Nonclassical excitation and quantum interference in a three level atom

Non-classical properties and quantum interference (QI) in two-photon excitation of a three level atom (|1〉), |2〉, |3〉) in a ladder configuration, illuminated by multiple fields in non-classical (squeezed) and/or classical (coherent) states, is studied. Fundamentally new effects associated with quantum correlations in the squeezed fields and QI due to multiple excitation pathways have been observed. Theoretical studies and extrapolations of these findings have revealed possible applications which are far beyond any current capabilities, including ultrafast nonlinear mixing, ultrafast homodyne detection and frequency metrology. The atom used throughout the experiments was Cesium, which was magneto-optically trapped in a vapor cell to produce a Doppler-free sample. For the first part of the work the |1〉 → |2〉 → |3〉 transition (corresponding to the 6S_1/2F = 4 → 6P_3/2F' = 5 → 6D_5/2F" = 6 transition) was excited by using the quantum-correlated signal (Ɛ_s) and idler (Ɛ_i) output fields of a subthreshold non-degenerate optical parametric oscillator, which was tuned so that the signal and idler fields were resonant with the |1〉 → |2〉 and |2〉 → |3〉 transitions, respectively. In contrast to excitation with classical fields for which the excitation rate as a function of intensity has always an exponent greater than or equal to two, excitation with squeezed-fields has been theoretically predicted to have an exponent that approaches unity for small enough intensities. This was verified experimentally by probing the exponent down to a slope of 1.3, demonstrating for the first time a purely non-classical effect associated with the interaction of squeezed fields and atoms. In the second part excitation of the two-photon transition by three phase coherent fields Ɛ₁ , Ɛ₂ and Ɛ₀, resonant with the dipole |1〉 → |2〉 and |2〉 → |3〉 and quadrupole |1〉 → |3〉 transitions, respectively, is studied. QI in the excited state population is observed due to two alternative excitation pathways. This is equivalent to nonlinear mixing of the three excitation fields by the atom. Realizing that in the experiment the three fields are spaced in frequency over a range of 25 THz, and extending this scheme to other energy triplets and atoms, leads to the discovery that ranges up to 100's of THz can be bridged in a single mixing step. Motivated by these results, a master equation model has been developed for the system and its properties have been extensively studied.

Phase conjugation via four-wave mixing in a resonant medium

This thesis describes the theoretical solution and experimental verification of phase conjugation via nondegenerate four-wave mixing in resonant media. The theoretical work models the resonant medium as a two-level atomic system with the lower state of the system being the ground state of the atom. Working initially with an ensemble of stationary atoms, the density matrix equations are solved by third-order perturbation theory in the presence of the four applied electro-magnetic fields which are assumed to be nearly resonant with the atomic transition. Two of the applied fields are assumed to be non-depleted counterpropagating pump waves while the third wave is an incident signal wave. The fourth wave is the phase conjugate wave which is generated by the interaction of the three previous waves with the nonlinear medium. The solution of the density matrix equations gives the local polarization of the atom. The polarization is used in Maxwell's equations as a source term to solve for the propagation and generation of the signal wave and phase conjugate wave through the nonlinear medium. Studying the dependence of the phase conjugate signal on the various parameters such as frequency, we show how an ultrahigh-Q isotropically sensitive optical filter can be constructed using the phase conjugation process.

In many cases the pump waves may saturate the resonant medium so we also present another solution to the density matrix equations which is correct to all orders in the amplitude of the pump waves since the third-order solution is correct only to first-order in each of the field amplitudes. In the saturated regime, we predict several new phenomena associated with degenerate four-wave mixing and also describe the ac Stark effect and how it modifies the frequency response of the filtering process. We also show how a narrow bandwidth optical filter with an efficiency greater than unity can be constructed.

In many atomic systems the atoms are moving at significant velocities such that the Doppler linewidth of the system is larger than the homogeneous linewidth. The latter linewidth dominates the response of the ensemble of stationary atoms. To better understand this case the density matrix equations are solved to third-order by perturbation theory for an atom of velocity v. The solution for the polarization is then integrated over the velocity distribution of the macroscopic system which is assumed to be a gaussian distribution of velocities since that is an excellent model of many real systems. Using the Doppler broadened system, we explain how a tunable optical filter can be constructed whose bandwidth is limited by the homogeneous linewidth of the atom while the tuning range of the filter extends over the entire Doppler profile.

Since it is a resonant system, sodium vapor is used as the nonlinear medium in our experiments. The relevant properties of sodium are discussed in great detail. In particular, the wavefunctions of the 3S and 3P states are analyzed and a discussion of how the 3S-3P transition models a two-level system is given.

Using sodium as the nonlinear medium we demonstrate an ultrahigh-Q optical filter using phase conjugation via nondegenerate four-wave mixing as the filtering process. The filter has a FWHM bandwidth of 41 MHz and a maximum efficiency of 4 x 10^-3. However, our theoretical work and other experimental work with sodium suggest that an efficient filter with both gain and a narrower bandwidth should be quite feasible.

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.

Spin dynamics of pulsed nuclear magnetic double resonance in solids

In the first part of this thesis, experiments utilizing an NMR phase interferometric concept are presented. The spinor character of two-level systems is explicitly demonstrated by using this concept. Following this is the presentation of an experiment which uses this same idea to measure relaxation times of off-diagonal density matrix elements corresponding to magnetic-dipole-forbidden transitions in a ^(13)C-^1H, AX spin system. The theoretical background for these experiments and the spin dynamics of the interferometry are discussed also.

The second part of this thesis deals with NMR dipolar modulated chemical shift spectroscopy, with which internuclear bond lengths and bond angles with respect to the chemical shift principal axis frame are determined from polycrystalline samples. Experiments using benzene and calcium formate verify the validity of the technique in heteronuclear (^(13)C-^1H) systems. Similar experiments on powdered trichloroacetic acid confirm the validity in homonuclear (^1H- ^1H) systems. The theory and spin dynamics are explored in detail, and the effects of a number of multiple pulse sequences are discussed.

The last part deals with an experiment measuring the ^(13)C chemical shift tensor in K_2Pt(CN)_4Br_(0.3) • 3H_2O, a one-dimensional conductor. The ^(13)C spectra are strongly affected by ^(14)N quadrupolar interactions via the ^(13)C - ^(14)N dipolar interaction. Single crystal rotation spectra are shown.

An appendix discussing the design, construction, and performance of a single-coil double resonance NMR sample probe is included.

First principles based multiparadigm modeling of electronic structures and dynamics

Electronic structures and dynamics are the key to linking the material composition and structure to functionality and performance.

An essential issue in developing semiconductor devices for photovoltaics is to design materials with optimal band gaps and relative positioning of band levels. Approximate DFT methods have been justified to predict band gaps from KS/GKS eigenvalues, but the accuracy is decisively dependent on the choice of XC functionals. We show here for CuInSe₂ and CuGaSe₂, the parent compounds of the promising CIGS solar cells, conventional LDA and GGA obtain gaps of 0.0-0.01 and 0.02-0.24 eV (versus experimental values of 1.04 and 1.67 eV), while the historically first global hybrid functional, B3PW91, is surprisingly the best, with band gaps of 1.07 and 1.58 eV. Furthermore, we show that for 27 related binary and ternary semiconductors, B3PW91 predicts gaps with a MAD of only 0.09 eV, which is substantially better than all modern hybrid functionals, including B3LYP (MAD of 0.19 eV) and screened hybrid functional HSE06 (MAD of 0.18 eV).

The laboratory performance of CIGS solar cells (> 20% efficiency) makes them promising candidate photovoltaic devices. However, there remains little understanding of how defects at the CIGS/CdS interface affect the band offsets and interfacial energies, and hence the performance of manufactured devices. To determine these relationships, we use the B3PW91 hybrid functional of DFT with the AEP method that we validate to provide very accurate descriptions of both band gaps and band offsets. This confirms the weak dependence of band offsets on surface orientation observed experimentally. We predict that the CBO of perfect CuInSe₂/CdS interface is large, 0.79 eV, which would dramatically degrade performance. Moreover we show that band gap widening induced by Ga adjusts only the VBO, and we find that Cd impurities do not significantly affect the CBO. Thus we show that Cu vacancies at the interface play the key role in enabling the tunability of CBO. We predict that Na further improves the CBO through electrostatically elevating the valence levels to decrease the CBO, explaining the observed essential role of Na for high performance. Moreover we find that K leads to a dramatic decrease in the CBO to 0.05 eV, much better than Na. We suggest that the efficiency of CIGS devices might be improved substantially by tuning the ratio of Na to K, with the improved phase stability of Na balancing phase instability from K. All these defects reduce interfacial stability slightly, but not significantly.

A number of exotic structures have been formed through high pressure chemistry, but applications have been hindered by difficulties in recovering the high pressure phase to ambient conditions (i.e., one atmosphere and room temperature). Here we use dispersion-corrected DFT (PBE-ulg flavor) to predict that above 60 GPa the most stable form of N₂O (the laughing gas in its molecular form) is a 1D polymer with an all-nitrogen backbone analogous to cis-polyacetylene in which alternate N are bonded (ionic covalent) to O. The analogous trans-polymer is only 0.03-0.10 eV/molecular unit less stable. Upon relaxation to ambient conditions both polymers relax below 14 GPa to the same stable non-planar trans-polymer, accompanied by possible electronic structure transitions. The predicted phonon spectrum and dissociation kinetics validate the stability of this trans-poly-NNO at ambient conditions, which has potential applications as a new type of conducting polymer with all-nitrogen chains and as a high-energy oxidizer for rocket propulsion. This work illustrates in silico materials discovery particularly in the realm of extreme conditions.

Modeling non-adiabatic electron dynamics has been a long-standing challenge for computational chemistry and materials science, and the eFF method presents a cost-efficient alternative. However, due to the deficiency of FSG representation, eFF is limited to low-Z elements with electrons of predominant s-character. To overcome this, we introduce a formal set of ECP extensions that enable accurate description of p-block elements. The extensions consist of a model representing the core electrons with the nucleus as a single pseudo particle represented by FSG, interacting with valence electrons through ECPs. We demonstrate and validate the ECP extensions for complex bonding structures, geometries, and energetics of systems with p-block character (C, O, Al, Si) and apply them to study materials under extreme mechanical loading conditions.

Despite its success, the eFF framework has some limitations, originated from both the design of Pauli potentials and the FSG representation. To overcome these, we develop a new framework of two-level hierarchy that is a more rigorous and accurate successor to the eFF method. The fundamental level, GHA-QM, is based on a new set of Pauli potentials that renders exact QM level of accuracy for any FSG represented electron systems. To achieve this, we start with using exactly derived energy expressions for the same spin electron pair, and fitting a simple functional form, inspired by DFT, against open singlet electron pair curves (H₂ systems). Symmetric and asymmetric scaling factors are then introduced at this level to recover the QM total energies of multiple electron pair systems from the sum of local interactions. To complement the imperfect FSG representation, the AMPERE extension is implemented, and aims at embedding the interactions associated with both the cusp condition and explicit nodal structures. The whole GHA-QM+AMPERE framework is tested on H element, and the preliminary results are promising.

Design of antenna-coupled lumped-element titanium nitride KIDs for long-wavelength multi-band continuum imaging

Many applications in cosmology and astrophysics at millimeter wavelengths including CMB polarization, studies of galaxy clusters using the Sunyaev-Zeldovich effect (SZE), and studies of star formation at high redshift and in our local universe and our galaxy, require large-format arrays of millimeter-wave detectors. Feedhorn and phased-array antenna architectures for receiving mm-wave light present numerous advantages for control of systematics, for simultaneous coverage of both polarizations and/or multiple spectral bands, and for preserving the coherent nature of the incoming light. This enables the application of many traditional "RF" structures such as hybrids, switches, and lumped-element or microstrip band-defining filters.

Simultaneously, kinetic inductance detectors (KIDs) using high-resistivity materials like titanium nitride are an attractive sensor option for large-format arrays because they are highly multiplexable and because they can have sensitivities reaching the condition of background-limited detection. A KID is a LC resonator. Its inductance includes the geometric inductance and kinetic inductance of the inductor in the superconducting phase. A photon absorbed by the superconductor breaks a Cooper pair into normal-state electrons and perturbs its kinetic inductance, rendering it a detector of light. The responsivity of KID is given by the fractional frequency shift of the LC resonator per unit optical power.

However, coupling these types of optical reception elements to KIDs is a challenge because of the impedance mismatch between the microstrip transmission line exiting these architectures and the high resistivity of titanium nitride. Mitigating direct absorption of light through free space coupling to the inductor of KID is another challenge. We present a detailed titanium nitride KID design that addresses these challenges. The KID inductor is capacitively coupled to the microstrip in such a way as to form a lossy termination without creating an impedance mismatch. A parallel plate capacitor design mitigates direct absorption, uses hydrogenated amorphous silicon, and yields acceptable noise. We show that the optimized design can yield expected sensitivities very close to the fundamental limit for a long wavelength imager (LWCam) that covers six spectral bands from 90 to 400 GHz for SZE studies.

Excess phase (frequency) noise has been observed in KID and is very likely caused by two-level systems (TLS) in dielectric materials. The TLS hypothesis is supported by the measured dependence of the noise on resonator internal power and temperature. However, there is still a lack of a unified microscopic theory which can quantitatively model the properties of the TLS noise. In this thesis we derive the noise power spectral density due to the coupling of TLS with phonon bath based on an existing model and compare the theoretical predictions about power and temperature dependences with experimental data. We discuss the limitation of such a model and propose the direction for future study.

I. Numerical solution of exact pair equations. II. Numerical solution of first-order pair equations

Part I

Numerical solutions to the S-limit equations for the helium ground state and excited triplet state and the hydride ion ground state are obtained with the second and fourth difference approximations. The results for the ground states are superior to previously reported values. The coupled equations resulting from the partial wave expansion of the exact helium atom wavefunction were solved giving accurate S-, P-, D-, F-, and G-limits. The G-limit is -2.90351 a.u. compared to the exact value of the energy of -2.90372 a.u.

Part II

The pair functions which determine the exact first-order wavefunction for the ground state of the three-electron atom are found with the matrix finite difference method. The second- and third-order energies for the (1s1s)¹S, (1s2s)³S, and (1s2s)¹S states of the two-electron atom are presented along with contour and perspective plots of the pair functions. The total energy for the three-electron atom with a nuclear charge Z is found to be E(Z) = -1.125•Z² +1.022805•Z-0.408138-0.025515•(1/Z)+O(1/Z²)a.u.

Atomic-level structure and deformation in metallic glasses

Metallic glasses (MGs) are a relatively new class of materials discovered in 1960 and lauded for its high strengths and superior elastic properties. Three major obstacles prevent their widespread use as engineering materials for nanotechnology and industry: 1) their lack of plasticity mechanisms for deformation beyond the elastic limit, 2) their disordered atomic structure, which prevents effective study of their structure-to-property relationships, and 3) their poor glass forming ability, which limits bulk metallic glasses to sizes on the order of centimeters. We focused on understanding the first two major challenges by observing the mechanical properties of nanoscale metallic glasses in order to gain insight into its atomic-level structure and deformation mechanisms. We found that anomalous stable plastic flow emerges in room-temperature MGs at the nanoscale in wires as little as ~100 nanometers wide regardless of fabrication route (ion-irradiated or not). To circumvent experimental challenges in characterizing the atomic-level structure, extensive molecular dynamics simulations were conducted using approximated (embedded atom method) potentials to probe the underlying processes that give rise to plasticity in nanowires. Simulated results showed that mechanisms of relaxation via the sample free surfaces contribute to tensile ductility in these nanowires. Continuing with characterizing nanoscale properties, we studied the fracture properties of nano-notched MGnanowires and the compressive response of MG nanolattices at cryogenic (~130 K) temperatures. We learned from these experiments that nanowires are sensitive to flaws when the (amorphous) microstructure does not contribute stress concentrations, and that nano-architected structures with MG nanoribbons are brittle at low temperatures except when elastic shell buckling mechanisms dominate at low ribbon thicknesses (~20 nm), which instead gives rise to fully recoverable nanostructures regardless of temperature. Finally, motivated by understanding structure-to-property relationships in MGs, we studied the disordered atomic structure using a combination of in-situ X-ray tomography and X-ray diffraction in a diamond anvil cell and molecular dynamics simulations. Synchrotron X-ray experiments showed the progression of the atomic-level structure (in momentum space) and macroscale volume under increasing hydrostatic pressures. Corresponding simulations provided information on the real space structure, and we found that the samples displayed fractal scaling (r^d ∝ V, d < 3) at short length scales (< ~8 Å), and exhibited a crossover to a homogeneous scaling (d = 3) at long length scales. We examined this underlying fractal structure of MGs with parallels to percolation clusters and discuss the implications of this structural analogy to MG properties and the glass transition phenomenon.

Interacting single atoms with nanophotonics for chip-integrated quantum networks

Underlying matter and light are their building blocks of tiny atoms and photons. The ability to control and utilize matter-light interactions down to the elementary single atom and photon level at the nano-scale opens up exciting studies at the frontiers of science with applications in medicine, energy, and information technology. Of these, an intriguing front is the development of quantum networks where N >> 1 single-atom nodes are coherently linked by single photons, forming a collective quantum entity potentially capable of performing quantum computations and simulations. Here, a promising approach is to use optical cavities within the setting of cavity quantum electrodynamics (QED). However, since its first realization in 1992 by Kimble et al., current proof-of-principle experiments have involved just one or two conventional cavities. To move beyond to N >> 1 nodes, in this thesis we investigate a platform born from the marriage of cavity QED and nanophotonics, where single atoms at ~100 nm near the surfaces of lithographically fabricated dielectric photonic devices can strongly interact with single photons, on a chip. Particularly, we experimentally investigate three main types of devices: microtoroidal optical cavities, optical nanofibers, and nanophotonic crystal based structures. With a microtoroidal cavity, we realized a robust and efficient photon router where single photons are extracted from an incident coherent state of light and redirected to a separate output with high efficiency. We achieved strong single atom-photon coupling with atoms located ~100 nm near the surface of a microtoroid, which revealed important aspects in the atom dynamics and QED of these systems including atom-surface interaction effects. We present a method to achieve state-insensitive atom trapping near optical nanofibers, critical in nanophotonic systems where electromagnetic fields are tightly confined. We developed a system that fabricates high quality nanofibers with high controllability, with which we experimentally demonstrate a state-insensitive atom trap. We present initial investigations on nanophotonic crystal based structures as a platform for strong atom-photon interactions. The experimental advances and theoretical investigations carried out in this thesis provide a framework for and open the door to strong single atom-photon interactions using nanophotonics for chip-integrated quantum networks.

Mechanistic studies of reactions at the single-molecule level using microfluidics with applications in molecular diagnostics

Motivated by needs in molecular diagnostics and advances in microfabrication, researchers started to seek help from microfluidic technology, as it provides approaches to achieve high throughput, high sensitivity, and high resolution. One strategy applied in microfluidics to fulfill such requirements is to convert continuous analog signal into digitalized signal. One most commonly used example for this conversion is digital PCR, where by counting the number of reacted compartments (triggered by the presence of the target entity) out of the total number of compartments, one could use Poisson statistics to calculate the amount of input target.

However, there are still problems to be solved and assumptions to be validated before the technology is widely employed. In this dissertation, the digital quantification strategy has been examined from two angles: efficiency and robustness. The former is a critical factor for ensuring the accuracy of absolute quantification methods, and the latter is the premise for such technology to be practically implemented in diagnosis beyond the laboratory. The two angles are further framed into a “fate” and “rate” determination scheme, where the influence of different parameters is attributed to fate determination step or rate determination step. In this discussion, microfluidic platforms have been used to understand reaction mechanism at single molecule level. Although the discussion raises more challenges for digital assay development, it brings the problem to the attention of the scientific community for the first time.

This dissertation also contributes towards developing POC test in limited resource settings. On one hand, it adds ease of access to the tests by incorporating massively producible, low cost plastic material and by integrating new features that allow instant result acquisition and result feedback. On the other hand, it explores new isothermal chemistry and new strategies to address important global health concerns such as cyctatin C quantification, HIV/HCV detection and treatment monitoring as well as HCV genotyping.

Computational modeling and psychophysics in low- and mid-level vision

This thesis addresses a series of topics related to the question of how people find the foreground objects from complex scenes. With both computer vision modeling, as well as psychophysical analyses, we explore the computational principles for low- and mid-level vision.

We first explore the computational methods of generating saliency maps from images and image sequences. We propose an extremely fast algorithm called Image Signature that detects the locations in the image that attract human eye gazes. With a series of experimental validations based on human behavioral data collected from various psychophysical experiments, we conclude that the Image Signature and its spatial-temporal extension, the Phase Discrepancy, are among the most accurate algorithms for saliency detection under various conditions.

In the second part, we bridge the gap between fixation prediction and salient object segmentation with two efforts. First, we propose a new dataset that contains both fixation and object segmentation information. By simultaneously presenting the two types of human data in the same dataset, we are able to analyze their intrinsic connection, as well as understanding the drawbacks of today’s “standard” but inappropriately labeled salient object segmentation dataset. Second, we also propose an algorithm of salient object segmentation. Based on our novel discoveries on the connections of fixation data and salient object segmentation data, our model significantly outperforms all existing models on all 3 datasets with large margins.

In the third part of the thesis, we discuss topics around the human factors of boundary analysis. Closely related to salient object segmentation, boundary analysis focuses on delimiting the local contours of an object. We identify the potential pitfalls of algorithm evaluation for the problem of boundary detection. Our analysis indicates that today’s popular boundary detection datasets contain significant level of noise, which may severely influence the benchmarking results. To give further insights on the labeling process, we propose a model to characterize the principles of the human factors during the labeling process.

The analyses reported in this thesis offer new perspectives to a series of interrelating issues in low- and mid-level vision. It gives warning signs to some of today’s “standard” procedures, while proposing new directions to encourage future research.

Hydrogen-Atom Transfer Photochemistry of Tetrakis(µ-pyrophosphito)diplatinate(II)

In many senses, the hydrogen-atom transfer reactions observed with the triplet excited state of pyrophosphito-bridged platinum(II) dimers resemble the reactions of organic ketone nπ* states. The first two chapters describe our attempts to understand the reactivity differences between these two chromophores. Reactivity of the metal dimers is strongly regulated by the detailed nature of the ligands that ring the axial site, the hydrogen-abstraction center. A hydrogen-bonded network linking the ligands facilitates H-atom transfer quenching with alcohols through the formation of a hydrogen-bonded complex between the alcohol and a dimer. For substrates of equal C-H bond strength that lack a hydroxyl group (e.g., benzyl hydrocarbons), the quenching rate is several orders of magnitude slower.

The shape and size of the axial site, as determined by the ligands, also discriminate among quenchers by their steric characteristics. Very small quenchers quench slowly because of high entropies of activation, while very large ones have large enthalpic barriers. The two effects find a balance with quenchers of "just the right size."

The third chapter discusses the design of a mass spectrometer that uses positron annihilation to ionize neutral molecules. The mass spectrometer creates positron-molecule adducts whose annihilation produces fragmentation products that may yield information on the bonding of positrons in such complexes.

Structure-, stereochemistry-, and metal-regulated DNA binding/cleaving molecules

In the cell, the binding of proteins to specific sequences of double helical DNA is essential for controlling the processes of protein synthesis (at the level of DNA transcription) and cell proliferation (at the level of DNA replication). In the laboratory, the sequence-specific DNA binding/cleaving properties of restriction endonuclease enzymes (secreted by microorganisms to protect them from foreign DNA molecules) have helped to fuel a revolution in molecular biology. The strength and specificity of a protein:DNA interaction depend upon structural features inherent to the protein and DNA sequences, but it is now appreciated that these features (and therefore protein:DNA complexation) may be altered (regulated) by other protein:DNA complexes, or by environmental factors such as temperature or the presence of specific organic molecules or inorganic ions. It is also now appreciated that molecules much smaller than proteins (including antibiotics of molecular weight less than 2000 and oligonucleotides) can bind to double-helical DNA in sequence-specific fashion. Elucidation of structural motifs and microscopic interactions responsible for the specific molecular recognition of DNA leads to greater understanding of natural processes and provides a basis for the design of novel sequence-specific DNA binding molecules. This thesis describes the synthesis and DNA binding/cleaving characteristics of molecules designed to probe structural, stereochemical, and environmental factors that regulate sequence-specific DNA recognition.

Chapter One introduces the DNA minor groove binding antibiotics Netropsin and Distamycin A, which are di- and tri(N-methylpyrrolecarboxamide) peptides, respectively. The method of DNA affinity cleaving, which has been employed to determine DNA binding properties of designed synthetic molecules is described. The design and synthesis of a series of Netropsin dimers linked in tail-to-tail fashion (by oxalic, malonic, succinic, or fumaric acid), or in head-to-tail fashion (by glycine, β-alanine, and γ-aminobutanoic acid (Gaba)) are presented. These Bis(Netropsin)s were appended with the iron-chelating functionality EDTA in order to make use of the technique of DNA affinity cleaving. Bis(Netropsin)-EDTA compounds are analogs of penta(N-methylpyrrolecarboxamide)-EDTA (P5E), which may be considered a head-to-tail Netropsin dimer linked by Nmethylpyrrolecarboxamide. Low- and high-resolution analysis of pBR322 DNA affinity cleaving by the iron complexes of these molecules indicated that small changes in the length and nature of the linker had significant effects on DNA binding/cleaving efficiency (a measure of DNA binding affinity). DNA binding/cleaving efficiency was found to decrease with changes in the linker in the order β-alanine > succinamide > fumaramide > N-methylpyrrolecarboxamide > malonamide >glycine, γ-aminobutanamide > oxalamide. In general, the Bis(Netropsin)-EDTA:Fe compounds retained the specificity for seven contiguous A:T base pairs characteristic of P5E:Fe binding. However, Bis(Netropsin)Oxalamide- EDTA:Fe exhibited decreased specificity for A:T base pairs, and Bis(Netropsin)-Gaba-EDT A:Fe exhibited some DNA binding sites of less than seven base pairs. Bis(Netropsin)s linked with diacids have C₂-symmmetrical DNA binding subunits and exhibited little DNA binding orientation preference. Bis(Netropsin)s linked with amino acids lack C₂-symmetrical DNA binding subunits and exhibited higher orientation preferences. A model for the high DNA binding orientation preferences observed with head-to-tail DNA minor groove binding molecules is presented.

Chapter Two describes the design, synthesis, and DNA binding properties of a series of chiral molecules: Bis(Netropsin)-EDTA compounds with linkers derived from (R,R)-, (S,S)-, and (RS,SR)-tartaric acids, (R,R)-, (S,S)-, and (RS,SR)-tartaric acid acetonides, (R)- and (S)-malic acids, N ,N-dimethylaminoaspartic acid, and (R)- and (S)-alanine, as well as three constitutional isomers in which an N-methylpyrrolecarboxamide (P1) subunit and a tri(N-methylpyrrolecarboxamide)-EDTA (P3-EDTA) subunit were linked by succinic acid, (R ,R)-, and (S ,S)-tartaric acids. DNA binding/cleaving efficiencies among this series of molecules and the Bis(Netropsin)s described in Chapter One were found to decrease with changes in the linker in the order β-alanine > succinamide > P1-succinamide-P3 > fumaramide > (S)-malicamide > N-methylpyrrolecarboxamide > (R)-malicamide > malonamide > N ,N-dimethylaminoaspanamide > glycine = Gaba = (S,S)-tartaramide = P1-(S,S)-tanaramide-P3 > oxalamide > (RS,SR)-tartaramide = P1- (R,R)-tanaramide-P3 > (R,R)-tartaramide (no sequence-specific DNA binding was detected for Bis(Netropsin)s linked by (R)- or (S)-alanine or by tartaric acid acetonides). The chiral molecules retained DNA binding specificity for seven contiguous A:T base pairs. From the DNA affinity cleaving data it could be determined that: 1) Addition of one or two substituents to the linker of Bis(Netropsin)-Succinamide resulted in stepwise decreases in DNA binding affinity; 2) molecules with single hydroxyl substituents bound DNA more strongly than molecules with single dimethylamino substituents; 3) hydroxyl-substituted molecules of (S) configuration bound more strongly to DNA than molecules of (R) configuration. This stereochemical regulation of DNA binding is proposed to arise from the inherent right-handed twist of (S)-enantiomeric Bis(Netropsin)s versus the inherent lefthanded twist of (R)-enantiomeric Bis(Netropsin)s, which makes the (S)-enantiomers more complementary to the right-handed twist of B form DNA.

Chapter Three describes the design and synthesis of molecules for the study of metalloregulated DNA binding phenomena. Among a series of Bis(Netropsin)-EDTA compounds linked by homologous tethers bearing four, five, or six oxygen atoms, the Bis(Netropsin) linked by a pentaether tether exhibited strongly enhanced DNA binding/cleaving in the presence of strontium or barium cations. The observed metallospecificity was consistent with the known affinities of metal cations for the cyclic hexaether 18-crown-6 in water. High-resolution DNA affinity cleaving analysis indicated that DNA binding by this molecule in the presence of strontium or barium was not only stronger but of different sequence-specificity than the (weak) binding observed in the absence of metal cations. The metalloregulated binding sites were consistent with A:T binding by the Netropsin subunits and G:C binding by a strontium or barium:pentaether complex. A model for the observed positive metalloregulation and novel sequence-specificity is presented. The effects of 44 different cations on DNA affinity cleaving by P5E:Fe were examined. A series of Bis(Netropsin)-EDTA compounds linked by tethers bearing two, three, four, or five amino groups was also synthesized. These molecules exhibited strong and specific binding to A:T rich regions of DNA. It was found that the iron complexes of these molecules bound and cleaved DNA most efficiently at pH 6.0-6.5, while P5E:Fe bound and cleaved most efficiently at pH 7.5-8.0. Incubating the Bis(Netropsin) Polyamine-EDTA:Fe molecules with K₂PdCl₄ abolished their DNA binding/cleaving activity. It is proposed that the observed negative metalloregulation arises from kinetically inert Bis(Netropsin) Polyamine:Pd(II) complexes or aggregates, which are sterically unsuitable for DNA complexation. Finally, attempts to produce a synthetic metalloregulated DNA binding protein are described. For this study, five derivatives of a synthetic 52 amino acid residue DNA binding/cleaving protein were produced. The synthetic mutant proteins carried a novel pentaether ionophoric amino acid residue at different positions within the primary sequence. The proteins did not exhibit significant DNA binding/cleaving activity, but they served to illustrate the potential for introducing novel amino acid residues within DNA binding protein sequences, and for the development of the tricyclohexyl ester of EDTA as a superior reagent for the introduction of EDT A into synthetic proteins.

Chapter Four describes the discovery and characterization of a new DNA binding/cleaving agent, [SalenMn(III)]OAc. This metal complex produces single- and double-strand cleavage of DNA, with specificity for A:T rich regions, in the presence of oxygen atom donors such as iodosyl benzene, hydrogen peroxide, or peracids. Maximal cleavage by [SalenMn(III)]OAc was produced at pH 6-7. A comparison of DNA singleand double-strand cleavage by [SalenMn(III)]⁺ and other small molecules (Methidiumpropyl-EDTA:Fe, Distamycin-EDTA:Fe, Neocarzinostatin, Bleomycin:Fe) is presented. It was found that DNA cleavage by [SalenMn(III)]⁺ did not require the presence of dioxygen, and that base treatment of DNA subsequent to cleavage by [SalenMn(III)]⁺ afforded greater cleavage and alterations in the cleavage patterns. Analysis of DNA products formed upon DNA cleavage by [SalenMn(III)] indicated that cleavage was due to oxidation of the sugar-phosphate backbone of DNA. Several mechanisms consistent with the observed products and reaction requirements are discussed.

Chapter Five describes progress on some additional studies. In one study, the DNA binding/cleaving specificities of Distamycin-EDTA derivatives bearing pyrrole N-isopropyl substituents were found to be the same as those of derivatives bearing pyrrole N-methyl substituents. In a second study, the design of and synthetic progress towards a series of nucleopeptide activators of transcription are presented. Five synthetic plasmids designed to test for activation of in vitro run-off transcription by DNA triple helix-forming oligonucleotides or nucleopeptides are described.

Chapter Six contains the experimental documentation of the thesis work.

I. The effects of variations in certain parameters upon the efficiency of in vivo hemodialysis with a Kiil dialyzer. II. Interfacial structure of concurrent air-water flow in a two-inch diameter horizontal tube.

Part I

Regression analyses are performed on in vivo hemodialysis data for the transfer of creatinine, urea, uric acid and inorganic phosphate to determine the effects of variations in certain parameters on the efficiency of dialysis with a Kiil dialyzer. In calculating the mass transfer rates across the membrane, the effects of cell-plasma mass transfer kinetics are considered. The concept of the effective permeability coefficient for the red cell membrane is introduced to account for these effects. A discussion of the consequences of neglecting cell-plasma kinetics, as has been done to date in the literature, is presented.

A physical model for the Kiil dialyzer is presented in order to calculate the available membrane area for mass transfer, the linear blood and dialysate velocities, and other variables. The equations used to determine the independent variables of the regression analyses are presented. The potential dependent variables in the analyses are discussed.

Regression analyses were carried out considering overall mass-transfer coefficients, dialysances, relative dialysances, and relative permeabilities for each substance as the dependent variables. The independent variables were linear blood velocity, linear dialysate velocity, the pressure difference across the membrane, the elapsed time of dialysis, the blood hematocrit, and the arterial plasma concentrations of each substance transferred. The resulting correlations are tabulated, presented graphically, and discussed. The implications of these correlations are discussed from the viewpoint of a research investigator and from the viewpoint of patient treatment.

Recommendations for further experimental work are presented.

Part II

The interfacial structure of concurrent air-water flow in a two-inch diameter horizontal tube in the wavy flow regime has been measured using resistance wave gages. The median water depth, r.m.s. wave height, wave frequency, extrema frequency, and wave velocity have been measured as functions of air and water flow rates. Reynolds numbers, Froude numbers, Weber numbers, and bulk velocities for each phase may be calculated from these measurements. No theory for wave formation and propagation available in the literature was sufficient to describe these results.

The water surface level distribution generally is not adequately represented as a stationary Gaussian process. Five types of deviation from the Gaussian process function were noted in this work. The presence of the tube walls and the relatively large interfacial shear stresses precludes the use of simple statistical analyses to describe the interfacial structure. A detailed study of the behavior of individual fluid elements near the interface may be necessary to describe adequately wavy two-phase flow in systems similar to the one used in this work.

The influence of freestream turbulence, freestream nuclei populations and a drag-reducing polymer on cavitation inception on two axisymmetric bodies

The influence upon the basic viscous flow about two axisymmetric bodies of (i) freestream turbulence level and (ii) the injection of small amounts of a drag-reducing polymer (Polyox WSR 301) into the test model boundary layer was investigated by the schlieren flow visualization technique. The changes in the type and occurrence of cavitation inception caused by the subsequent modifications in the viscous flow were studied. A nuclei counter using the holographic technique was built to monitor freestream nuclei populations and a few preliminary tests investigating the consequences of different populations on cavitation inception were carried out.

Both test models were observed to have a laminar separation over their respective test Reynolds number ranges. The separation on one test model was found to be insensitive to freestream turbulence levels of up to 3.75 percent. The second model was found to be very susceptible having its critical velocity reduced from 30 feet per second at a 0.04 percent turbulence level to 10 feet per second at a 3.75 percent turbulence level. Cavitation tests on both models at the lowest turbulence level showed the value of the incipient cavitation number and the type of cavitation were controlled by the presence of the laminar separation. Cavitation tests on the second model at 0.65 percent turbulence level showed no change in the inception index, but the appearance of the developed cavitation was altered.

The presence of Polyox in the boundary layer resulted in a cavitation suppression comparable to that found by other investigators. The elimination of the normally occurring laminar separation on these bodies by a polymer-induced instability in the laminar boundary layer was found to be responsible for the suppression of inception.

Freestream nuclei populations at test conditions were measured and it was found that if there were many freestream gas bubbles the normally present laminar separation was elminated and travelling bubble type cavitation occurred - the value of the inception index then depended upon the nuclei population. In cases where the laminar separation was present it was found that the value of the inception index was insensitive to the free stream nuclei populations.