During animal development from zygote to adult, a limited set of regulatory molecules are autonomously deployed in the service of tissue-specific gene expression (reviewed in chapter 1). Inherent in the process is the tension that single cells sample heterogeneous expression states while robustly maintaining a collective final outcome. This thesis addresses theoretical issues that help resolve the paradox that one cell simultaneously contains the fate information of many.
\r\n\r\nPrevious models of development have likened cell fate to minima on a smooth potential energy surface. Such static pictures can be misleading because they suggest the egg knows the path it will take to the adult before it divides even once. Recognition that the potential analogy is an oversimplification has led others to propose that the surface is actually nonsmooth. Chapter 2 reviews the theoretical basis for smooth potentials and resolves these problems by appealing to the tangent space of gene expression. It is then shown that if the potential difference is sufficient to characterize the difference between egg and adult, then the tangent space controls on gene expression are one-dimensional. Furthermore, a shortcoming of models ignoring the connectivity and common origin of dividing cells is that they erect artificial barriers between alternative fates. A fundamentally different picture is sketched wherein the difference between egg and adult is schematized as the shape of the locus of equipotential fates accessible at the same point in time. The conjugacy of space and time is invoked to explain how the requirement that each fate be on a line of equipotential is the same as requiring that each alternative fate move the same distance down the surface at each step. The developmental trajectory is deterministic but not known in advance because it needs to be ascertained at each step which way cells \"turn\" in order to maintain their equipotential relationship. Chapters 3 and 4 refine this sequential model of collective development with specific examples.
\r\n\r\nA simple solution to the problem of cell-type specific gene expression is combinatorial binding of transcription factors at promoters. It is shown in chapter 3 that such models result in substantial information bottlenecks, because all cell fate information is concentrated at the start. We explore a novel, noncommutative model of gene regulation—known as sequential logic—that spreads the information out over time. It is shown using time sequences of noncommutative controllers that targets which otherwise would have been activated together can be regulated independently. We derive scaling laws for two noncommutative models of regulation, motivated by phosphorylation/neural networks and chromosome folding, respectively, and show that they scale super-exponentially in the number of regulators. It is also shown that specificity in control is robust to loss of a regulator. Consequently, sequential logic overcomes the information bottleneck in complex problems and enables novel solutions through roundabout strategies. The theoretical results are connected to real biological networks demonstrating specificity in the context of promiscuity.
\r\n\r\nNoncommutative sequential logic has improved storage capacity, but it does not specify who or what supplies the sequences of input that determine cell fate. Chapter 4 offers a solution by way of the seemingly unrelated problem of looping in twisted strings. Cells and strings obey a set of common space-time constraints, ultimately due to the conservation of energy. It is argued that the most parsimonious allocation of energy from the straight to strained string is the one in which each segment sees the same share of the total. Planar looping is shown to be a consequence of the parsimony principle and the Euler-Poincaré equations for rotational motion in the presence an applied torque. We then solve the problem for the looping of a twisted string; with two strains, the Euler-Poincaré predict a different answer than the classical Frenet-Serret equations. Using the results of chapter 2, it is concluded that the Frenet-Serret curvatures assigned ahead of time are not guaranteed to generate space curves that conserve energy: the predicted string has localized strains the Euler-Poincaré solution lacks. Rotational dynamics of strings are connected to developing organisms by postulating conserved RNA polymerase as an analog of angular momentum, and transcriptional activity as energy. Alternative fates along a one-dimensional \"string\" of dividing cells are possible by finding the RNAP distribution that conserves transcriptional activity along a curve of constant developmental potential. Consequently, each alternative fate samples a different sequence of changes to the distribution as it follows a local gradient downhill from high to low developmental potential over time.
\r\n\r\nIn conclusion, regulation in the tangent space of gene expression resolves the paradox that development has a unique solution specified in the DNA of the egg which cannot be determined with certainty until completion of the adult. Noncommutative sequential logic generates complexity that cannot be realized at the start, while interdependent cells (and strings) require time to ensure that each fate is at the same potential difference from a common ancestor. This fundamental reimagining of the Waddington framework can be tested using new multiplexed mRNA imaging technologies that preserve the spatial context of cells in developing tissue.
", "doi": "10.7907/9B5E-F105", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:11028", "collection": "thesis", "collection_id": "11028", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06062018-120951718", "type": "thesis", "title": "Laboratory and Astronomical Rotational Spectroscopy", "author": [ { "family_name": "Carroll", "given_name": "Paul Brandon", "orcid": "0000-0002-3191-5401", "clpid": "Carroll-Paul-Brandon" } ], "thesis_advisor": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "orcid": "0000-0003-0079-8000", "clpid": "Weitekamp-D-P" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" } ], "local_group": [ { "literal": "Astronomy Department" }, { "literal": "div_chem" } ], "abstract": "Rotational spectroscopy is a capable technique with a rich history in a variety of chemical physics applications that is undergoing a renaissance thanks to new approaches and powerful new experimental capabilities. This thesis demonstrates that flexibility by examining multiple uses of rotational spectroscopy from instrument development, analytical chemistry, fundamental chemical physics, and astrochemistry.
\r\n\r\nIn chapter 2 we discuss the development of two novel coherent microwave spectrometers. These low cost instruments have only recently become feasible thanks to the burgeoning development of highly flexible digital electronics. The first instrument is designed for undergraduate teaching labs and can be used to demonstrate many new concepts of coherent spectroscopy that are used in modern spectroscopy. It is a rotational spectrometer and can, therefore, also be used for a variety of basic spectroscopy experiments. The second instrument uses the stability and consistency of waveguides and broadband microwave instruments to measure the rotational spectrum and abundance of isotopologues to high accuracy.
\r\n\r\nChapter 3 describes the measurement of the rotational spectrum of the cyclopentanol--water dimer. Using microwave spectroscopy, the spectrum is measured and assigned, and the structure of the dimer is determined. The cyclopentanol--water dimer shows a structure dominated by both strong hydrogen bonding and multiple weaker hydrogen bonds from the hydrocarbon ring. The monomer spectrum is measured, though unassigned due to the strong perturbation from the motion of the ring. Dimerization with water is shown to suppress this motion. This system is shown to be an excellent example of the effect of weak hydrogen bonding on the secondary structure and dynamics of molecular systems.
\r\n\r\nChapter 4 moves to astronomical observations of rotational transitions with the detection of a new species: propylene oxide. Measuring the inventory, abundance, and distribution of molecular species provides tests of our understanding of interstellar chemistry. Propylene oxide is an important addition to this inventory because it is the first chiral species detected beyond our solar system. Chiral species play an enormously important role in biology on Earth, and it is believed that interstellar chemistry may contribute to the early inventory of prebiotic species on newly formed planets. The detection of propylene oxide is discussed in the context of the origin and distribution of chiral molecules in the universe.
\r\n\r\nChapter 5 discusses recent data from the Atacama Large Millimeter/Submillimeter Array. The data maps the distribution of CH3CN isotopologues at incredibly high spatial resolution toward the Orion KL region. The measurement of isotopic ratios in CH3CN is used to inform our understanding the formation mechanisms of cyanides in star forming regions. More broadly, the maps are used to show the extreme spatial heterogeneity of the region, with numerous dense clumps roughly the size of a solar system, each with their own unique chemical and physical structure that reflects their distinct evolutionary histories.
\r\n\r\nFinally, chapter 6 discusses the non-detection of trans ethylmethyl ether. Ethylmethyl ether is one of the largest molecules claimed to be detected in the interstellar medium. Due to its size, it is believed to be produced on grain surfaces as a secondary or tertiary product from dissociation of ice constituents. Given its complexity, its abundance may be an important metric of the accuracy of chemical models of ice chemistry. The study claiming its detection reported an unusually high abundance of the species toward W51 e1/e2. Follow up observations and analysis showed that the original detection was mistaken, likely caused by interference from other features.
", "doi": "10.7907/8Y1M-6C76", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:11075", "collection": "thesis", "collection_id": "11075", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06122018-090745040", "type": "thesis", "title": "Analysis of Metal-Oxide Protected Photoelectrochemical Systems for Water Splitting", "author": [ { "family_name": "Lichterman", "given_name": "Michael Yang", "orcid": "0000-0002-0710-7068", "clpid": "Lichterman-Michael-Frankston-Yang" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Brunschwig", "given_name": "Bruce S.", "clpid": "Brunschwig-B-S" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "local_group": [ { "literal": "JCAP" }, { "literal": "div_chem" } ], "abstract": "The photoelectrochemical splitting of water into oxygen and hydrogen gas is one pathway toward the renewable and economic generation of a fuel which is sufficiently scalable to power a large fraction, or even a majority, of the power requirements of\r\nmodern society. In order to make such a device economically promising, it must be sufficiently cheap, have sufficiently high efficiency, or some combination thereof. In this work, two primary routes toward such a device are discussed; the first is the use of a cheaply prepared photoanode material, BiVO4, the interactions of this material with cobalt oxide based catalysts, and the use of such structures in more extreme pH ranges than have previous been reported. The second route details the application of a protective layer, TiO2, on otherwise unstable materials such as GaP and CdTe when operated as\r\nphotoanodes in alkaline media. The further work herein applies operando ambientpressure x-ray photoelectron spectroscopy (AP-XPS) to understand the nature of the energetics which allow conduction in the aforementioned TiO2, as well as other\r\nenergetics in the electrochemical double layer in the adjacent electrolyte. Further experiments using Raman spectroscopy on associated III-V photoanode devices are also described.", "doi": "10.7907/aq89-jv13", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:9805", "collection": "thesis", "collection_id": "9805", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05272016-171126982", "primary_object_url": { "basename": "Boyu Li's thesis.pdf", "content": "final", "filesize": 6823920, "license": "other", "mime_type": "application/pdf", "url": "/9805/1/Boyu Li's thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Ring/Chain versus Network: Architecture Induced by Self- versus Pairwise-Association of Telechelic Polymers", "author": [ { "family_name": "Li", "given_name": "Boyu", "orcid": "0000-0002-7648-3745", "clpid": "Li-Boyu" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Non-covalent associations, including hydrophobic interaction or ionic interaction for self-association, and metal coordination or hydrogen-bonding for complementary-association, have been widely used as key interactions in supramolecules formation with telechelic associative polymers. And a specific application of long associative telechelic polymers has been developed by our group for the mist-control and drag-reduction of liquid fuels. During the research on this project, self- and pairwise-associative telechelic polymers are able to be compared for the first time, and are shown to display distinct associative patterns. In order to design materials with the desired properties, it is imperative to understand the relationships between polymer chemical structure and their topology and dynamics.
\r\n\r\nIn this thesis, self-associative telechelic polymer refers to \u03b1,\u03c9-di(isophthalic acid) polycyclooctadiene (DA-PCOD), which can associate with itself through its acid ends. When tertiary amine-ended polymer is added into the mixture, isophthalic acid preferably associates pairwisely with tertiary amine due to the higher binding strength of charge-assisted hydrogen bond. And the 1:1 molar ratio mixture of \u03b1,\u03c9-di(isophthalic acid) and \u03b1,\u03c9-di(di(tertiary amine)) PCOD (DA/DB-PCOD) is named as pairwise-associative telechelic polymers. DA-PCOD is capable of multimeric association via directional hydrogen bonding due to the specific chemical structure of the isophthalic acid end, while DA/DB-PCOD exhibits dynamics that strikingly resembles that for linear covalent polymers. Temperature determines the binding strength of self- and pairwise- end association, and furthermore, the fraction of unbound ends and the distribution and topology of formed supramolecules/aggregates. Polymer length affects the dynamics of DA-PCOD mainly through determining the concentration of the end groups. And the net effect of chain length on the dynamics of DA/DB-PCOD is non-monotonic and varies with the specific temperature and concentration. The knowledge of structure-property relationships obtained from this work will enable future design of end group entities and other properties of these associative telechelic polymers for their specific applications.
\r\n", "doi": "10.7907/Z9NS0RTW", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:6432", "collection": "thesis", "collection_id": "6432", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252011-091250250", "primary_object_url": { "basename": "Thesis_Peigen.pdf", "content": "final", "filesize": 11678980, "license": "other", "mime_type": "application/pdf", "url": "/6432/8/Thesis_Peigen.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Surface Chemistry at the Nanometer Scale", "author": [ { "family_name": "Cao", "given_name": "Peigen", "clpid": "Cao-Peigen" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "Kavli Nanoscience Institute" }, { "literal": "div_chem" } ], "abstract": "This thesis describes research towards understanding surface chemical and physical processes, as well as their effects on the underlying substrate properties, at the nanometer and atomic scales. We demonstrate a method to tune the density of etch pits on Si(111) during the chlorination process so as to change the surface reactivity. Subsequent grafting of an azide group to replace chlorine demonstrates an example of non-oxidative passivation of silicon surfaces with new functionalities. Depending upon the solvent used in the azidation process, it is shown to yield different azidation kinetic rates, different final azide coverages, and different surface-area distributions. Scanning tunneling spectroscopy studies show that both chlorination and azidation processes significantly modify the surface electronic structures, with the former leading to a non-zero density of states at the Fermi level.\r\n
\r\nOur studies on a new class of corrugation, i.e., wrinkles, in exfoliated graphene on SiO2 show that a \"three-for-six\" triangular pattern of atoms is exclusively and consistently observed on wrinkles, suggesting the local curvature of the wrinkle is a perturbation that breaks the six-fold symmetry of the graphene lattice. Lower electrical conductance is also found on the top of wrinkles compared to other regions of graphene. The wrinkles are characterized by the presence of midgap states, which is in agreement with recent theoretical predictions. A general method is also reported for reliably fabricating ultrahigh-density graphene nanoribbon (GNR) arrays. We have clearly observed how the properties of GNRs evolve as a function of number of graphene layers. The band gap (and so the on-off ratio) decreases as the number of layers increases. These results suggest that, in addition to single layer graphene, properties of GNRs of different thicknesses can also be harnessed for engineering GNRs as different building blocks towards FET applications.\r\n
\r\nA novel imaging technique, graphene-templated scanning probe microscopy, has been developed and applied for the study on the condensation process of water and small organic molecules on mica. We found that these molecular adlayers grow epitaxially on the mica substrate in a layer-by-layer fashion. In particular, submonolayers of water form atomically flat, faceted islands of height 0.37 plus or minus 0.02 nm, in agreement with the height of a monolayer of ice. The second adlayers also appear ice-like, and thicker layers appear liquid-like. This general mechanism, however, is not universal. Exclusively three-dimensional droplets of water are observed on chemically modified (hydrophobic) mica surfaces, suggesting a 3D growth mechanism.\r\n
\r\nThis thesis also includes my work on the design of a quartz-tuning-fork-based force sensor and related electronics for applications on low-temperature atomic force microscopy. Results show that the force-sensor-global-feedback circuit detector system induced lowest noise floor. The high detection sensitivity of this system demonstrates its ability to be used in frequency-modulated AFM at cryogenic temperatures. Surface topographic imaging of H-terminated Si(111) has been achieved at low temperatures.\r\n
", "doi": "10.7907/7EFV-V231", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:5824", "collection": "thesis", "collection_id": "5824", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05212010-154212167", "primary_object_url": { "basename": "thesis_VAN.pdf", "content": "final", "filesize": 1671048, "license": "other", "mime_type": "application/pdf", "url": "/5824/1/thesis_VAN.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Efficient Generation of Hyperpolarized Molecules Utilizing the Scalar Order of Parahydrogen", "author": [ { "family_name": "Norton", "given_name": "Valerie Ann", "clpid": "Norton-Valerie-Ann" } ], "thesis_advisor": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Reisman", "given_name": "Sarah E.", "clpid": "Reisman-S-E" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation describes methods that polarize the spin of a specific nucleus in molecules synthesized by molecular addition of parahydrogen to a precursor molecule. Nuclear magnetic resonance (NMR) pulse sequences are designed to perform efficient transfer of spin order by way of the scalar spin couplings between the two nascent protons and a heteronuclear spin label target. The result is an increase in the NMR signal from that nucleus by several orders of magnitude, approaching unity polarization. Algorithms are presented to effect the desired unitary evolution of this three-spin system over the range of couplings found in diverse molecules and in the presence of interfering spins. These methods are explored theoretically and comparisons are made to select the most advantageous method given a specific problem.
\r\n\r\nIssues concerning the choice of target molecule, portable equipment, and automation are discussed. Some design choices made for convenience in one aspect of the execution of the methods raise difficulties in other aspects. These difficulties are elucidated and methods of mitigation are discussed.
\r\n\r\nPulse design issues are elucidated with numerical calculations which confirm analytical results for the time dependence obtained in the multiply rotating frame approximation. Failures of this approximation at low frequencies are explored numerically leading to novel pulse sequence design rules which ameliorate undesirable phenomena peculiar to low field NMR, enabling its employment for this and other applications requiring precise control of the spin degrees of freedom. Experimental results, primarily aimed at biomedical applications, are reviewed.
\r\n", "doi": "10.7907/57FW-1060", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5234", "collection": "thesis", "collection_id": "5234", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06112008-065533", "primary_object_url": { "basename": "10Thesis.pdf", "content": "final", "filesize": 1432379, "license": "other", "mime_type": "application/pdf", "url": "/5234/11/10Thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Novel Methods for Force-Detected Nuclear Magnetic Resonance", "author": [ { "family_name": "Butler", "given_name": "Mark Cheiron", "clpid": "Butler-Mark-Cheiron" } ], "thesis_advisor": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Shan", "given_name": "Shu-ou", "clpid": "Shan-Shu-ou" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis is concerned with the problem of extending methods for force-detected nuclear magnetic resonance (NMR) to the nanoscale regime. A magnetic mechanical resonator can be used both as a sensitive detector of spins and a means of inducing spin relaxation between detected transients. At the mK temperatures achievable in a dilution refrigerator, spin-lattice interactions are \"frozen out,\" and resonator-induced relaxation can replace spin-lattice relaxation in returning the spins to equilibrium between detected transients. We analyze resonator-induced spin relaxation and the sensitivity of schemes which use a nanoscale mechanical resonator to detect spins.
\r\n\r\nRelaxation equations are derived from first principles, and a physical interpretation of the processes contributing to resonator-induced relaxation is given. The intrinsically quantum mechanical nature of the relaxation is highlighted by comparing the quantum mechanical relaxation equations with analogous equations derived using a semiclassical model in which all spin components have a definite value simultaneously. In the case where the spins all experience the same field, the semiclassical spins cannot become polarized as a result of their interaction with the resonator, and a quantum mechanical model is necessary even for a qualitative description of the polarization process.
\r\n\r\nResonator-induced relaxation of spin systems is complicated by the fact that an indirect spin-spin interaction is present when all spins are coupled to the same resonator, since the resonator's field at a given spin is determined by the interactions which have occurred between the resonator and the other spins of the system. This indirect interaction can prevent the spins from relaxing to a thermal state characterized by a spin temperature. We present a physical interpretation of the mechanism by which an indirect spin-spin torque develops during resonator-induced relaxation, and we estimate the magnitude of this torque and the time T_corr required for it to induce strong spin-spin correlations. A perturbation in the spin Hamiltonian which periodically reverses the direction of the indirect torques within a time period shorter than T_corr will prevent the development of resonator-induced correlations and allow the spins to relax to a thermal state.
\r\n\r\nThe mechanisms by which the spin Hamiltonian H_s modifies resonator-induced relaxation are characterized. In the case where the eigenstates of H_s are weakly perturbed from product states, the system will relax exponentially to thermal equilibrium with the resonator, provided that resonator-induced couplings between populations and certain zero-quantum coherences are suppressed by terms in H_s which shift the frequencies of these coherences sufficiently far from zero. Analysis of longitudinal relaxation in example systems containing three dipole-dipole coupled spins shows that the relaxation occurs in two stages governed by different physical processes, and the three-spin systems do not relax to a thermal state. For substantially larger dipole-dipole coupled system (e.g., N = 50), we propose the hypotheses that the secular dipolar Hamiltonian will quickly equalize the population of states which lie in the same eigenspace of I_z. Simulations of the longitudinal relaxation predicted by this hypothesis suggest that a single resonator could efficiently relax dipole-dipole coupled systems to a thermal state.
\r\n\r\nArguments based on general properties of the master equation suggest that the transverse relaxation induced by the mechanical resonator could occur on a shorter time scale than that of the longitudinal relaxation. We derive conditions which guarantee that the time constant for transverse relaxation will be 2/R_h, where 1/R_h is the time constant for resonator-induced longitudinal relaxation of a single-spin sample to thermal equilibrium. Under these conditions, transverse relaxation can be interpreted as the \"lifetime broadening\" associated with the shortened lifetime of energy eigenstates due to coupling with the resonator. For a two-spin system, however, we show analytically that \"turning on\" the dipolar coupling can accelerate resonator-induced transverse relaxation, and we give an interpretation of the mechanism by which this occurs. Simulations of four-spin systems also show that the presence of dipolar couplings can substantially accelerate resonator-induced transverse relaxation, and that this accelerated relaxation can be distinguished from so-called radiation damping. In addition, we find that spin-locking limits the rate of resonator-induced transverse relaxation. In the case where the spin-locking field is large enough to average the dipolar Hamiltonian and the superoperator responsible for resonator-induced relaxation, we have T_1rho = 2/R_h.
\r\n\r\nWe propose a general definition of signal-to-noise ratio (SNR) which can be used to compare the sensitivity of methods that measure the amplitude of a signal with the sensitivity of methods that yield a continuous record of a signal. This definition is used to compare the sensitivity of three schemes for detecting the NMR signal of a sample consisting of a few spins: spin-locked detection of a transverse dipole, detection of a freely-precessing dipole, and detection of a correlated product. The dependence of SNR and acquisition time on resonator parameters is analyzed. We find that when the time constant for decay of the signal during the detection period is 2/R_h, with instrument noise substantially larger than spin noise, the only resonator parameter which appears in the SNR expressions is the ratio of the mechanical frequency to the temperature. This result suggests, in particular, that SNR for spin-locked detection will be insensitive to details of resonator design.
\r\n\r\nA torsional mechanical resonator design is presented. We discuss the advantages of using soft magnetic material and eliminating relative motion between the sample and the resonator, as well as the validity of the models used to characterize the resonator. The possibility of using non-metallic magnetic material as the source of the resonator's magnetic field is introduced. A numerical example is presented for which the calculated time constant for the longitudinal relaxation of a single-spin sample is 1/R_h = 0.77 s. Simulations of detected NMR spectra for two-spin samples suggest the possibility of chemical studies in which force-detected NMR spectroscopy is used with single-spin sensitivity.
\r\n\r\nThe final chapter studies the possibility of using hyperpolarized spins to cool a single mechanical mode. Numerical examples suggest that cooling would be negligible for resonators of size scale ~ 10 um or larger. In the regime characterized by these examples, substantial cooling requires sufficiently strong spin-resonator coupling that neither a mechanical mode nor a spin mode can be distinguished in the spin-resonator system; instead, the modes of the system include equal contributions from the spins and the mechanical resonator. The spin-resonator correlations responsible for cooling make a significant contribution to the symmetric correlation function of the resonator coordinate, with the result that the noisy \"thermal torque\" acting on the resonator is increased rather than diminished by the presence of the hyperpolarized spins.
\r\n", "doi": "10.7907/S5K2-NH54", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:667", "collection": "thesis", "collection_id": "667", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02172007-172548", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 8027534, "license": "other", "mime_type": "application/pdf", "url": "/667/1/Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Continuous Quantum Measurement of Cold Alkali-Atom Spins", "author": [ { "family_name": "Stockton", "given_name": "John Kenton", "clpid": "Stockton-John-Kenton" } ], "thesis_advisor": [ { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" } ], "thesis_committee": [ { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Refael", "given_name": "Gil", "clpid": "Refael-G" }, { "family_name": "Libbrecht", "given_name": "Kenneth George", "clpid": "Libbrecht-K-G" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "The field of quantum metrology concerns the physical measurement of sensors with a precision comparable to fundamental limits set by quantum mechanics. It is possible to outperform naive interpretations of these limits by using entangled states of the sensor system. One example is that of a spin-squeezed state, in which the uncertainty of one variable is decreased at the expense of another while still obeying Heisenberg's uncertainty principle, improving rotation sensitivity along a chosen axis. These states are potentially useful in devices including atomic clocks, inertial sensors, and magnetometers.
\r\n\r\nAny model of a quantum metrology device must respect the fact that physical measurements are not passive, as imagined classically, but necessarily invasive. Far from being a negative feature, well-understood quantum measurement can conditionally drive a system into desirable entangled states, including spin-squeezed states. Furthermore, the fundamental randomness of this process can, in principle, be removed with real-time feedback control, motivating an adaptation of classical feedback concepts to the quantum realm.
\r\n\r\nIn this thesis, I describe these ideas in the context of one experimental example. A laser-cooled cloud of cesium spins is polarized along one axis via optical pumping and, subsequently, a linearly polarized far-off resonant probe beam traverses the sample. Due to the interaction Hamiltonian, the optical polarization rotates by an amount nominally proportional to one spin component of the collective spin state, enacting a weak, continuous, nondemolition measurement of that collective variable. This optical Faraday rotation is then measured with a polarimeter and the inherently noisy result used to condition the collective atomic state via a quantum filter, or stochastic master equation. Ideally, this process is capable of producing spin-squeezed states via the measurement itself.
\r\n\r\nThe details of this measurement are investigated in depth, including a derivation of the nonideal polarizability Hamiltonian, an analysis of the projection process with control, and a derivation of the magnetometry sensitivity. Experimentally, we demonstrate continuous measurement of the collective spin state with a large single-shot signal-to-noise ratio and verify many predictions of the model. Finally, we describe attempts to observe the atomic projection noise, which would infer the preparation of spin-squeezed states.
", "doi": "10.7907/7PTX-AB16", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:1455", "collection": "thesis", "collection_id": "1455", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04222006-220215", "primary_object_url": { "basename": "JAD-PhD_Front_Matter.pdf", "content": "final", "filesize": 251182, "license": "other", "mime_type": "application/pdf", "url": "/1455/5/JAD-PhD_Front_Matter.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Modulation of Magnetic Properties in Magnetic Resonance Imaging Contrast Agents and Molecular Magnetic Materials", "author": [ { "family_name": "Duimstra", "given_name": "Joseph Anthony", "clpid": "Duimstra-Joseph-Anthony" } ], "thesis_advisor": [ { "family_name": "Meade", "given_name": "Thomas J.", "clpid": "Meade-T-J" }, { "family_name": "Fraser", "given_name": "Scott E.", "clpid": "Fraser-S-E" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Fraser", "given_name": "Scott E.", "clpid": "Fraser-S-E" }, { "family_name": "Meade", "given_name": "Thomas J.", "clpid": "Meade-T-J" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation focuses on fundamental research in two areas of magnetism, the technologically advanced field of magnetic resonance imaging (MRI) and the nascent discipline of molecular magnetic materials. Contrast agents for MRI based on the gadolinium(III) ion were designed and studied to gain insight into the parameters that may be modulated to control contrast agent efficacy. Two parameters in particular, the inner-sphere coordination environment and the electronic relaxation of the gadolinium(III) ion, were examined. Investigations into the electronic relaxation of the gadolinium(III) ion led to insights that were applied to the synthesis and evaluation of a low dimensional magnetic material based on ruthenium(III) and nickel(II) ions.
\r\n\r\nManipulation of the gadolinium(III) coordination sphere provided the basis for an MRI contrast agent designed to be sensitive to the oncologically relevant enzyme beta-glucuronidase. This agent functions by restricting water access to the inner-sphere coordination sites of the gadolinium(III) ion. The design, synthesis, magnetic properties and biochemistry of the agent are described in detail. The agent displays good enzyme kinetics and complicated coordination equilibria with water and carbonate ion.
\r\n\r\nA second approach to modulating contrast agent efficacy consisted of varying the electronic relaxation time of the gadolinium(III) ion. Towards this goal, ligand frameworks were designed and synthesized to influence the relaxation time of the gadolinium(III) ion via remote redox activity. Structural characterization and in vitro assays of these ligand-metal constructs indicated more robust ligands were required for complex stability. Initial steps toward a ligand that fulfills these requirements proved successful.
\r\n\r\nThe structural data from the electronic relaxation studies led to the synthesis of a one-dimensional coordination polymer comprised of chelated ruthenium(III) and nickel(II) ions bridged by cyanide ligands. The compound was studied by X-ray crystallography and its magnetic properties indicated that the ions were ferromagnetically coupled.
", "doi": "10.7907/vc42-nh03", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:5177", "collection": "thesis", "collection_id": "5177", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02182006-145814", "type": "thesis", "title": "Theoretical and Experimental Investigations in MEMS-Based Force-Detected NMR", "author": [ { "family_name": "Elgammal", "given_name": "Ramez Ahmed", "orcid": "0000-0002-6382-6817", "clpid": "Elgammal-Ramez-Ahmed" } ], "thesis_advisor": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes a method of mechanically detecting magnetic resonance. The detector consists of a ferromagnet harmonically bound to a mechanical resonator and measures a magnetic force of interaction with a nearby sample via dipole-dipole coupling. Flexural modes of vibration of the resonator are induced by inversion of the sample magnetization at the mechanical resonance frequency of the device. In this method, a nominally homogeneous field at the sample allows coherent spectroscopy over the entire sample volume.
\r\n\r\nSensitivity analyses suggest that encoding an NMR signal into mechanical oscillations favors inductive detection at the micron scale and below with Brownian motion of the detection being the predominant source of noise and azimuthal eddy currents being the predominant source of damping. As such, the design issues of a MEMS-based spectrometer optimized for 50 micron samples have been investigated. Finite element methods were used and the results for magnetic softening effects, mechanical stresses, field homogeneity, magnet design, radiofrequency excitation, and the utility of capacitive transduction to provide tuning of the oscillator\u2019s mechanical resonance frequency and active shimming are discussed. A piezeoelectrically actuated microvalve is proposed as part of a microfluidic device to allow shuttling of liquid samples. We present a new means of fiber-optic interferometry for geometrically confined regions in which the light exits transverse to core axis. The use of a composite magnetic array of packed nanoparticles may reduce the damping by 104.
\r\n\r\nThe portability of the spectrometer will allow in situ spectroscopy and towards that end 14N overtone experiments were simulated. Force-detection of this transition is superior not only at reduced size scales, but over a broad range of magnetic field strengths. The line narrowing observed by detecting the overtone transition should allow detailed spectroscopic analysis not possible by observing the quadrupolar broadened first-order spectrum. Simulations for a representative class of tholins suggest that the overtone linewidths is of order tens of kHz.
\r\n\r\nWe conclude by discussing the feasibility of nanoscale NMR using torque detection of spin-locked, transverse magnetization, include a derivation of the signal-to-noise and detector optimization, and comment on the fundamental limitations of quantum statistical noise.
", "doi": "10.7907/4FSQ-YP59", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2360", "collection": "thesis", "collection_id": "2360", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06012005-194621", "primary_object_url": { "basename": "bml_thesis.pdf", "content": "final", "filesize": 26761199, "license": "other", "mime_type": "application/pdf", "url": "/2360/1/bml_thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Force-Detected, Single-Molecule Spectroscopy and Imaging Using Nanoscale Mechanical Resonators", "author": [ { "family_name": "Lambert", "given_name": "Bruce Michael", "clpid": "Lambert-Bruce-Michael" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Novel methods for spectroscopic probing of single-molecules are described that sense the optically induced, molecular dipole through the force/torque it generates on a submicron mechanical probe. The probe comprises a mechanical resonator with a high-Q mode of oscillation at frequency vh, to which is attached a nanoparticle with dipole moment p. This dipole is either the optically induced dipole of a metal nanoparticle irradiated at plasmon resonance, or the static dipole moment of a ferroelectric nanocrystal. The electric force or torque between the probe dipole and molecular dipole drives the motion of the resonator at the resonance frequency. Three novel optical scattering mechanisms, which encode the mechanical motion into the phase, amplitude, or polarization of the light scattered by the resonator are investigated and quantified. A novel single-molecule sensor will also be described that comprises a mechanical torsional resonator with an attached ferroelectric nanoparticle. The observable quantity is the shift in the oscillation frequency of the mechanical resonator as a molecule becomes polarized by the rf near-field of the ferroelectric particle. The ferroelectric particle couples electrostatically to a nearby nanoscale capacitor which is used to electrically drive and detect the resonant mechanical motion. Due to this coupling, the electric and mechanical coordinates, which specify the state of this electromechanical device, are no longer the eigenmodes of the system. This gives rise to interesting dynamical effects that are best analyzed using the Lagrange formulation of mechanics. Finally, we discuss experimental progress toward fiber-optic interferometric detection of submicron mechanical resonators.", "doi": "10.7907/SN22-ZZ77", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2000", "collection": "thesis", "collection_id": "2000", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05242005-144900", "primary_object_url": { "basename": "Front_Matter.pdf", "content": "final", "filesize": 108480, "license": "other", "mime_type": "application/pdf", "url": "/2000/9/Front_Matter.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Gas Phase Reaction Dynamics and Design of Molecular Clusters and Bioconjugates", "author": [ { "family_name": "Sumner", "given_name": "Heather Ann", "clpid": "Sumner-Heather-Ann" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "clpid": "Blake-G-A" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter 1 serves as an introduction to the design of molecular clusters and bioconjugates that exhibit interesting reactivity in the gas phase. In Chapter 2, gas-phase reactions of clusters of alkylammonium ions with triphosphate, DNA, and peptides are examined. Alkylation of both phosphate and carboxylate groups is observed. In Chapter 3, the gas phase reactions of methyl phosphate noncovalently bound clusters are studied in detail. The presence of sodium ions in methyl phosphate clusters stabilizes the clusters, facilitating intermolecular condensation reactions between methyl phosphates.
\r\n\r\nIn Chapter 4, the first gas-phase phosphorylation of molecules containing hydroxyl substituents is reported. Gas-phase reactions of triphosphate with hydroxyl-containing molecules result in phosphorylation of the hydroxyl substituent. In the absence of a hydroxyl substituent, the C-terminus of a peptide can be phosphorylated. Otherwise, hydroxyl residues are selectively phosphorylated.
\r\n\r\nChapter 5 considers the possibility of free radical initiated peptide sequencing, or FRIPS, in the gas phase. A free radical initiator is conjugated to the N-terminus of peptides or proteins, forming a bioconjugate. Collision-induced dissociation of the conjugated species results in free radical formation. The free radical then fragments on further collisional activation to yield backbone fragmentation products. This technique may allow selective cleavage of peptides at specific amino acid residues, with applications to gas-phase proteomics sequencing efforts.
\r\n\r\nChapters 6 deals with experiments conducted on solvated ions, specifically focusing on the evaporation kinetics and the relative intensities of differently solvated species. Water cluster distributions are used to discriminate between isomers and enantiomers. Chapter 6 also includes data on the reaction of t-butyl chloride in water clusters, as well as data on doubly charged cationic species showing pairwise evaporation of water.
\r\n\r\nChapter 7 uses H/D exchange experiments to examine the behavior of sodiated glycine oligomers, ranging from Gly1 to Gly5. It is found that H/D exchange dynamics do not directly reflect the structure of sodiated glycine oligomers, as the solvation energy provided by the exchange reagent can allow the ion-molecule complex to access high-energy states. Therefore, interpretations of H/D exchange results should be conducted with detailed examinations of possible exchange mechanisms.
", "doi": "10.7907/AVWS-B055", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:5197", "collection": "thesis", "collection_id": "5197", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05242005-172142", "primary_object_url": { "basename": "thesis_ch1.pdf", "content": "final", "filesize": 273247, "license": "other", "mime_type": "application/pdf", "url": "/5197/1/thesis_ch1.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "A Solid-state Atomic Frequency Standard", "author": [ { "family_name": "White", "given_name": "Christopher John", "clpid": "White-Christopher-John" } ], "thesis_advisor": [ { "family_name": "Hajimiri", "given_name": "Ali", "clpid": "Hajimiri-A" } ], "thesis_committee": [ { "family_name": "Hajimiri", "given_name": "Ali", "clpid": "Hajimiri-A" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Rutledge", "given_name": "David B.", "clpid": "Rutledge-D-B" }, { "family_name": "Roukes", "given_name": "Michael Lee", "clpid": "Roukes-M-L" }, { "family_name": "Weinreb", "given_name": "Sander", "clpid": "Weinreb-S" }, { "family_name": "Bridges", "given_name": "William B.", "clpid": "Bridges-W-B" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The thesis describes a new class of frequency reference. The frequency source uses the same operating principle as a passive atomic frequency standard; however, the device is entirely solid-state, removing many cost and reliability issues associated with gas-phase atomic clocks. More specifically, the \"atomic resonance\" is derived from zero-field magnetic resonance transitions of the vanadium ion in a cubic crystal lattice. The characteristics of these resonances will be described in detail. The apparatus for measuring the \"atomic\" resonances uses a radio-frequency resonant cavity and frequency discriminator circuit. Using integrated circuits, the radio-frequency signal processing functions can be implemented at very low cost in a reliable manufacturing process. We discuss the system design and the measurement sensitivity. Advantages of the new frequency reference may include immunity to vibration and reduced aging compared to crystal oscillators.", "doi": "10.7907/ATKE-YX40", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2238", "collection": "thesis", "collection_id": "2238", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292003-175447", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 1542424, "license": "other", "mime_type": "application/pdf", "url": "/2238/11/Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Force-Detected Nuclear Magnetic Resonance Independent of Field Gradients", "author": [ { "family_name": "Leskowitz", "given_name": "Garett Michael", "clpid": "Leskowitz-Garett-Michael" } ], "thesis_advisor": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes a new method of magnetic resonance detection based on mechanical displacements caused by magnetic forces, which is general with respect to sample and pulse sequence. A spin-bearing sample placed inside a flexible magnet assembly distorts that assembly in proportion to the sample's magnetization. Radio-frequency fields that modulate the sample's spin magnetization at this detector's mechanical resonance frequency encode magnetic resonance spectra into the detector's trajectory. A key insight is that such mechanical detection can be performed within optimized detectors with no need for field gradients inside the sample volume, circumventing the deleterious consequences of such gradients for sensitivity and resolution. The new method is called Better Observation of Magnetization, Enhanced Resolution, and No Gradient (BOOMERANG), and its sensitivity is predicted to exceed that of inductive detection at microscopic size scales.\r\n\r\nA prototype BOOMERANG spectrometer optimized for 3 mm diameter liquid and solid samples is described. The device uses direct digital synthesis of radio-frequency waveforms in its operation and fiber-optic interferometry to detect picometer-scale motions of a detector magnet. This magnet is bound to a tuned mechanical oscillator inside a magnet assembly designed for homogeneity of the magnetic field in the sample. Several types of time-domain FT-NMR spectra on test samples are presented. The data confirm theory and design principles.\r\n\r\nThe favorable scaling of BOOMERANG's sensitivity and the numerous potential uses for NMR at reduced size scales motivate construction of spectrometers optimized for microscopic samples. Geometric concerns in scaling down BOOMERANG are addressed quantitatively. At size scales where the number of spins is such that mean magnetization is smaller than fluctuations, such fluctuations, if not accounted for, can dominate the noise regardless of the physical detection method used. A measurement paradigm using correlations of these fluctuations to encode spectra is proposed to suppress this quantum noise, and the sensitivity of this method, which we call Correlated Observations Narrow Quantum Uncertainty, Enhancing Spectroscopic Transients (CONQUEST), is analyzed. BOOMERANG and CONQUEST promise to extend the applicability of nuclear magnetic resonance (NMR) for chemical analysis to samples and problems that are currently inaccessible by NMR due to poor sensitivity.", "doi": "10.7907/8GH1-CC08", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:4432", "collection": "thesis", "collection_id": "4432", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11072002-135150", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 1523959, "license": "other", "mime_type": "application/pdf", "url": "/4432/9/Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Impact-Ionization Mass Spectrometry of Cosmic Dust", "author": [ { "family_name": "Austin", "given_name": "Daniel Ephraim", "clpid": "Austin-Daniel-Ephraim" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Collier", "given_name": "C. Patrick", "clpid": "Collier-C-P" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Ahrens", "given_name": "Thomas J.", "clpid": "Ahrens-T-J" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In situ characterization of cosmic dust grains typically involves impact-ionization time-of-flight mass spectrometry. Considering the performance and limitations of previous instruments, I designed and tested a novel, compact time-of-flight mass spectrometer for cosmic dust analysis. The instrument, Dustbuster, incorporates a large target area with a reflectron, simultaneously optimizing mass resolution, particle detection, and ion collection. Dust particles hit the 65-cm\u00b2 target plate and are partially ionized by the impact. The resulting ions, with broad energy and angular distributions, are accelerated through the modified reflectron, focusing ions spatially and temporally to produce high-resolution spectra.
\r\n\r\nInitial performance tests of the Dustbuster used laser desorption ionization of embedded metal and mineral samples to simulate particle impacts. Mass resolution (mass/peakwidth) in these experiments ranged from 60 to 180, permitting resolution of isotopes. Subsequent experiments included hypervelocity microparticle impacts. Charged iron and copper microparticles, accelerated to 2-20 km/s in a 2 MV van de Graaff accelerator, impacted the Dustbuster. Mass resolution in these experiments ranged from 150 to 300 for iron and copper. Hydrogen, carbon, and oxygen ions appeared in many spectra. Field-induced emission of electrons immediately before impact is a possible cause of ion formation from species with high ionization potentials. The implications of this ionization effect are discussed in relation to interpretation of mass spectra from other in situ dust analyzers.
\r\n\r\nAnother time-of-flight instrument, originally designed as an energy analyzer, shows promise as a high-resolution mass spectrometer for high-flux cosmic dust environments.
\r\n\r\nIce is an important component of particulates ejected from comets and other icy bodies in the solar system. Due to limited experimental data on ice particle impacts, I built an ice particle source based on a vibrating orifice aerosol generator connected directly to vacuum. Ice particles produced in this manner can be electrostatically accelerated for impact ionization studies.
\r\n\r\nHypervelocity impact vaporization may have played a key role in the mass extinction that occurred at the Cretaceous-Tertiary (K-T) boundary. In order to study the speciation of gases that may have been produced in such an asteroid impact, I designed a specialized orthogonal extraction mass spectrometer for future laboratory impact experiments.
", "doi": "10.7907/2E8R-G492", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:1811", "collection": "thesis", "collection_id": "1811", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05152003-115814", "primary_object_url": { "basename": "The_thesis2.pdf", "content": "final", "filesize": 2144737, "license": "other", "mime_type": "application/pdf", "url": "/1811/1/The_thesis2.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Laboratory Studies of Atmospherically Important Gas-Phase Peroxy Radical Reactions", "author": [ { "family_name": "Christensen", "given_name": "Lance Eric", "clpid": "Christensen-L-E" } ], "thesis_advisor": [ { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Peroxy radicals (HO\u2082, RO\u2082) are important intermediates in Earth's atmosphere. They are intermediates in the oxidation of alkanes and CO in combustion and atmospheric chemical processes. In earth's atmosphere, the rates of their self and cross reactions are often the dominant loss processes when NOx concentrations fall below tens of pptv. These reactions have proven difficult to study in laboratory experiments, due to complex secondary chemistry and ambiguities in radical detection.
\r\n\r\nThis thesis describes a new laser-photolysis apparatus to measure the rates of peroxy radical reactions under atmospheric conditions that employs simultaneous UV direct absorption and IR wavelength-modulation spectroscopy to detect the peroxy radicals. Prior kinetic measurements of gas-phase peroxy radical reactions have typically employed flash-photolysis methods coupled with detection of the radicals only by UV absorption spectroscopy. However, uncertainties can arise because several different species often contribute to the absorption signal. The IR channel provides an independent means of monitoring HO\u2082 radicals by detection of specific rovibrational transitions.
\r\n\r\nWith this apparatus, the rates of the reactions HO\u2082 + NO\u2082, HO\u2082 + CH\u2083O\u2082, CH\u2083O\u2082 + CH\u2083O\u2082, and HO\u2082 + HO\u2082 were studied at temperatures from 219 K to 300 K. Our measurements have, in some cases, led to significant revision of previously accepted rate constants, mechanisms, or product yields, especially at conditions relevant to the upper atmosphere. The new rate coefficients for the HO\u2082 + HO\u2082 reaction are shown to account for a long-standing discrepancy in modeled vs. observed hydrogen peroxide in the stratosphere.
\r\n\r\nA key finding has been the observation that many previous measurements of HO\u2082 reactions at low temperatures have suffered from problems due to complexation between HO\u2082 and methanol, a precursor used to generate HO\u2082. Direct kinetic evidence is presented for the formation of the HO\u2082\u2022CH\u2083OH complex; the rate coefficients, equilibrium constant, and enthalpy of reaction for HO\u2082 + CH\u2083OH \u2194 HO\u2082\u2022CH\u2083OH were measured. These results are the first direct study of the chaperone effect proposed to explain the enhancement of the observed rates of the HO\u2082 self-reaction by hydrogen-bonding species.
\r\n\r\nThe effects of methanol enhancement on the HO\u2082 + NO\u2082, HO\u2082 + CH\u2083O\u2082, CH\u2083O\u2082 + CH\u2083O\u2082, and HO\u2082 + HO\u2082 reaction rates were measured. For the HO\u2082 + NO\u2082 reaction, overlapping, time-dependent signals in the UV due to the equilibrium between NO\u2082 and N\u2082O\u2084 were observed that may not have been properly accounted for in previous measurements. Other studies of NO\u2082 reactions conducted at temperatures below 250 K may be subject to similar errors. In the CH\u2083O2 + CH\u2083O2 reaction, detection of HO\u2082 products has raised questions concerning the product yields and reaction mechanisms.
", "doi": "10.7907/6QP1-YM37", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:4932", "collection": "thesis", "collection_id": "4932", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12102007-114331", "primary_object_url": { "basename": "Miller_ma_2001.PDF", "content": "final", "filesize": 67396101, "license": "other", "mime_type": "application/pdf", "url": "/4932/1/Miller_ma_2001.PDF", "version": "v3.0.0" }, "type": "thesis", "title": "Laser Synchronized Optical Nuclear Magnetic Resonance via Larmor Beat Detection : Imaging Electronic Wavefunctions in Gallium Arsenide Device Structures", "author": [ { "family_name": "Miller", "given_name": "Michael Andrew", "clpid": "Miller-Michael-Andrew" } ], "thesis_advisor": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "orcid": "0000-0003-0079-8000", "clpid": "Weitekamp-D-P" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "orcid": "0000-0003-0079-8000", "clpid": "Weitekamp-D-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We have accomplished Optical Nuclear Magnetic Resonance (ONMR) experiments in an Al0.36Ga0.64As/GaAs heterojunction sample at ~2K with rf-optical pulse synchronization. The hyperfine coupling of the electron spin to the nuclear spins enable this spectroscopy in several ways, which are discussed herein. Moreover, the interactions experienced by nuclear spins in III-V semiconductors, in general, and the phenomena encountered when they are in the vicinity of a shallow donor or pseudo-donor, specifically, are developed. Furthermore, the most accurate calculation of spin diffusion in a spin-three-halves system to date is developed and presented using a methodology can be readily applied to any spin-larger-than-one-half system to a yield a set of coupled differential equations for a set of orthogonal polarizations. The behavior of these equations under a number of physical situations is also investigated.
\r\n\r\nWe have captured the first ever radially resolved Knight shift images from the nuclei near a point defect in GaAs using laser synchronized ONMR. A deconvolution of these images into their constituent physical interactions has been approximately carried out using the theoretical advances developed and presented in this thesis, yielding the shape and size of the electronic orbital in which the electron is trapped, the occupancy of that electronic orbital, and the quadrupolar interactions in the vicinity of the defect, including the charge state of the defect.
\r\n\r\nComputational approaches include both full, real-time analyses of every one of the hundreds of thousands of nuclei surrounding a defect in GaAs, modeling the time domain evolution for each individual nucleus including its Knight shift, quadrupolar interactions (both secular and nonsecular), individual optical polarization conditions, optical detection weighting, and rigorously exact rf effects, and analyses of a variety of continuous medium approximations. The only computations that fit the experimental spectra are those that calculate spin diffusion along a radial line of spins, and use this approximation to the radial profile of nuclear polarization in a continuous medium approximation. The successful interface of this spin diffusion calculation and the single nucleus calculations, leveraging their individual strengths, is clearly a desirable route to further increase computational accuracy.
", "doi": "10.7907/ARCE-F837", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:3255", "collection": "thesis", "collection_id": "3255", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08282001-123851", "primary_object_url": { "basename": "JGK_Thesis_for_DBLsided_printing.pdf", "content": "final", "filesize": 3984594, "license": "other", "mime_type": "application/pdf", "url": "/3255/1/JGK_Thesis_for_DBLsided_printing.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Probing Quantum Confinement at the Atomic Scale with Optically Detected Nuclear Magnetic Resonance", "author": [ { "family_name": "Kempf", "given_name": "James G.", "clpid": "Kempf-James-G" } ], "thesis_advisor": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "orcid": "0000-0003-0079-8000", "clpid": "Weitekamp-D-P" } ], "thesis_committee": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "orcid": "0000-0003-0079-8000", "clpid": "Weitekamp-D-P" }, { "family_name": "Anson", "given_name": "Fred C.", "clpid": "Anson-F-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Near-band-gap circularly polarized excitation in III-V semiconductors provides spin-polarized electrons that transfer spin order to lattice nuclei via fluctuations in the contact hyperfine interaction. This process of optical nuclear polarization and the complementary technique of optical detection of nuclear magnetic resonance (NMR) provide extreme sensitivity enhancement and spatial selectivity in structured samples, enabling collection of NMR spectra from samples such as single quantum wells or dots containing as few as ~10^5 nuclei.
\r\n\r\nCombining these advances with novel techniques for high spectral resolution, we have probed quantum-confined electronic states near the interface of a single epitaxially grown Al(1-x)Ga(x)As/GaAs (x = 0.36) heterojunction. Using a novel strategy that we refer to as POWER (perturbations observed with enhanced resolution) NMR, multiple-pulse time suspension is synchronized with bandgap optical irradiation to reveal spectra of effective spin Hamiltonians that are differences between those of the occupied and unoccupied photoexcited electronic state. The underlying NMR linewidth is reduced by three orders of magnitude in these experiments, enabling resolution of an asymmetric line shape due to light-induced hyperfine interactions. The results are successfully fit with the coherent nuclear spin evolution and relaxation theoretically expected for sites distributed over the volume of an electronic excitation weakly localized at a point defect. This analysis establishes a one-to-one relationship, which can be used to follow nuclear spin diffusion, between optical Knight shift and the radial position of lattice nuclei.
\r\n\r\nWe have also introduced POWER NMR techniques to characterize the change in electric field associated with cycling from light-on to light-off states via a linear quadrupole Stark effect (LQSE) of the nuclear spins. Simulations of these NMR spectra in terms of the radial electric fields of either donor-bound electrons or excitons indicate differences, where the bound-exciton model provides a significantly better fit to the data. The same spin physics enabled our measurement of the heterojunction interfacial field, which we find to be less than 1.3 kV/cm at the sites responsible for optical NMR. Other simulations show the promise of optical NMR as a tool in future studies aimed at atomic-level characterization of quantum-confined systems such as quantum dots and wells.
", "doi": "10.7907/0JZB-N948", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:13592", "collection": "thesis", "collection_id": "13592", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11212019-155237296", "primary_object_url": { "basename": "lee-h-n-1999.pdf", "content": "final", "filesize": 2538727, "license": "other", "mime_type": "application/pdf", "url": "/13592/1/lee-h-n-1999.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "I. Gas Phase Proton Affinity of Zwitterionic Betaine. II. High Resolution Spectroscopy of Trapped Ions: Concept and Design", "author": [ { "family_name": "Lee", "given_name": "Hak-No", "clpid": "Lee-Hak-No" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In an ideal experiment, the system being investigated is isolated from the environment. The only external influences allowed on the system are the parameters that the experimenter chooses to vary, in effort to study their effects on the observables. Moreover, these parameters can be controlled with all the accuracy and precision desired by the experimenter. In chemistry, ion cyclotron resonance (ICR) mass spectrometry may come closer to replicating this ideal condition than any other experimental technique. An ion isolated in an ICR trap is under ultra high vacuum, devoid of physical contact with other atomic and molecular systems, as well as with the apparatus itself. Confined to a small volume and for a practically unlimited length of time, its few connections with the external environment, such as temperature and the electric and magnetic trapping fields, are well under the experimenter's control. And since the motion of a charged particle in electric and magnetic fields is completely known, the ion can be manipulated with an unequaled freedom and certainty. In this dissertation, two experimental methods which utilize these unique capabilities of ICR spectrometry are explored.
\r\n\r\nIn Chapter 1, the kinetic method is applied to determine the gas phase proton affinity of the zwitterion betaine, (CH\u2083)\u2083N\u207aCH\u2082CO\u2082\u207b. Protonated dimers of betaine with reference bases of known proton affinities are formed by Cs\u207a bombardment of a glycerol solution in an external ion source FT-ICR. Product distributions resulting from off-resonance collisional activation of isolated adducts are analyzed to yield a value of 242 \u00b1 1 kcal/mol for the gas phase proton affinity of betaine. This is 103 kcal/mol less than that of the isoelectronic tert-butylacetate anion, (CH\u2083)\u2083CCH\u2082CO\u2082\u207b, and the difference can be attributed to the electrostatic dipolar stabilization of the carboxylate anion in betaine. In addition, a general analysis of the kinetic method is presented based on RRKM unimolecular reaction theory. This analysis does not assume a Boltzmann distribution of internal energies in the reactant ion and provides a rationalization for the success of the method even when different experimental techniques are used.
\r\n\r\nWhile ICR has proven to be a powerful technique for studying the chemical properties of gas phase ions, it suffers from a serious weakness which prevents full realization of its unique capabilties: The only observable it measures is the mass. This has kept ICR from being widely used to investigate the physical properties of molecular ions. In Chapter 2, a novel method for obtaining high-resolution r.f. and microwave spectra of ions in ICR trap is proposed. Termed internally resonant ion trapping excitation (IRITE), it uses spatially inhomogeneous a.c. electric fields to couple the internal energy states with the ion's translation motion. The resonance absorption of radiation is detected by its effect on the oscillations of the trapped ions, rather than on the radiation. The theoretical concept behind IRITE is introduced, and an experiment designed to demonstrate its feasibility by observing r.f. transitions in HCl\u207a is discussed in details. Combined with ICR's unsurpassed ability to isolate and manipulate chemical systems, this new technique promises to allow chemists to study phenomena previously unobservable even in neutral molecules.
", "doi": "10.7907/8gqa-0x72", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:4709", "collection": "thesis", "collection_id": "4709", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12022003-155839", "primary_object_url": { "basename": "Carson_pj_1997.pdf", "content": "final", "filesize": 5409881, "license": "other", "mime_type": "application/pdf", "url": "/4709/1/Carson_pj_1997.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. Ultrasensitive surface NMR using parahydrogen spin labeling. II. High-resolution optical NMR of semiconductor heterostructures using larmor beat detection", "author": [ { "family_name": "Carson", "given_name": "Paul Jonathan", "clpid": "Carson-P-J" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "abstract": "This dissertation presents two techniques for ultrasensitive high-resolution nuclear magnetic resonance. The first exploits the spin order inherent in spin-symmetry enriched H2 to achieve orders of magnitude improvement in the sensitivity of surface NMR over traditional techniques. The second uses a Larmor beat method to allow real-time optical detection of NMR transients in single epitaxial heterostructures and achieves orders of magnitude improvement in spectral resolution over previous steady-state techniques.\r\n\r\nMolecular addition of para-enriched hydrogen to sites in which the protons are magnetically inequivalent results in large nonequilibrium spin population differences, detected as enhanced NMR signals in coupled spin systems. This PASADENA technique (parahydrogen and synthesis allow dramatically enhanced nuclear alignment) has previously been applied to liquids, with the potential for improvement in sensitivity of up to four orders of magnitude. The extension of the technique to the solid state is described here. Enhanced spectra of hydrogen chemisorbed on powdered ZnO are observed, revealing a reversible binding site. The spectra show a strong dipolar coupling which is not detected without PASADENA enhancement. This indicates the selectivity of the method for molecular binding and its potential for structural and mechanistic studies. A random comparison of theoretical lineshapes with the data yields clustering of possible interproton distances around 1.8 [angstroms], and 2.3-2.5[angstroms], although other distances are not rigorously excluded. The inverse technique, in which the branching fraction of ortho and para molecules desorbed after spin evolution reports on the surface NMR spectrum, is also discussed.\r\n\r\nNext, the Larmor beat method for optical detection of NMR in III-V semiconductors is presented. The technique utilizes modulation of the circular polarization of luminescence, via a Hanle effect, at the difference in Larmor precession frequencies of two nuclear species. Order-of-magnitude improvements in both sensitivity and resolution over previous methods for studying single epitaxial structures are observed. High-resolution spectra of a GaAs heterojunction reveal weak quadrupole splittings that report on the electric field gradient at nuclear sites. The spectra also allow spin thermometry, indicating that optically pumped nuclear spin polarizations on the order of 10% are achieved with less than 5 seconds of optical nuclear polarization", "doi": "10.7907/8382-QF81", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:4847", "collection": "thesis", "collection_id": "4847", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12072007-093730", "primary_object_url": { "basename": "Hwang_jy_1994.pdf", "content": "final", "filesize": 5152396, "license": "other", "mime_type": "application/pdf", "url": "/4847/1/Hwang_jy_1994.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "NMR of dilute sites in GaAs", "author": [ { "family_name": "Hwang", "given_name": "Jack Yanchai", "clpid": "Hwang-J-Y" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "abstract": "The presence of a point defect in the zincblende lattice of GaAs breaks the tetrahedral symmetry and induces a range of quadrupole splittings into the NMR spectra of the surrounding Ga and As sites (all spin 3/2). Two-dimensional NMR nutation experiments are used to observe the resulting resonances in the case of an isovalent dopant. Differences in the nutation frequency of resonances near the unperturbed Zeeman frequency allow separation of the contributions from sites with large and small electric field gradients. Rotation studies allow the determination of field gradient tensor components in the crystal frame and provide clues to the assignment to specific sites. The inability to observe the NMR of the indium dopant at a concentration of 1 x 10^20/cm3 highlights the insensitivity of conventional NMR to the study of defects found at the concentrations present in device quality materials or to the low number of sites present at a single-crystal surface or interface.\n\nOptical nuclear polarization (ONP) and optical detection (OD) of nuclear magnetic resonance (NMR) in III-V semiconductors have proven to be effective methods for increasing the sensitivity of NMR over that of conventional methods. The combination of ONP and OD into one optical NMR experiment has led to sensitivity enhancements of at least 10^5 in several GaAs-based materials. The quasi steady-state optically detected NMR (ODNMR) method used in all of these studies has resulted in NMR lineshapes which were either distorted by the high rf fields needed to see signals or broadened by the presence of spin-polarized electrons during NMR. The previous introduction of time-sequenced optical NMR (TSONMR) by the Weitekamp group, in which ONP, NMR, and OD occur in successive periods and are thus separately optimizable, has allowed the full implementation of multiple-pulse NMR. Several such methods are demonstrated on sub-ppm donor sites in epitaxial p-GaAs. These results suggest that TSONMR may contribute to defect identification at sensitivities of technological relevance.\n\nIn conventional rf-detected Fourier transform (FT) NMR, the entire dipole- allowed spectrum is obtained from a single free induction decay. In contrast, FT time- sequenced optical NMR methods have necessarily been pointwise methods in which a period of coherent NMR evolution is incremented on successive repetitions to map out the desired interferogram. This method has the disadvantage, relative to ordinary NMR, that even simple experiments are time-consuming and susceptible to signal drift, giving rise to t1 noise. This restriction has now been lifted by introducing a circularly-polarized transverse rf reference field so that the magnitude of the vector sum field (reference plus nuclear field of interest) is modulated at the difference frequencies of its Fourier components. The circular polarization of the luminescence is thus likewise modulated, due to the Hanle effect. This method allows real-time collection of NMR transients. To simultaneously optimize sensitivity and linearity, it is desirable to have a reference field which is larger than the signal field and comparable to the total longitudinal field. This is achieved by tuning the frequency of the applied reference field into resonance with one isotope so that the spin-locked nuclear hyperfine field, which can be orders of magnitude larger than practical applied rf fields, becomes the effective reference field. The circularly polarized luminescence signals at the difference frequencies are demodulated by a heterodyne rf spectrometer and digitized.\n", "doi": "10.7907/0C96-JQ24", "publication_date": "1994", "thesis_type": "phd", "thesis_year": "1994" }, { "id": "thesis:7722", "collection": "thesis", "collection_id": "7722", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05172013-114618257", "primary_object_url": { "basename": "Ross 1994.pdf", "content": "final", "filesize": 24975103, "license": "other", "mime_type": "application/pdf", "url": "/7722/1/Ross 1994.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Insights into the Mechanism of Human Erythrocyte Hexose Transport: a Transferred NOE Study of Glucose Binding to GLUT1", "author": [ { "family_name": "Ross", "given_name": "Scott Alan", "clpid": "Ross-Scott-Alan" } ], "thesis_advisor": [ { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" } ], "thesis_committee": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "orcid": "0000-0003-0079-8000", "clpid": "Weitekamp-D-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This study examines binding of \u03b1- and \u03b2-D-glucose in their equilibrium mixture to the glucose transporter (GLUT1) in human erythrocyte membrane preparations by an ^1H NMR method, the transferred NOE (TRNOE). This method is shown theoretically and experimentally to be a sensitive probe of weak ligand-macromolecule interactions. The TRNOEs observed are shown to arise solely from glucose binding to GLUT1. Sites at both membrane faces contribute to the TRNOEs. Binding curves obtained are consistent with a homogeneous class of sugar sites, with an apparent KD which varies (from ~30 mM to ~70 mM for both anomers) depending on the membrane preparation examined. Preparations with a higher proportion of the cytoplasmic membrane face exposed to bulk solution yield higher apparent KKDs. The glucose transport inhibitor cytochalasin B essentially eliminates the TRNOE. Nonlinearity was found in the dependence on sugar concentration of the apparent inhibition constant for cytochalasin B reversal of the TRNOE observed in the \u03b1 anomer (and probably the \u03b2 anomer); such nonlinearity implies the existence of ternary complexes of sugar, inhibitor and transporter. The inhibition results furthermore imply the presence of a class of relatively high-affinity (KD < 2mM) sugar sites specific for the \u03b1 anomer which do not contribute to NMR-observable binding. The presence of two classes of sugar-sensitive cytochalasin B sites is also indicated. These results are compared with predictions of the alternating conformer model of glucose transport. Variation of apparent KD in the NMR-observable sites, the formation of ternary complexes and the presence of an anomer-specific site are shown to be inconsistent with this model. An alternate model is developed which reconciles these results with the known transport behavior of GLUT1. In this model, the transporter possesses (at minimum) three classes of sugar sites: (i) transport sites, which are alternately exposed to the cytoplasmic or the extracellular compartment, but never to both simultaneously, (ii) a class of sites (probably relatively low-affinity) which are confined to one compartment, and (iii) the high-affinity \u03b1 anomer-specific sites, which are confined to the cytoplasmic compartment.\r\n", "doi": "10.7907/nb45-1b79", "publication_date": "1994", "thesis_type": "phd", "thesis_year": "1994" }, { "id": "thesis:4468", "collection": "thesis", "collection_id": "4468", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11092004-164546", "primary_object_url": { "basename": "Buratto_sk_1993.pdf", "content": "final", "filesize": 8196488, "license": "other", "mime_type": "application/pdf", "url": "/4468/1/Buratto_sk_1993.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Time-sequenced optical nuclear magnetic resonance of gallium arsenide", "author": [ { "family_name": "Buratto", "given_name": "Steven Keith", "clpid": "Buratto-S-K" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThis dissertation describes the development of a new method of optical NMR, time-sequenced optical NMR (TSONMR), of GaAs for which both sensitivity and resolution are optimized. In this method, the three processes of optical nuclear polarization (ONP), nuclear magnetic resonance (NMR), and optical detection (OD) occur in distinct sequential periods achieving order-ofmagnitude improvements insensitivity and resolution relative to the earlier quasi-steady-state methods. The TSONMR experiment is also flexible, allowing both continuous wave (CW) and time-domain TSONMR experiments to be performed. The underlying physics is used to develop a quantitative theory of sensitivity which is in good agreement with experiment.\n\nApplications to epitaxial p-type GaAs samples show that the CW and Fourier transform (FT) versions of TSONMR are sensitive to different nuclear sites. The locus of the method is an unknown optically relevant defect (ORD) present at [...]. The CW experiment is sensitive to the more numerous bulk spins far from the ORD, while the FT experiment is sensitive to the low abundance sites which are quadrupole-perturbed by proximity to the ORD. The difference between the two experiments can be understood by accounting for and manipulating the role of spin diffusion. Nutation experiments and the dependence on sample orientation rule out the alternative interpretation that only strongly perturbed sites are seen. Thus, the range of the optically induced hyperfine coupling at the ORD far exceeds that of valence-band electric field perturbations.\n\nThe FT-TSONMR experiment is sample specific as is demonstrated for two electrically-equivalent p-type samples (both containing [...]). One sample exhibits much stronger electric field gradient perturbations than the other indicating differences at the atomic level in the defects responsible for localization. \n\nIt is also shown on a bulk sample that the method allows high-resolution measurement of the optically induced Knight shift which is proportional to the electron density at the nucleus. Extensions of these observations to quantum wells are proposed. For a [...] quantum well, sample calculations show that the optical Knight shift will provide spectral resolution of individual atomic layers. Optical-rf multiple-pulse sequences are described to minimize other contributions to the linewidth. It should therefore be possible to map out the electron probability across the GaAs layer of a quantum well and give great insight into the electronic wavefunction near the interface as well as the center of the well.", "doi": "10.7907/HHY0-JX87", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:4627", "collection": "thesis", "collection_id": "4627", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11212006-091334", "primary_object_url": { "basename": "Werner_mh_1993.pdf", "content": "final", "filesize": 18730514, "license": "other", "mime_type": "application/pdf", "url": "/4627/1/Werner_mh_1993.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "NMR imaging of solids with multiple-pulse line narrowing and radiofrequency gradients", "author": [ { "family_name": "Werner", "given_name": "Margat Hoppe", "clpid": "Werner-M-H" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "abstract": "The usual methods of magnetic resonance imaging fail in rigid solids due to the line shape contributions of dipolar coupling, chemical shift dispersion and anisotropy, and bulk magnetic susceptibility. This dissertation presents a new method of solid-state imaging by nuclear magnetic resonance which averages away these contributions with multiple-pulse line-narrowing and encodes spatial information with pulsed radiofrequency field gradients. This method is closely related to simultaneously developed methods utilizing pulsed DC gradients, and offers similar improvements in sensitivity and resolution. The advantage of rf gradients is that they can be rapidly switched without inducing eddy currents in the probe or the magnet. In addition, the phases and amplitudes of the rf gradients can be switched by equipment which is already part of an NMR spectrometer capable of solid-state spectroscopy. The line-narrowing and gradient pulses originate in separate rf circuits tuned to the same frequency. Interactions between the circuits have been minimized by a method of active Q-switching which employs PIN diodes in the matching networks of these circuits.\n\nBoth one- and two-dimensional images are presented. The latter are obtained by a novel method in which the two dimensions of imaging transverse to the static magnetic field are encoded by two orthogonal components of a single rf gradient. A [pi]/2 phase shift of the rf phase relative to that of the line-narrowing pulses selects one component or the other. This arrangement allows the solid-state analogs of versatile imaging sequences based on Fourier imaging and eliminates the need for sample rotation and back-projection methods.\n\nCoherent averaging theory is used to analyze this imaging technique and exact numerical simulations on several coupled spins are discussed. These lend insight to the residual linewidth and its dependence on pixel position as well as to the range of applicability of this technique.\n", "doi": "10.7907/E4BV-9D83", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:1405", "collection": "thesis", "collection_id": "1405", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04172006-141634", "primary_object_url": { "basename": "Bowers_cr_1991.pdf", "content": "final", "filesize": 8094021, "license": "other", "mime_type": "application/pdf", "url": "/1405/1/Bowers_cr_1991.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Parahydrogen and Synthesis Allow Dramatically Enhanced Nuclear Alignment", "author": [ { "family_name": "Bowers", "given_name": "Clifford Russell", "orcid": "0000-0001-6155-5163", "clpid": "Bowers-Clifford-Russell" } ], "thesis_advisor": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "thesis_committee": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Chan", "given_name": "David C.", "clpid": "Chan-D-C" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The PASADENA effect is a method for transient high-sensitivity proton spin-labelling by molecular addition of dihydrogen. When the parahydrogen mole fraction differs from the high-temperature limit of 1/4, this population difference constitutes a form of spin order which can be converted to magnetization observable by NMR. Large NMR signals are observed, if subsequent to the hydrogen addition, the two protons experience magnetic inequivalence and spin-spin coupling and if observation is made before spin-lattice relaxation restores the equilibrium spin order. The analogous effect for D2 is also possible.
\r\n\r\nThe kinetic mechanisms of the homogeneous hydrogenation catalysts which permit the realization of the PASADENA effect have been the target of the experimental applications. The enhancement of the NMR transitions has facilitated the determination of true molecular rate constants. Ordinarily, the activity of a catalyst is assessed by dividing the observed rate by the total catalyst concentration. However, the question as to whether most of the catalytic rate is due to a tiny fraction of active species or a large fraction with a relatively low molecular rate is not clearly addressed by such an analysis. This ambiguity is entirely avoided in the PASADENA studies, since only active catalyst molecules can contribute to the enhanced signals from which all kinetic inferences are made.
\r\n\r\nThe sensitivity enhancement has also led to the identification of a novel intermediate in the mechanism for the Rh(DIPHOS)+ catalyzed hydrogenation of styrene. The rate of conversion of this species into product and starting material has been studied using two-dimensional NMR. The dramatically improved sensitivity should make it possible to observe key catalytic intermediates which do not build up in sufficient quantity to allow detection by conventional NMR arising from Curie-Law magnetization.
\r\n\r\nThe study of surface sites which bind pairwise with H2 is also a potentially fruitful area for future experimental work. The ambient temperature NMR spectroscopy of surfaces is not often feasible due to sensitivity limitations. Simulations have been performed using typical shift and coupling parameters in an effort to characterize the enhanced lineshapes which can be expected.
\r\n\r\nThe inverse of the PASADENA effect has also been proposed, whereby the spin order of a molecule containing hydrogen is probed by measuring the branching ratio to ortho and para dihydrogen. This RAYMOND phenomenon (radiowave application yields modulated ortho number desorbed) has the potential for measuring precursor NMR with extraordinary sensitivity, since it finesses the need for detection of radiowaves.
", "doi": "10.7907/R5TV-Z220", "publication_date": "1991", "thesis_type": "phd", "thesis_year": "1991" }, { "id": "thesis:4693", "collection": "thesis", "collection_id": "4693", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11302006-091037", "type": "thesis", "title": "Time-Resolved Studies of Molecular Reaction Dynamics and Development of Experimental Methodology", "author": [ { "family_name": "Scherer", "given_name": "Norbert Franz", "clpid": "Scherer-Norbert-Franz" } ], "thesis_advisor": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "thesis_committee": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The six research topics presented in the following chapters are concerned with several diverse problems of molecular reaction dynamics in isolated gas-phase environments. The scope of the studies ranges from performing direct measurements of bond-breakage on electronically dissociative potential energy surfaces, to monitoring the time-course of a restricted geometry bimolecular reaction. The common experimental method used in all of the studies has been a variant of pump-probe time-resolved spectroscopy. The underlying theme of the endeavors has been threefold: 1) To gain a better understanding of the role of intramolecular dynamics that precede or are commensurate with the reaction dynamics; 2) To begin to appreciatiate the observable manifestations of specific features of the reactive potential energy surface; and 3) To utilize the specific temporal behavior to elucidate quantitative information for the said potential surface.
\r\n\r\nThe studies of molecular dissociation on repulsive electronic surfaces has lead to a quantification of the timescale for primary steps in reaction processes. Moreover, transform limited temporal/spectral studies have begun to focus on specific long-range reaction fragment interactions in a state-specific manner. The latter endeavor has identified a mechanism for the reaction-fragment(s) interaction in the near-asymptotic product region.
\r\n\r\nPredissociative reaction and intramolecular dynamical behavior has been studied on ground potential energy surfaces. Overtone excitation of the OH-stretch mode of hydrogen peroxide enables molecular ground state excitation and state-specific detection of the OH reaction product. These investigations point out the potential of this picosecond pump-probe method for directly elucidating the intramolecular energy redistribution process and the possibility for direct investigation of the long-range tail region of the free-radical recombination potential surface.
\r\n\r\nThe investigation of a spatially oriented bimolecular reaction has conclusively shown that the IH-OCO reaction proceeds by way of the [HOCO]\u2020 reaction complex species. The close proximity of the van der Waals bound reactants produces unique multi-body interactions not found in the gas phase but which may arise in condensed phases. Moreover, these investigations have obtained evidence for a unique reaction reasonance (which is analogous to a shape-resonance) feature. The presence of such a resonance in the reaction entrance channel region affects the temporal behavior and yield of product formation.
", "doi": "10.7907/5JGV-E964", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:5370", "collection": "thesis", "collection_id": "5370", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11122009-115104264", "type": "thesis", "title": "Experimental and Theoretical Studies of Silylenes, Silicenium Ions, and Organometallic Reactive Intermediates", "author": [ { "family_name": "Shin", "given_name": "Seung Koo", "clpid": "Shin-Seung-Koo" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Fourier transform ion cyclotron resonance spectroscopy has been used to investigate thermochemistry and relative stabilities of silylenes, silaethylene, and silicenium ions in the gas phase. Proton affinities of silylene, methylsilylene and silaethylene have been derived from studies of kinetics and thermochemistry of proton transfer from the corresponding silicenium ions to a series of n-donor bases with well-established gas-phase base strengths. Values of proton affinities combined with the known heats of formation of the corresponding silicenium ions yield heats of formation of silylene, methylsilylene, and silaethylene. Experimental results for the relative stability between methylsilylene and silaethylene are corroborated by ab initio generalized valence bond (GVB)-configuration interaction (CI) calculations which indicate that silaethylene is more stable than methylsilylene. Hydride affinities of the methyl-substituted silicenium ions have been precisely determined from examination of kinetics and equilibria of hydride-transfer reactions of methyl-substituted silanes with various hydrocarbons having well-established gas-phase hydride affinities. The result shows that the silicenium ions are significantly more stable than the corresponding carbonium ions in the gas phase with H\u207b as a reference base.
\r\n\r\nPhotoelectron spectroscopy and mass spectrometry have been employed to identify the gas-phase reactive intermediate in the chiorosilane chemical vapor deposition under the heterogeneous flash vacuum pyrolytic condition. The result indicates that dichlorosilylene and hydrogen chloride are the major gas-phase products and monochlorosilylene is not an abundant gas-phase intermediate.
\r\n\r\nThe ab initio theoretical methods have been used to calculate the equlibrium ge-ometries and singlet-triplet splittings of chlorine- and fluorine-substituted silylenes and methylenes. The GVB-dissociation consistent CI (DCCI) method has been developed to accurately predict singlet-triplet energy gaps within 1 kcal/mol error.
\r\n\r\nFinally, we have employed Fourier transform ion cyclotron resonance spec-troscopy combined with a line tunable CW CO\u2082 laser to isolate the coordinatively unsaturated organometallic intermediates and examine structures, reactivities, and spectroscopic properties of the isolated intermediates for the methyl-migratory decarbonylation reaction and ligand displacement reaction. The results show that the CF\u2083 group is an ideal infrared chromophore to investigate the infrared photochemistry of organometallic complexes, L\u2099M-CF\u2083, structures, and reaction mechanisms of their coordinatively unsaturated intermediates containing metal-bonded CF\u2083 groups. The infrared multiphoton dissociation spectra of the isolated intermediates containing metal-bonded CF\u2083 group are presented.
", "doi": "10.7907/sdj1-2y57", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:8005", "collection": "thesis", "collection_id": "8005", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10232013-093350784", "type": "thesis", "title": "Electron Energy-Loss Spectroscopy Study of Polyatomic Molecular Systems Under Pyrolytic Conditions", "author": [ { "family_name": "Xavier", "given_name": "Isaac de Melo, Jr.", "clpid": "Xavier-Isaac-de-Melo-Jr" } ], "thesis_advisor": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "orcid": "0000-0003-0079-8000", "clpid": "Weitekamp-D-P" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The technique of variable-angle, electron energy-loss spectroscopy has been used to study the electronic spectroscopy of the diketene molecule. The experiment was performed using incident electron beam energies of 25 eV and 50 eV, and at scattering angles between 10\u00b0 and 90\u00b0. The energy-loss region from 2 eV to 11 eV was examined. One spin-forbidden transition has been observed at 4.36 eV and three others that are spin-allowed have been located at 5.89 eV, 6.88 eV and 7.84 eV. Based on the intensity variation of these transitions with impact energy and scattering angle, and through analogy with simpler molecules, the first three transitions are tentatively assigned to an n \u2192 \u03c0* transition, a \u03c0 - \u03c3* (3s) Rydberg transition and a \u03c0 \u2192 \u03c0* transition.
\r\n\r\nThermal decomposition of chlorodifluoromethane, chloroform, dichloromethane and chloromethane under flash-vacuum pyrolysis conditions (900-1100\u00b0C) was investigated by the technique of electron energy-loss spectroscopy, using the impact energy of 50 eV and a scattering angle of 10\u00b0. The pyrolytic reaction follows a hydrogen-chloride \u03b1-elimination pathway. The difluoromethylene radical was produced from chlorodifluoromethane pyrolysis at 900\u00b0C and identified by its X̃\u00b9A\u2081 \u2192 Ã\u00b9B\u2081 band at 5.04 eV.
\r\n\r\nFinally, a number of exploratory studies have been performed. The thermal decomposition of diketene was studied under flash vacuum pressures (1-10 mTorr) and temperatures ranging from 500\u00b0C to 1000\u00b0C. The complete decomposition of the diketene molecule into two ketene molecules was achieved at 900\u00b0C. The pyrolysis of trifluoromethyl iodide molecule at 1000\u00b0C produced an electron energy-loss spectrum with several iodine-atom, sharp peaks and only a small shoulder at 8.37 eV as a possible trifluoromethyl radical feature. The electron energy-loss spectrum of trichlorobromomethane at 900\u00b0C mainly showed features from bromine atom, chlorine molecule and tetrachloroethylene. Hexachloroacetone decomposed partially at 900\u00b0C, but showed well-defined features from chlorine, carbon monoxide and tetrachloroethylene molecules. Bromodichloromethane molecule was investigated at 1000\u00b0C and produced a congested, electron energy-loss spectrum with bromine-atom, hydrogen-bromide, hydrogen-chloride and tetrachloroethylene features.
", "doi": "10.7907/4wx9-6j66", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:8065", "collection": "thesis", "collection_id": "8065", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02072014-135012645", "primary_object_url": { "basename": "Watnick 1989.pdf", "content": "final", "filesize": 31758236, "license": "other", "mime_type": "application/pdf", "url": "/8065/1/Watnick 1989.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Cooperative Properties of Lipid Bilayers: Collective Director Fluctuations and the Effects of Hydrophobic Mismatch in Protein/Lipid Membrane Systems", "author": [ { "family_name": "Watnick", "given_name": "Paula Ivonne", "clpid": "Watnick-Paula-Ivonne" } ], "thesis_advisor": [ { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "orcid": "0000-0003-0079-8000", "clpid": "Weitekamp-D-P" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Cooperative director fluctuations in lipid bilayers have been postulated for many years. \u00b2H-NMR T\u2081\u207b\u00b9, T\u2081\u03c1\u207b\u00b9, and T\u2082\u207b\u00b9; measurements have been used identify these motions and to determine the origin of increased slow bilayer motion upon addition of unlike lipids or proteins to a pure lipid bilayer.
\r\n\r\nThe contribution of cooperative director fluctuations to NMR relaxation in lipid bilayers has been expressed mathematically using the approach of Doane et al.\u00b9 and Pace and Chan.\u00b2 The T\u2082\u207b\u00b9's of pure dimyristoyllecithin (DML) bilayers deuterated at the 2, 9 and 10, and all positions on both lipid hydrocarbon chains have been measured. Several characteristics of these measurements indicate the presence of cooperative director fluctuations. First of all, T\u2082\u207b\u00b9 exhibits a linear dependence on S\u00b2CD. Secondly, T\u2082\u207b\u00b9 varies across the \u00b2H-NMR powder pattern as sin\u00b2 (2\u03b2), where , \u03b2 is the angle between the average bilayer director and the external magnetic field. Furthermore, these fluctuations are restricted near the lecithin head group suggesting that the head group does not participate in these motions but, rather, anchors the hydrocarbon chains in the bilayer.
\r\n\r\nT\u2082\u207b\u00b9 has been measured for selectively deuterated liquid crystalline DML hilayers to which a host of other lipids and proteins have been added. The T\u2082\u207b\u00b9 of the DML bilayer is found to increase drastically when chlorophyll a (chl a) and Gramicidin A' (GA') are added to the bilayer. Both these molecules interfere with the lecithin head group spacing in the bilayer. Molecules such as myristic acid, distearoyllecithin (DSL), phytol, and cholesterol, whose hydrocarbon regions are quite different from DML but which have small,neutral polar head groups, leave cooperative fluctuations in the DML bilayer unchanged.
\r\n\r\n\r\nThe effect of chl a on cooperative fluctuations in the DML bilayer has been examined in detail using \u00b2H-NMR T\u2081\u207b\u00b9, T\u2081\u03c1\u207b\u00b9, and T\u2082\u207b\u00b9; measurements. Cooperative fluctuations have been modelled using the continuum theory of the nematic state of liquid crystals. Chl a is found to decrease both the correlation length and the elastic constants in the DML bilayer.
\r\n\r\nA mismatch between the hydrophobic length of a lipid bilayer and that of an added protein has also been found to change the cooperative properties of the lecithin bilayer. Hydrophobic mismatch has been studied in a series GA'/lecithin bilayers. The dependence of \u00b2H-NMR order parameters and relaxation rates on GA' concentration has been measured in selectively deuterated DML, dipalmitoyllecithin (DPL), and DSL systems. Order parameters, cooperative lengths, and elastic constants of the DML bilayer are most disrupted by GA', while the DSL bilayer is the least perturbed by GA'. Thus, it is concluded that the hydrophobic length of GA' best matches that of the DSL bilayer. Preliminary Raman spectroscopy and Differential Scanning Calorimetry experiments of GA'/lecithin systems support this conclusion. Accommodation of hydrophobic mismatch is used to rationalize the absence of HII phase formation in GA'/DML systems and the observation of HII phase in GA'/DPL and GA'/DSL systems.
\r\n\r\n1. J. W. Doane and D. L. Johnson, Chem. Phys. Lett., 6, 291-295 (1970).
\r\n\r\n2. R. J. Pace and S. I. Chan, J. Chem. Phys., 76, 4217-4227 (1982).
", "doi": "10.7907/j3wj-vz40", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:7485", "collection": "thesis", "collection_id": "7485", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02202013-105931312", "type": "thesis", "title": "Photoelectron Spectroscopy of Reactive Intermediates", "author": [ { "family_name": "Kruppa", "given_name": "Gary Hermann", "clpid": "Kruppa-Gary-Hermann" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Photoelectron Spectroscopy (PES) has been used to investigate the structure and thermochemistry of a number of alkyl radicals and their corresponding carbonium ions. The radicals have been produced by flash vacuum pyrolysis of alkyl nitrites. The shape of the first band in the photoelectron spectrum of a free radical is related to the structural changes that take place in forming the carbonium ion from the radical. The ionization potentials obtained from the photoelectron spectra of the radicals are combined with gas phase ion thermochemistry data to obtain alkyl radical heats of formation. The thermochemical data thus obtained is used to discuss substituent and structural effects on the stability of radicals and carbonium ions. In many cases the thermolytic decomposition pathways of the alkyl radicals have been elucidated using PES. The application of the PES technique to the analysis of reactive intermediates present in heterogeneous thermolysis mixtures is also discussed.
\r\n\r\nChapter 1 presents an introduction to the technique employed in these studies, and a review of the studies performed in this laboratory. Chapter 2 presents results on the thermochemistry and structure of the 1- and 2-adamantyl radicals. The tricyclic 1-adamantyl radical and carbonium ion are important as model bridgehead compounds, and the question of the amount of strain energy caused by the non-planarity of the radical and ion center has been of great interest. The first bands in the photoelectron spectra of the o-, m- and p-methylbenzyl radicals are presented in Chapter 3. The methyl substituent effects on the stabilities of the radicals and ions are discussed.
\r\n\r\nIn Chapter 4 results on investigations of heterogeneous processes in Chemical Vapor Deposition (CVD) systems using the chlorosilanes as feed gases are discussed. SiCl\u2082 is found to be the major silicon containing reactive intermediate produced by surface reactions at 600 - 1100 \u00b0C in CVD systems using dichlorosilane and trichlorosilane as feed gases.
\r\n\r\nChapter 5 presents the spectra of the 1- and 2-methylnaphthyl radicals. The relative stabilities of the radicals and carbonium ions are discussed based on proton affinities determined by Fourier transform mass spectrometric equilibrium studies, combined with ionization potentials obtained from photoelectron spectra of the radicals.
\r\n", "doi": "10.7907/jytn-vs45", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:7411", "collection": "thesis", "collection_id": "7411", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01182013-144750308", "primary_object_url": { "basename": "Dubs_rl_1988.pdf", "content": "final", "filesize": 20048491, "license": "other", "mime_type": "application/pdf", "url": "/7411/1/Dubs_rl_1988.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Single- and Multiphoton Ionization Processes in Molecules", "author": [ { "family_name": "Dubs", "given_name": "Richard Leslie", "clpid": "Dubs-Richard-Leslie" } ], "thesis_advisor": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation is theoretical in nature and can be separated into two main areas: 1) single- and multiphoton ionization studies of a novel photoelectron effect, and 2) single-photon ionization studies of simple clusters as models for adsorbate photoemission. The first area centers on the phenomenon of circular dichroism in photoelectron angular distributions (CDAD). CDAD is shown to exist from oriented linear molecules, adsorbed atoms, and aligned atoms and molecules in the gas phase. The calculations presented here are the first to demonstrate the experimental feasability of CDAD studies. CDAD is shown to be a measurable effect which exists because the photoelectron collection direction can break the symmetry of these otherwise highly symmetric systems. As a direct result of the work presented here, CDAD has now been observed experimentally. Coupled with resonantly enhanced multiphoton ionization (REMPI), CDAD is shown to be a powerful probe of unknown alignment in gas phase atomic and molecular samples. The second area of research focuses on the simple oriented molecules NiCO and NiN\u2082 as models for the corresponding adsorbate systems. These simple models provide insight into features observed in the experimental angle-resolved photoemission spectra.
", "doi": "10.7907/63a3-d438", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:7510", "collection": "thesis", "collection_id": "7510", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03122013-093032947", "primary_object_url": { "basename": "Parker_gr_1988.pdf", "content": "final", "filesize": 97733769, "license": "other", "mime_type": "application/pdf", "url": "/7510/1/Parker_gr_1988.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Determination of Nascent H\u2082 Rovibrational Distributions by Laser Induced Fluorescence: Applications to Formaldehyde Photodissociation and Hydrogen Exchange Reactions", "author": [ { "family_name": "Parker", "given_name": "Garth Rockwood, Jr.", "clpid": "Parker-Garth-Rockwood-Jr" } ], "thesis_advisor": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Individual quantum states of H\u2082 have been detected using the technique of Laser Induced Fluorescence. This technique is extremely sensitive, with a detection sensitivity of 6 x 10\u2078 states cm\u207b\u00b3 in a probed volume of 0.029 cm\u00b3 with a signal-to-noise ratio of 3. This technique is also accurate. A spectrum of room temperature H\u2082 had a rotational temperature of 305.8 \u00b1 3.0 K. LIF detection of H\u2082 was used to study the H\u2082CO photodissociation reaction under essentially collision-free conditions. Following excitation of the rR\u2083 bandhead of the 2\u00b9\u20804\u00b3\u2080 transition at 30388.5 cm\u207b\u00b9, the principal product was ortho-H\u2082. States as high as v = 4, J = 5 were seen. Within the v = 1 channel, the rotational distribution peaked at J = 3. Following excitation of the rR\u2084 bandhead of the 2\u00b9\u20804\u00b3\u2080 transition at 30396.7 cm\u207b\u00b9, the principal product was para-H\u2082. This is the first report of the para-H\u2082 distribution following H\u2082CO dissociation. The rotational distribution is similar to that for ortho-H\u2082 and peaks at J = 4 within v = 1 channel. This result contradicts a recent theoretical calculation that predicted that the para-H\u2082 distribution would be bimodal with a minimum at J = 6. Quantitative analysis of higher vibrational levels was hampered by a lack of spectroscopic knowledge (both transition energies and intensities) when the the B̅ and C̅ states perturb each other. Attempts to use LIF to study the hydrogen exchange reaction have been unsuccessful.
", "doi": "10.7907/ht1t-df04", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:17586", "collection": "thesis", "collection_id": "17586", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08012025-212202129", "primary_object_url": { "basename": "Lynch_DL_1987.pdf", "content": "final", "filesize": 60867116, "license": "other", "mime_type": "application/pdf", "url": "/17586/1/Lynch_DL_1987.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Dynamics of Single and Multiphoton Ionization Processes in Molecules", "author": [ { "family_name": "Lynch", "given_name": "Diane Lynn", "clpid": "Lynch-Diane-Lynn" } ], "thesis_advisor": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" } ], "thesis_committee": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "orcid": "0000-0003-0079-8000", "clpid": "Weitekamp-D-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Single-photon and resonant multiphoton ionization\r\nstudies, which can now be carried out using synchrotron\r\nradiation and lasers, respectively, are providing important\r\ndynamical information on molecular photoionization. We\r\nhave studied the underlying dynamical features of these\r\nionization processes using Hartree-Fock continuum orbitals\r\ngenerated using the Iterative Schwinger Variational method\r\nfor solving the photoelectron collisional equations. Our\r\nsingle-photon studies examine the important role that\r\nshape and autoionizing resonances play in molecular photoionization,\r\nwhile the multiphoton studies investigate the\r\nionization dynamics of excited electronic states.
\r\n\r\nWe have demonstrated the subtle nature of shape\r\nresonances in polyatomic systems such as C2H2 and C2N2,\r\nwhere the possibility of multiple resonances in a single\r\nchannel is observed. In addition, these resonant states\r\ninduce the breakdown of the Franck-Condon approximation as\r\nwell as the frozen core approximation in K-shell\r\nionization, as illustrated in our vibrationally resolved\r\nstudies of CO and the K-Shell studies of N2 and CO2,\r\nrespectively. Critical comparisons with other theoretical\r\nresults and available experimental data have been made for\r\nthese systems.
\r\n\r\nMolecular autoionizing resonances are known to\r\ndominate regions of the photoionization spectra. We have\r\nadapted and applied a generalization of the Fane treatment\r\nfor autoionization to molecular systems. Results for H2\r\nand C2H2 autoionizing resonances are presented and\r\ndiscussed.
\r\n\r\nResonant enhanced multiphoton ionization (REMPI) is\r\ncurrently being used to study the dynamics of state-selected\r\nphotoionization processes by laser excitation to\r\nspecific vibrational and rotational levels. As first\r\napplications of a quantitative analysis for molecular\r\nREMPI we have studied several ionization schemes in H2,\r\nsuch as (3+1) REMPI via the C1\u220fu state, (2+1) REMPI via\r\nthe B1\u03a3u+ state, and (2+1) REMPI via the double-well\r\nE,F1\u03a3g+ state. These ab initio studies are very useful in g\r\nunderstanding the underlying dynamics of molecular REMPI,\r\ne.g., the observed non-Franck-Condon behavior of the\r\nvibrational branching ratios in the C1\u220fu and E,F1\u03a3g+\r\nstates can be primarily attributed to the internuclear\r\ndistance dependence of the electronic transition moments.\r\nWe compare and discuss our theoretical results with the\r\navailable experimental data.
", "doi": "10.7907/7grh-zk17", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:11851", "collection": "thesis", "collection_id": "11851", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10232019-145508172", "type": "thesis", "title": "Elastic, Inelastic, and Photofragment Scattering from Crossed Molecular Beams", "author": [ { "family_name": "Reid", "given_name": "Brian Paul", "clpid": "Reid-Brian-Paul" } ], "thesis_advisor": [ { "family_name": "Sparks", "given_name": "Randal K.", "clpid": "Sparks-Randal-K" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Sparks", "given_name": "Randal K.", "clpid": "Sparks-Randal-K" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Weitekamp", "given_name": "Daniel P.", "orcid": "0000-0003-0079-8000", "clpid": "Weitekamp-D-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Three sets of crossed molecular beam scattering experiments are described. In the first experiment, total differential cross sections are measured for collisions between two methane molecules. Treating the scattering as elastic, these cross sections are used to determine an isotropic intermolecular potential energy function for the methane-methane system. The second experiment involves the measurement of total differential cross sections and time-of-flight spectra for neon-chlorine scattering. These data are modeled using the infinite order sudden approximation for rotationally inelastic scattering, and an anisotropic potential function for neon-chlorine is determined. In the third experiment, the angular and time-of-flight distributions for the products of the three-body photofragmentation of 1,2-diiodotetrafluoroethane at 266 nm are measured. These data are analyzed to determine the product translational energy distributions.
", "doi": "10.7907/xz77-2x37", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" } ]