I. Electronic states of heavily-doped molecular crystals--naphthalene. I. Theoretical. II. Experimental. II. Lowest singlet and triplet excited states of pyrazine

PART I

The energy spectrum of heavily-doped molecular crystals was treated in the Green’s function formulation. The mixed crystal Green’s function was obtained by averaging over all possible impurity distributions. The resulting Green’s function, which takes the form of an infinite perturbation expansion, was further approximated by a closed form suitable for numerical calculations. The density-of-states functions and optical spectra for binary mixtures of normal naphthalene and deuterated naphthalene were calculated using the pure crystal density-of-state functions. The results showed that when the trap depth is large, two separate energy bands persist, but when the trap depth is small only a single band exists. Furthermore, in the former case it was found that the intensities of the outer Davydov bands are enhanced whereas the inner bands are weakened. Comparisons with previous theoretical calculations and experimental results are also made.

PART II

The energy states and optical spectra of heavily-doped mixed crystals are investigated. Studies are made for the following binary systems: (1) naphthalene-h₈ and d₈, (2) naphthalene--h₈ and αd₄, and (3) naphthalene--h₈ and βd₁, corresponding to strong, medium and weak perturbations. In addition to ordinary absorption spectra at 4˚K, band-to-band transitions at both 4˚K and 77˚K are also analyzed with emphasis on their relations to cooperative excitation and overall density-of-states functions for mixed crystals. It is found that the theoretical calculations presented in a previous paper agree generally with experiments except for cluster states observed in system (1) at lower guest concentrations. These features are discussed semi-quantitatively. As to the intermolecular interaction parameters, it is found that experimental results compare favorably with calculations based on experimental density-of-states functions but not with those based on octopole interactions or charge-transfer interactions. Previous experimental results of Sheka and the theoretical model of Broude and Rashba are also compared with present investigations.

PART III

The phosphorescence, fluorescence and absorption spectra of pyrazine-h₄ and d₄ have been obtained at 4˚K in a benzene matrix. For comparison, those of the isotopically mixed crystal pyrazine-h₄ in d₄ were also taken. All these spectra show extremely sharp and well-resolved lines and reveal detailed vibronic structure.

The analysis of the weak fluorescence spectrum resolves the long-disputed question of whether one or two transitions are involved in the near-ultraviolet absorption of pyrazine. The “mirror-image relationship” between absorption and emission shows that the lowest singlet state is an allowed transition, properly designated as ¹B_3u ← ¹A_1g. The forbidden component ¹B_2g, predicted by both “exciton” and MO theories to be below the allowed component, must lie higher. Its exact location still remains uncertain.

The phosphorescence spectrum when compared with the excitation phosphorescence spectra, indicates that the lowest triplet state is also symmetry allowed, showing a strong 0-0 band and a “mirror-image relationship” between absorption and emission. In accordance with previous work, the triplet state is designated as ³B_3u.

The vibronic structure of the phosphorescence spectrum is very complicated. Previous work on the analysis of this spectrum all concluded that a long progression of v_6a exists. Under the high resolution attainable in our work, the supposed v_6a progression proves to have a composite triplet structure, starting from the second member of the progression. Not only is the v_9a hydrogen-bending mode present as shown by the appearance of the C-D bending mode in the d₄ spectrum, but a band of 1207 cm^-1 in the pyrazine in benzene system and 1231 cm^-1 in the mixed crystal system is also observed. This band is assigned as 2v_6b and of a_1g symmetry. Its anonymously strong intensity in the phosphorescence spectrum is interpreted as due to the Fermi resonance with the 2v_6a and v_9a band.

To help resolve the present controversy over the crystal phosphorescence spectrum of pyrazine, detailed vibrational analyses of the emission spectra were made. The fluorescence spectrum has essentially the same vibronic structure as the phosphorescence spectrum.

Synthesis and characterization of 1,1-di-tert-butyldiazene

The synthesis and direct observation of 1,1-di-tert-butyldiazene (16) at -127°C is described. The absorption spectrum of a red solution of 1,1-diazene 16 reveals a structured absorption band with λ max at 506 run (Me_2O, -125°C). The vibrational spacing in S_1 is about 1200 cm^(-1). The excited state of 16 emits weakly with a single maximum at 715 run observed in the fluorescence spectrum (Me_2O:CD_2Cl_2, -196°C). The proton NMR spectrum of 16 occurs as a singlet at 1.41 ppm. Monitoring this NMR absorption at -94^0 ± 2°C shows that 1,1-diazene 16 decomposes with a first-order rate of 1.8 x 10^(-3) sec(-1) to form isobutane, isobutylene and hexarnethylethane. This rate is 10^8 and 10^(34) times faster than the thermal decomposition of the corresponding cis and trans 1,2-di-tert-butyldiazene isomers. The free energy of activation for decomposition of 1,1-diazene 16 is found to be 12.5 ± 0.2 kcal/mol at -94°C which is much lower than the values of 19.1 and 19.4 kcal/lmole calculated at -94°C for N-(2,2,6,6- tetramethylpiperidyl)nitrene (3) and N-(2,2,5,5- tetrarnethylpyrrolidyl)nitrene (4), respectively. This difference between 16 and the cyclic-1,1-diazenes 3 and 4 can be attributed to a large steric interaction between the tert-butyl groups in 1,1-diazene 16.

In order to investigate the nature of the singlet-triplet gap in 1,1-diazenes, 2,5-di-tert-butyl-N-pyrrolynitrene (22) was generated but was found to be too reactive towards dimerization to be persistent. In the presence of dimethylsulfoxide, however, N-pyrrolynitrene (22) can be trapped as N-(2,5-di-tert-butyl- N'-pyrrolyl)dimethylsulfoxirnine (38). N-(2,5-di-tert-butyl-N'-pyrrolyl)dimethylsulfoximine (38-d^6) exchanges with free dimethylsulfoxide at 50°C in solution, presumably by generation and retrapping of pyrrolynitrene 22.

Applications of nuclear magnetic resonance spectroscopy to the study of medium-sized rings. I. Conformational properties of cycloheptane. II. Conformational properties of cycloöctane

Conformational equilibrium in medium-sized rings has been investigated by the temperature variation of the fluorine-19 n.m.r. spectra of 1, 1-difluorocycloalkanes and various substituted derivatives of them. Inversion has been found to be fast on the n.m.r. time scale at -180˚ for 1, 1-difluorocycloheptane, but slow for 1, 1-difluoro-4, 4-dimethylcycloheptane at -150˚. At low temperature, the latter compound affords a single AB pattern with a chemical-shift difference of 841 cps. which has been interpreted in terms of the twist-chair conformation with the methyl groups on the axis position and the fluorine atoms in the 4-position. At room temperature, the n.m.r. spectrum of 1, 1-difluoro-4-t-butylcycloheptane affords an AB pattern with a chemical-shift difference of 185 cps. The presence of distinct trans and gauche couplings from the adjacent hydrogens has been interpreted to suggest the existence of a single predominant form, the twist chair with the fluorine atoms on the axis position.

Investigation of 1, 1-difluorocycloöctane and 1, 1, 4, 4-tetrafluorocycloöctane has led to the detection of two kinetic processes both having activation energies of 8-10 kcal./mole but quite different A values. In light of these results eleven different conformations of cycloöctane along with a detailed description of the ways in which they may be interconverted are discussed. An interpretation involving the twist-boat conformation rapidly equilibrating through the saddle and the parallel-boat forms at room temperature is compatible with the results.

Spin wave resonance in ferromagnetic films

The objective of this investigation has been a theoretical and experimental understanding of ferromagnetic resonance phenomena in ferromagnetic thin films, and a consequent understanding of several important physical properties of these films. Significant results have been obtained by ferromagnetic resonance, hysteresis, torque magnetometer, He ion backscattering, and X-ray fluorescence measurements for nickel-iron alloy films.

Taking into account all relevant magnetic fields, including the applied, demagnetizing, effective anisotropy and exchange fields, the spin wave resonance condition applicable to the thin film geometry is presented. On the basis of the simple exchange interaction model it is concluded that the normal resonance modes of an ideal film are expected to be unpinned. The possibility of nonideality near the surface of a real film was considered by means of surface anisotropy field, inhomogeneity in demagnetizing field and inhomogeneity of magnetization models. Numerical results obtained for reasonable parameters in all cases show that they negligibly perturb the resonance fields and the higher order mode shapes from those of the unpinned modes of ideal films for thicknesses greater than 1000 Å. On the other hand for films thinner than 1000 Å the resonance field deviations can be significant even though the modes are very nearly unpinned. A previously unnoticed but important feature of all three models is that the interpretation of the first resonance mode as the uniform mode of an ideal film allows an accurate measurement of the average effective demagnetizing field over the film volume. Furthermore, it is demonstrated that it is possible to choose parameters which give indistinguishable predictions for all three models, making it difficult to uniquely ascertain the source of spin pinning in real films from resonance measurements alone.

Spin wave resonance measurements of 81% Ni-19% Fe coevaporated films 30 to 9000 Å thick, at frequencies from 1 to 8 GHz, at room temperature, and with the static magnetic field parallel and perpendicular to the film plane have been performed. A self-consistent analysis of the results for films thicker than 1000 Å, in which multiple excitations can be observed, shows for the first time that a unique value of exchange constant A can only be obtained by the use of unpinned mode assignments. This evidence and the resonance behavior of films thinner than 1000 Å strongly imply that the magnetization at the surfaces of permalloy films is very weakly pinned. However, resonance measurements alone cannot determine whether this pinning is due to a surface anisotropy, an inhomogeneous demagnetizing field or an inhomogeneous magnetization. The above analysis yields a value of 4πM=10,100 Oe and A = (1.03 ± .05) x 10^-6 erg/cm for this alloy. The ability to obtain a unique value of A suggests that spin wave resonance can be used to accurately characterize the exchange interaction in a ferromagnet.

In an effort to resolve the ambiguity of the source of pinning of the magnetization, a correlation of the ratio of magnetic moment and X-ray film thickness with the value of effective demagnetizing field 4πNM as determined from resonance, for films 45 to 300 Å has been performed. The remarkable agreement of both quantities and a comparison with the predictions of five distinct models, strongly imply that the thickness dependence of both quantities is related to a thickness dependent average saturation magnetization, which is far below 10,100 Oe for very thin films. However, a series of complementary experiments shows that this large decrease of average saturation magnetization cannot be simply explained by either oxidation or interdiffusion processes. It can only be satisfactorily explained by an intrinsic decrease of the average saturation magnetization for very thin films, an effect which cannot be justified by any simple physical considerations.

Recognizing that this decrease of average saturation magnetization could be due to an oxidation process, a correlation of resonance measurements, He ion backscattering, X-ray fluorescence and torque magnetometer measurements, for films 40 to 3500 Å thick has been performed. On basis of these measurements it is unambiguously established that the oxide layer on the surface of purposefully oxidized 81% Ni-19% Fe evaporated films is predominantly Fe-oxide, and that in the oxidation process Fe atoms are removed from the bulk of the film to depths of thousands of angstroms. Extrapolation of results for pure Fe films indicates that the oxide is most likely α-Fe₂O₃. These conclusions are in agreement with results from old metallurgical studies of high temperature oxidation of bulk Fe and Ni-Fe alloys. However, X-ray fluorescence results for films oxidized at room temperature, show that although the preferential oxidation of Fe also takes place in these films, the extent of this process is by far too small to explain the large variation of their average saturation magnetization with film thickness.

Nuclear magnetic resonance studies of protein conformation: I. Ribonuclease S. II. Hemoglobin

Fluorine nuclear magnetic resonance techniques have been used to study conformational processes in two proteins labeled specifically in strategic regions with covalently attached fluorinated molecules. In ribonuclease S, the ϵ-amino groups of lysines 1 and 7 were trifluoroacetylated without diminishing enzymatic activity. As inhibitors bound to the enzyme, changes in orientation of the peptide segment containing the trifluoroacetyl groups were detected in the nuclear magnetic resonance spectrum. pH Titration of one of the histidines in the active site produced a reversal of the conformational process.

Hemoglobin was trifluoroacetonylated at the reactive cysteine 93 of each β chain. The nuclear magnetic resonance spectrum of the fluorine moiety reflected changes in the equilibrium position of the β chain carboxy terminus upon binding of heme ligands and allosteric effectors. The chemical shift positions observed in deoxy- and methemoglobin were pH dependent, undergoing an abnormally steep apparent titration which was not observed in hemoglobin from which histidine β 146 had been removed enzymatically. The abnormal sharpness of these pH dependent processes is probably due to interactions between several ionizing groups.

The carbon monoxide binding process was studied by concurrent observation of the visible and nuclear magnetic resonance spectra of trifluoroacetonylated hemoglobin at fractional ligand saturations throughout the range 0-1.0. Comparison of the ligand binding process observed in these two ways yields evidence for a specific order of ligand binding. The sequence of events is sensitive to the pH and organic phosphate concentration of the medium, demonstrating the delicately balanced control system produced by interactions between the hemoglobin subunits and the effectors.

2,4-dimethylene-1,3-cyclobutanediyl and 2,4-dimethylenebicyclobutane. Synthesis, spectroscopy, and reactivity of a triplet biradical and its covalent isomer

The preparation and direct observation of triplet 2,4-dimethylene-1,3- cyclobutanediyl (1), the non-Kekule isomer of benzene, is described. The biradical was generated by photolysis of 5,6-dimethylene-2,3- diazabicyclo[2.1.1]hex-2-ene (2) (which was synthesized in several steps from benzvalene) under cryogenic, matrix-isolation conditions. Biradical 1 was characterized by EPR spectroscopy (‌‌‌‌‌│D/hc│ =0.0204 cm^(-1), │E/hc│ =0.0028 cm^(-1)) and found to have a triplet ground state. The Δm_s= 2 transition displays hyperfine splitting attributed to a 7.3-G coupling to the ring methine and a 5.9-G coupling to the exocyclic methylene protons. Several experiments, including application of the magnetophotoselection (mps) technique in the generation of biradical 1, have allowed a determination of the zero-field triplet sublevels as x = -0.0040, y = +0.0136, and z = -0.0096 cm^(-1), where x and y are respectively the long and short in-plane axes and z the out-of-plane axis of 1.

Triplet 1 is yellow-orange and displays highly structured absorption (λ_(max)= 506 nm) and fluorescence (λ_(max) = 510 nm) spectra, with vibronic spacings of 1520 and 620 cm^(-1) for absorption and 1570 and 620 cm^(-1) for emission. The spectra were unequivocally assigned to triplet 1 by the use of a novel technique that takes advantage of the biradical's photolability. The absorption є = 7200 M^(-1) cm^(-1) and f = 0.022, establishing that the transition is spin-allowed. Further use of the mps technique has demonstrated that the transition is x-polarized, and the excited state 1s therefore of B_(1g) symmetry, in accord with theoretical predictions.

Thermolysis or direct photolysis of diazene 2 in fluid solution produces 2,4- dimethylenebicyclo[l.l.0]butane (3), whose ^(l)H NMR spectrum (-80°C, CD_(2)Cl_(2)) consists of singlets at δ 4.22 and 3.18 in a 2:1 ratio. Compound 3 is thermally unstable and dimerizes with second-order kinetics between -80 and -25°C (∆H^(‡) = 6.8 kcal mol^(-1), (∆s^(‡) = -28 eu) by a mechanism involving direct combination of two molecules of 3 in the rate-determining step. This singlet-manifold reaction ultimately produces a mixture of two dimers, 3,8,9- trimethylenetricyclo[5.1.1.0^(2,5)]non-4-ene (75) and trans-3,10-dimethylenetricyclo[6.2.0.0^(2,5)]deca-4,8-diene (76t), with the former predominating. In contrast, triplet-sensitized photolysis of 2, which leads to triplet 1, provides, in addition to 75 and 76t, a substantial amount of trans-5,10- dimethylenetricyclo[6.2.0.0^(3,6)]deca-3,8-diene (77t) and small amounts of two unidentified dimers.

In addition, triplet biradical 1 ring-closes to 3 in rigid media both thermally (77-140 K) and photochemically. In solution 3 forms triplet 1 upon energy transfer from sensitizers having relatively low triplet energies. The implications of the thermal chemistry for the energy surfaces of the system are discussed.

Genetically engineered sensors of cell signaling

Measuring electrical activity in large numbers of cells with high spatial and temporal resolution is a fundamental problem for the study of neural development and information processing. To address this problem, we have constructed FlaSh: a novel, genetically-encoded probe that can be used to measure trans-membrane voltage in single cells. We fused a modified green fluorescent protein (GFP) into a voltage-sensitive potassium channel so that voltage dependent rearrangements in the potassium channel induce changes in the fluorescence of GFP. A voltage sensor encoded into DNA has the advantage that it may be introduced into an organism non-invasively and targeted to specific developmental stages, brain regions, cell types, and sub-cellular compartments.

We also describe modifications to FlaSh that shift its color, kinetics, and dynamic range. We used multiple green fluorescent proteins to produce variants of the FlaSh sensor that generate ratiometric signal output via fluorescence resonance energy transfer (FRET). Finally, we describe initial work toward FlaSh variants that are sensitive to G-protein coupled receptor (GPCR) activation. These sensors can be used to design functional assays for receptor activation in living cells.

Response of multiple simultaneously recorded macaque area LIP neurons in a memory saccade task

Cells in the lateral intraparietal cortex (LIP) of rhesus macaques respond vigorously and in spatially-tuned fashion to briefly memorized visual stimuli. Responses to stimulus presentation, memory maintenance, and task completion are seen, in varying combination from neuron to neuron. To help elucidate this functional segmentation a new system for simultaneous recording from multiple neighboring neurons was developed. The two parts of this dissertation discuss the technical achievements and scientific discoveries, respectively.

Technology. Simultanous recordings from multiple neighboring neurons were made with four-wire bundle electrodes, or tetrodes, which were adapted to the awake behaving primate preparation. Signals from these electrodes were partitionable into a background process with a 1/f-like spectrum and foreground spiking activity spanning 300-6000 Hz. Continuous voltage recordings were sorted into spike trains using a state-of-the-art clustering algorithm, producing a mean of 3 cells per site. The algorithm classified 96% of spikes correctly when tetrode recordings were confirmed with simultaneous intracellular signals. Recording locations were verified with a new technique that creates electrolytic lesions visible in magnetic resonance imaging, eliminating the need for histological processing. In anticipation of future multi-tetrode work, the chronic chamber microdrive, a device for long-term tetrode delivery, was developed.

Science. Simultaneously recorded neighboring LIP neurons were found to have similar preferred targets in the memory saccade paradigm, but dissimilar peristimulus time histograms, PSTH). A majority of neighboring cell pairs had a difference in preferred directions of under 45° while the trial time of maximal response showed a broader distribution, suggesting homogeneity of tuning with het erogeneity of function. A continuum of response characteristics was present, rather than a set of specific response types; however, a mapping experiment suggests this may be because a given cell's PSTH changes shape as well as amplitude through the response field. Spike train autocovariance was tuned over target and changed through trial epoch, suggesting different mechanisms during memory versus background periods. Mean frequency-domain spike-to-spike coherence was concentrated below 50 Hz with a significant maximum of 0.08; mean time-domain coherence had a narrow peak in the range ±10 ms with a significant maximum of 0.03. Time-domain coherence was found to be untuned for short lags (10 ms), but significantly tuned at larger lags (50 ms).

Fluorescence optofluidic microscopy and fluorescence microscopy based on the Talbot effect

Light microscopy has been one of the most common tools in biological research, because of its high resolution and non-invasive nature of the light. Due to its high sensitivity and specificity, fluorescence is one of the most important readout modes of light microscopy. This thesis presents two new fluorescence microscopic imaging techniques: fluorescence optofluidic microscopy and fluorescent Talbot microscopy. The designs of the two systems are fundamentally different from conventional microscopy, which makes compact and portable devices possible. The components of the devices are suitable for mass-production, making the microscopic imaging system more affordable for biological research and clinical diagnostics.

Fluorescence optofluidic microscopy (FOFM) is capable of imaging fluorescent samples in fluid media. The FOFM employs an array of Fresnel zone plates (FZP) to generate an array of focused light spots within a microfluidic channel. As a sample flows through the channel and across the array of focused light spots, a filter-coated CMOS sensor collects the fluorescence emissions. The collected data can then be processed to render a fluorescence microscopic image. The resolution, which is determined by the focused light spot size, is experimentally measured to be 0.65 μm.

Fluorescence Talbot microscopy (FTM) is a fluorescence chip-scale microscopy technique that enables large field-of-view (FOV) and high-resolution imaging. The FTM method utilizes the Talbot effect to project a grid of focused excitation light spots onto the sample. The sample is placed on a filter-coated CMOS sensor chip. The fluorescence emissions associated with each focal spot are collected by the sensor chip and are composed into a sparsely sampled fluorescence image. By raster scanning the Talbot focal spot grid across the sample and collecting a sequence of sparse images, a filled-in high-resolution fluorescence image can be reconstructed. In contrast to a conventional microscope, a collection efficiency, resolution, and FOV are not tied to each other for this technique. The FOV of FTM is directly scalable. Our FTM prototype has demonstrated a resolution of 1.2 μm, and the collection efficiency equivalent to a conventional microscope objective with a 0.70 N.A. The FOV is 3.9 mm × 3.5 mm, which is 100 times larger than that of a 20X/0.40 N.A. conventional microscope objective. Due to its large FOV, high collection efficiency, compactness, and its potential for integration with other on-chip devices, FTM is suitable for diverse applications, such as point-of-care diagnostics, large-scale functional screens, and long-term automated imaging.

Deep tissue fluorescence imaging with time-reversed light

Advances in optical techniques have enabled many breakthroughs in biology and medicine. However, light scattering by biological tissues remains a great obstacle, restricting the use of optical methods to thin ex vivo sections or superficial layers in vivo. In this thesis, we present two related methods that overcome the optical depth limit—digital time reversal of ultrasound encoded light (digital TRUE) and time reversal of variance-encoded light (TROVE). These two techniques share the same principle of using acousto-optic beacons for time reversal optical focusing within highly scattering media, like biological tissues. Ultrasound, unlike light, is not significantly scattered in soft biological tissues, allowing for ultrasound focusing. In addition, a fraction of the scattered optical wavefront that passes through the ultrasound focus gets frequency-shifted via the acousto-optic effect, essentially creating a virtual source of frequency-shifted light within the tissue. The scattered ultrasound-tagged wavefront can be selectively measured outside the tissue and time-reversed to converge at the location of the ultrasound focus, enabling optical focusing within deep tissues. In digital TRUE, we time reverse ultrasound-tagged light with an optoelectronic time reversal device (the digital optical phase conjugate mirror, DOPC). The use of the DOPC enables high optical gain, allowing for high intensity optical focusing and focal fluorescence imaging in thick tissues at a lateral resolution of 36 µm by 52 µm. The resolution of the TRUE approach is fundamentally limited to that of the wavelength of ultrasound. The ultrasound focus (~ tens of microns wide) usually contains hundreds to thousands of optical modes, such that the scattered wavefront measured is a linear combination of the contributions of all these optical modes. In TROVE, we make use of our ability to digitally record, analyze and manipulate the scattered wavefront to demix the contributions of these spatial modes using variance encoding. In essence, we encode each spatial mode inside the scattering sample with a unique variance, allowing us to computationally derive the time reversal wavefront that corresponds to a single optical mode. In doing so, we uncouple the system resolution from the size of the ultrasound focus, demonstrating optical focusing and imaging between highly diffusing samples at an unprecedented, speckle-scale lateral resolution of ~ 5 µm. Our methods open up the possibility of fully exploiting the prowess and versatility of biomedical optics in deep tissues.

Trapped ion magnetic resonance: concepts and designs

A novel spectroscopy of trapped ions is proposed which will bring single-ion detection sensitivity to the observation of magnetic resonance spectra. The approaches developed here are aimed at resolving one of the fundamental problems of molecular spectroscopy, the apparent incompatibility in existing techniques between high information content (and therefore good species discrimination) and high sensitivity. Methods for studying both electron spin resonance (ESR) and nuclear magnetic resonance (NMR) are designed. They assume established methods for trapping ions in high magnetic field and observing the trapping frequencies with high resolution (<1 Hz) and sensitivity (single ion) by electrical means. The introduction of a magnetic bottle field gradient couples the spin and spatial motions together and leads to a small spin-dependent force on the ion, which has been exploited by Dehmelt to observe directly the perturbation of the ground-state electron's axial frequency by its spin magnetic moment.

A series of fundamental innovations is described m order to extend magnetic resonance to the higher masses of molecular ions (100 amu = 2x 10^5 electron masses) and smaller magnetic moments (nuclear moments = 10^(-3) of the electron moment). First, it is demonstrated how time-domain trapping frequency observations before and after magnetic resonance can be used to make cooling of the particle to its ground state unnecessary. Second, adiabatic cycling of the magnetic bottle off between detection periods is shown to be practical and to allow high-resolution magnetic resonance to be encoded pointwise as the presence or absence of trapping frequency shifts. Third, methods of inducing spindependent work on the ion orbits with magnetic field gradients and Larmor frequency irradiation are proposed which greatly amplify the attainable shifts in trapping frequency.

The dissertation explores the basic concepts behind ion trapping, adopting a variety of classical, semiclassical, numerical, and quantum mechanical approaches to derive spin-dependent effects, design experimental sequences, and corroborate results from one approach with those from another. The first proposal presented builds on Dehmelt's experiment by combining a "before and after" detection sequence with novel signal processing to reveal ESR spectra. A more powerful technique for ESR is then designed which uses axially synchronized spin transitions to perform spin-dependent work in the presence of a magnetic bottle, which also converts axial amplitude changes into cyclotron frequency shifts. A third use of the magnetic bottle is to selectively trap ions with small initial kinetic energy. A dechirping algorithm corrects for undesired frequency shifts associated with damping by the measurement process.

The most general approach presented is spin-locked internally resonant ion cyclotron excitation, a true continuous Stern-Gerlach effect. A magnetic field gradient modulated at both the Larmor and cyclotron frequencies is devised which leads to cyclotron acceleration proportional to the transverse magnetic moment of a coherent state of the particle and radiation field. A preferred method of using this to observe NMR as an axial frequency shift is described in detail. In the course of this derivation, a new quantum mechanical description of ion cyclotron resonance is presented which is easily combined with spin degrees of freedom to provide a full description of the proposals.

Practical, technical, and experimental issues surrounding the feasibility of the proposals are addressed throughout the dissertation. Numerical ion trajectory simulations and analytical models are used to predict the effectiveness of the new designs as well as their sensitivity and resolution. These checks on the methods proposed provide convincing evidence of their promise in extending the wealth of magnetic resonance information to the study of collisionless ions via single-ion spectroscopy.

Studying conscious and unconscious vision with functional Magnetic Resonance Imaging : the BOLD promise

Waking up from a dreamless sleep, I open my eyes, recognize my wife’s face and am filled with joy. In this thesis, I used functional Magnetic Resonance Imaging (fMRI) to gain insights into the mechanisms involved in this seemingly simple daily occurrence, which poses at least three great challenges to neuroscience: how does conscious experience arise from the activity of the brain? How does the brain process visual input to the point of recognizing individual faces? How does the brain store semantic knowledge about people that we know? To start tackling the first question, I studied the neural correlates of unconscious processing of invisible faces. I was unable to image significant activations related to the processing of completely invisible faces, despite existing reports in the literature. I thus moved on to the next question and studied how recognition of a familiar person was achieved in the brain; I focused on finding invariant representations of person identity – representations that would be activated any time we think of a familiar person, read their name, see their picture, hear them talk, etc. There again, I could not find significant evidence for such representations with fMRI, even in regions where they had previously been found with single unit recordings in human patients (the Jennifer Aniston neurons). Faced with these null outcomes, the scope of my investigations eventually turned back towards the technique that I had been using, fMRI, and the recently praised analytical tools that I had been trusting, Multivariate Pattern Analysis. After a mostly disappointing attempt at replicating a strong single unit finding of a categorical response to animals in the right human amygdala with fMRI, I put fMRI decoding to an ultimate test with a unique dataset acquired in the macaque monkey. There I showed a dissociation between the ability of fMRI to pick up face viewpoint information and its inability to pick up face identity information, which I mostly traced back to the poor clustering of identity selective units. Though fMRI decoding is a powerful new analytical tool, it does not rid fMRI of its inherent limitations as a hemodynamics-based measure.

I. Impact spallation experiments: fracture patterns and spall velocities. II. Craters in carbonate rocks: an electron paramagnetic resonance analysis of shock damage

This work is divided into two independent papers.

PAPER 1.

Spall velocities were measured for nine experimental impacts into San Marcos gabbro targets. Impact velocities ranged from 1 to 6.5 km/sec. Projectiles were iron, aluminum, lead, and basalt of varying sizes. The projectile masses ranged from a 4 g lead bullet to a 0.04 g aluminum sphere. The velocities of fragments were measured from high-speed films taken of the events. The maximum spall velocity observed was 30 m/sec, or 0.56 percent of the 5.4 km/sec impact velocity. The measured velocities were compared to the spall velocities predicted by the spallation model of Melosh (1984). The compatibility between the spallation model for large planetary impacts and the results of these small scale experiments are considered in detail.

The targets were also bisected to observe the pattern of internal fractures. A series of fractures were observed, whose location coincided with the boundary between rock subjected to the peak shock compression and a theoretical "near surface zone" predicted by the spallation model. Thus, between this boundary and the free surface, the target material should receive reduced levels of compressive stress as compared to the more highly shocked region below.

PAPER 2.

Carbonate samples from the nuclear explosion crater, OAK, and a terrestrial impact crater, Meteor Crater, were analyzed for shock damage using electron para- magnetic resonance, EPR. The first series of samples for OAK Crater were obtained from six boreholes within the crater, and the second series were ejecta samples recovered from the crater floor. The degree of shock damage in the carbonate material was assessed by comparing the sample spectra to spectra of Solenhofen limestone, which had been shocked to known pressures.

The results of the OAK borehole analysis have identified a thin zone of highly shocked carbonate material underneath the crater floor. This zone has a maximum depth of approximately 200 ft below sea floor at the ground zero borehole and decreases in depth towards the crater rim. A layer of highly shocked material is also found on the surface in the vicinity of the reference bolehole, located outside the crater. This material could represent a fallout layer. The ejecta samples have experienced a range of shock pressures.

It was also demonstrated that the EPR technique is feasible for the study of terrestrial impact craters formed in carbonate bedrock. The results for the Meteor Crater analysis suggest a slight degree of shock damage present in the β member of the Kaibab Formation exposed in the crater walls.

Bright-field and fluorescence chip-scale microscopy for biological imaging

Optical microscopy is an essential tool in biological science and one of the gold standards for medical examinations. Miniaturization of microscopes can be a crucial stepping stone towards realizing compact, cost-effective and portable platforms for biomedical research and healthcare. This thesis reports on implementations of bright-field and fluorescence chip-scale microscopes for a variety of biological imaging applications. The term “chip-scale microscopy” refers to lensless imaging techniques realized in the form of mass-producible semiconductor devices, which transforms the fundamental design of optical microscopes.

Our strategy for chip-scale microscopy involves utilization of low-cost Complementary metal Oxide Semiconductor (CMOS) image sensors, computational image processing and micro-fabricated structural components. First, the sub-pixel resolving optofluidic microscope (SROFM), will be presented, which combines microfluidics and pixel super-resolution image reconstruction to perform high-throughput imaging of fluidic samples, such as blood cells. We discuss design parameters and construction of the device, as well as the resulting images and the resolution of the device, which was 0.66 µm at the highest acuity. The potential applications of SROFM for clinical diagnosis of malaria in the resource-limited settings is discussed.

Next, the implementations of ePetri, a self-imaging Petri dish platform with microscopy resolution, are presented. Here, we simply place the sample of interest on the surface of the image sensor and capture the direct shadow images under the illumination. By taking advantage of the inherent motion of the microorganisms, we achieve high resolution (~1 µm) imaging and long term culture of motile microorganisms over ultra large field-of-view (5.7 mm × 4.4 mm) in a specialized ePetri platform. We apply the pixel super-resolution reconstruction to a set of low-resolution shadow images of the microorganisms as they move across the sensing area of an image sensor chip and render an improved resolution image. We perform longitudinal study of Euglena gracilis cultured in an ePetri platform and image based analysis on the motion and morphology of the cells. The ePetri device for imaging non-motile cells are also demonstrated, by using the sweeping illumination of a light emitting diode (LED) matrix for pixel super-resolution reconstruction of sub-pixel shifted shadow images. Using this prototype device, we demonstrate the detection of waterborne parasites for the effective diagnosis of enteric parasite infection in resource-limited settings.

Then, we demonstrate the adaptation of a smartphone’s camera to function as a compact lensless microscope, which uses ambient illumination as its light source and does not require the incorporation of a dedicated light source. The method is also based on the image reconstruction with sweeping illumination technique, where the sequence of images are captured while the user is manually tilting the device around any ambient light source, such as the sun or a lamp. Image acquisition and reconstruction is performed on the device using a custom-built android application, constructing a stand-alone imaging device for field applications. We discuss the construction of the device using a commercial smartphone and demonstrate the imaging capabilities of our system.

Finally, we report on the implementation of fluorescence chip-scale microscope, based on a silo-filter structure fabricated on the pixel array of a CMOS image sensor. The extruded pixel design with metal walls between neighboring pixels successfully guides fluorescence emission through the thick absorptive filter to the photodiode layer of a pixel. Our silo-filter CMOS image sensor prototype achieves 13-µm resolution for fluorescence imaging over a wide field-of-view (4.8 mm × 4.4 mm). Here, we demonstrate bright-field and fluorescence longitudinal imaging of living cells in a compact, low-cost configuration.

Protein-protein recognition: The neonatal Fe receptor and immunoglobulin G

The neonatal Fe receptor (FeRn) binds the Fe portion of immunoglobulin G (IgG) at the acidic pH of endosomes or the gut and releases IgG at the alkaline pH of blood. FeRn is responsible for the maternofetal transfer of IgG and for rescuing endocytosed IgG from a default degradative pathway. We investigated how FeRn interacts with IgG by constructing a heterodimeric form of the Fe (hdFc) that contains one FeRn binding site. This molecule was used to characterize the interaction between one FeRn molecule and one Fe and to determine under what conditions FeRn forms a dimer. The hdFc binds one FeRn molecule at pH 6.0 with a K_d of 80 nM. In solution and with FeRn anchored to solid supports, the heterodimeric Fe does not induce a dimer of FeRn molecules. FcRnhdFc complex crystals were obtained and the complex structure was solved to 2.8 Å resolution. Analysis of this structure refined the understanding of the mechanism of the pH-dependent binding, shed light on the role played by carbohydrates in the Fe binding, and provided insights on how to design therapeutic IgG antibodies with longer serum half-lives. The FcRn-hdFc complex in the crystal did not contain the FeRn dimer. To characterize the tendency of FeRn to form a dimer in a membrane we analyzed the tendency of the hdFc to induce cross-phosphorylation of FeRn-tyrosine kinase chimeras. We also constructed FeRn-cyan and FeRn-yellow fluorescent proteins and have analyzed the tendency of these molecules to exhibit fluorescence resonance energy transfer. As of now, neither of these analyses have lead to conclusive results. In the process of acquiring the context to appreciate the structure of the FcRn-hdFc interface, we developed a study of 171 other nonobligate protein-protein interfaces that includes an original principal component analysis of the quantifiable aspects of these interfaces.