive antagonist, was studied at the nicotinic acetycholine receptor of Electrophorus electroplaques using voltage-jump and light-flash techniques.

2. 2BQ, at concentrations below 3 μΜ, reduced the amplitude of voltage-jump relaxations but had little effect on the voltage-jump relaxation time constants under all experimental conditions. At higher concentrations and voltages more negative than -150 mV, 2BQ caused significant open channel blockade.

3. Dose-ratio studies showed that the cis and trans isomers of 2BQ have equilibrium binding constants (K _ᵢ) of .33 and 1.0 μΜ, respectively. The binding constants determined for both isomers are independent of temperature, voltage, agonist concentration, and the nature of the agonist.

4. In a solution of predominantly cis-2BQ, visible-light flashes led to a net cis→trans isomerization and caused an increase in the agonist-induced current. This increase had at least two exponential components; the larger amplitude component had the same time constant as a subsequent voltage-jump relaxation; the smaller amplitude component was investigated using ultraviolet light flashes.

5. In a solution of predominantly trans-2BQ, UV-light flashes led to a net trans→cis isomerization and caused a net decrease in the agonist-induced current. This effect had at least two exponential components. The smaller and faster component was an increase in agonist-induced current and had a similar time constant to the voltage-jump relaxation. The larger component was a slow decrease in the agonist-induced current with rate constant approximately an order of magnitude less than that of the voltage-jump relaxation. This slow component provided a measure of the rate constant for dissociation of cis-2BQ (k_ = 60/s at 20°C). Simple modelling of the slope of the dose-rate curves yields an association rate constant of 1.6 x 10⁸/M/s. This agrees with the association rate constant of 1.8 x 10⁸/M/s estimated from the binding constant (K_i). The Q₁₀ of the dissociation rate constant of cis-2BQ was 3.3 between 6° and 20°C. The rate constants for association and dissociation of cis-28Q at receptors are independent of voltage, agonist concentration, and the nature of the agonist.

6. We have measured the molecular rate constants of a competitive antagonist which has roughly the same K _ᵢ as d-tubocurarine but interacts more slowly with the receptor. This leads to the conclusion that curare itself has an association rate constant of 4 x 10⁹/M/s or roughly as fast as possible for an encounter-limited reaction.

Magnetic field and pressure effects in a saturated gas laser amplifier

Theoretical and experimental studies of a gas laser amplifier are presented, assuming the amplifier is operating with a saturating optical frequency signal. The analysis is primarily concerned with the effects of the gas pressure and the presence of an axial magnetic field on the characteristics of the amplifying medium. Semiclassical radiation theory is used, along with a density matrix description of the atomic medium which relates the motion of single atoms to the macroscopic observables. A two-level description of the atom, using phenomenological source rates and decay rates, forms the basis of our analysis of the gas laser medium. Pressure effects are taken into account to a large extent through suitable choices of decay rate parameters.

Two methods for calculating the induced polarization of the atomic medium are used. The first method utilizes a perturbation expansion which is valid for signal intensities which barely reach saturation strength, and it is quite general in applicability. The second method is valid for arbitrarily strong signals, but it yields tractable solutions only for zero magnetic field or for axial magnetic fields large enough such that the Zeeman splitting is much larger than the power broadened homogeneous linewidth of the laser transition. The effects of pressure broadening of the homogeneous spectral linewidth are included in both the weak-signal and strong-signal theories; however the effects of Zeeman sublevel-mixing collisions are taken into account only in the weak-signal theory.

The behavior of a He-Ne gas laser amplifier in the presence of an axial magnetic field has been studied experimentally by measuring gain and Faraday rotation of linearly polarized resonant laser signals for various values of input signal intensity, and by measuring nonlinearity - induced anisotropy for elliptically polarized resonant laser signals of various input intensities. Two high-gain transitions in the 3.39-μ region were used for study: a J = 1 to J = 2 (3s₂ → 3p₄) transition and a J = 1 to J = 1 (3s₂ → 3p₂) transition. The input signals were tuned to the centers of their respective resonant gain lines.

The experimental results agree quite well with corresponding theoretical expressions which have been developed to include the nonlinear effects of saturation strength signals. The experimental results clearly show saturation of Faraday rotation, and for the J = 1 t o J = 1 transition a Faraday rotation reversal and a traveling wave gain dip are seen for small values of axial magnetic field. The nonlinearity induced anisotropy shows a marked dependence on the gas pressure in the amplifier tube for the J = 1 to J = 2 transition; this dependence agrees with the predictions of the general perturbational or weak signal theory when allowances are made for the effects of Zeeman sublevel-mixing collisions. The results provide a method for measuring the upper (neon 3s₂) level quadrupole moment decay rate, the dipole moment decay rates for the 3s₂ → 3p₄ and 3s₂ → 3p₂ transitions, and the effects of various types of collision processes on these decay rates.

An Optically recombined laser interferometer for gravitational wave detection

Kilometer scale interferometers for the detection of gravitational waves are currently under construction by the LIGO (Laser Interferometer Gravitational-wave Observatory) and VIRGO projects. These interferometers will consist of two Fabry-Perot cavities illuminated by a laser beam which is split in half by a beam splitter. A recycling mirror between the laser and the beam splitter will reflect the light returning from the beam splitter towards the laser back into the interferometer. The positions of the optical components in these interferometers must be controlled to a small fraction of a wavelength of the laser light. Schemes to extract signals necessary to control these optical components have been developed and demonstrated on the tabletop. In the large scale gravitational wave detectors the optical components must be suspended from vibration isolation platforms to achieve the necessary isolation from seismic motion. These suspended components present a new class of problems in controlling the interferometer, but also provide more exacting test of interferometer signal and noise models.

This thesis discusses the first operation of a suspended-mass Fabry-Perot-Michelson interferometer, in which signals carried by the optically recombined beams are used to detect and control all important mirror displacements. This interferometer uses an optical configuration and signal extraction scheme that is planned for the full scale LIGO interferometers with the simplification of the removal of the recycling mirror. A theoretical analysis of the performance that is expected from such an interferometer is presented and the experimental results are shown to be in generally good agreement.

Gas laser discharge noise and its effect on the laser output

A large portion of the noise in the light output of a laser oscillator is associated with the noise in the laser discharge. The effect of the discharge noise on the laser output has been studied. The discharge noise has been explained through an ac equivalent circuit of the laser discharge tube.

The discharge noise corresponds to time-varying spatial fluctuations in the electron density, the inverted population density and the dielectric permittivity of the laser medium from their equilibrium values. These fluctuations cause a shift in the resonant frequencies of the laser cavity. When the fluctuation in the dielectric permittivity of the laser medium is a longitudinally traveling wave (corresponding to the case in which moving striations exist in the positive column of the laser discharge), the laser output is frequency modulated.

The discharge noise has been analyzed by representing the laser discharge by an equivalent circuit. An appropriate ac equivalent circuit of a laser discharge tube has been obtained by considering the frequency spectrum of the current response of the discharge tube to an ac voltage modulation. It consist of a series ρLC circuit, which represents the discharge region, in parallel with a capacitance C', which comes mainly from the stray wiring. The equivalent inductance and capacitance of the discharge region have been calculated from the values of the resonant frequencies measured on discharge currents, gas pressures and lengths of the positive column. The experimental data provide for a set of typical values and dependencies on the discharge parameters for the equivalent inductance and capacitance of a discharge under laser operating conditions. It has been concluded from the experimental data that the equivalent inductance originates mainly from the positive column while the equivalent capacitance is due to the discharge region other than the positive column.

The ac equivalent circuit of the laser discharge has been shown analytically and experimentally to be applicable to analyzing the internal discharge noise. Experimental measurements have been made on the frequency of moving striations in a laser discharge. Its experimental dependence on the discharge current agrees very well with the expected dependence obtained from an analysis of the circuit and the experimental data on the equivalent circuit elements. The agreement confirms the validity of representing a laser discharge tube by its ac equivalent circuit in analyzing the striation phenomenon and other low frequency noises. Data have also been obtained for the variation of the striation frequency with an externally-applied longitudinal magnetic field and the increase in frequency has been attributed to a decrease in the equivalent inductance of the laser discharge.