The biological sense of smell: olfactory search behavior and a metabolic view for olfactory perception

Part I of the thesis describes the olfactory searching and scanning behaviors of rats in a wind tunnel, and a detailed movement analysis of terrestrial arthropod olfactory scanning behavior. Olfactory scanning behaviors in rats may be a behavioral correlate to hippocampal place cell activity.

Part II focuses on the organization of olfactory perception, what it suggests about a natural order for chemicals in the environment, and what this in tum suggests about the organization of the olfactory system. A model of odor quality space (analogous to the "color wheel") is presented. This model defines relationships between odor qualities perceived by human subjects based on a quantitative similarity measure. Compounds containing Carbon, Nitrogen, or Sulfur elicit odors that are contiguous in this odor representation, which thus allows one to predict the broad class of odor qualities a compound is likely to elicit. Based on these findings, a natural organization for olfactory stimuli is hypothesized: the order provided by the metabolic process. This hypothesis is tested by comparing compounds that are structurally similar, perceptually similar, and metabolically similar in a psychophysical cross-adaptation paradigm. Metabolically similar compounds consistently evoked shifts in odor quality and intensity under cross-adaptation, while compounds that were structurally similar or perceptually similar did not. This suggests that the olfactory system may process metabolically similar compounds using the same neural pathways, and that metabolic similarity may be the fundamental metric about which olfactory processing is organized. In other words, the olfactory system may be organized around a biological basis.

The idea of a biological basis for olfactory perception represents a shift in how olfaction is understood. The biological view has predictive power while the current chemical view does not, and the biological view provides explanations for some of the most basic questions in olfaction, that are unanswered in the chemical view. Existing data do not disprove a biological view, and are consistent with basic hypotheses that arise from this viewpoint.

Measurement of the direct CP asymmetry in b-->s+gamma via sum of exclusive B Meson decays using the BABAR detector

We perform a measurement of direct CP violation in b to s+gamma Acp, and the measurement of a difference between Acp for neutral B and charged B mesons, Delta A_{X_s\gamma}, using 429 inverse femtobarn of data recorded at the Upsilon(4S) resonance with the BABAR detector. B mesons are reconstructed from 16 exclusive final states. Particle identification is done using an algorithm based on Error Correcting Output Code with an exhaustive matrix. Background rejection and best candidate selection are done using two decision tree-based classifiers. We found $\acp = 1.73%+-1.93%+-1.02% and Delta A_X_sgamma = 4.97%+-3.90%+-1.45% where the uncertainties are statistical and systematic respectively. Based on the measured value of Delta A_X_sgamma, we determine a 90% confidence interval for Im C_8g/C_7gamma, where C_7gamma and C_8g are Wilson coefficients for New Physics amplitudes, at -1.64 < Im C_8g/C_7gamma < 6.52.

A measurement of inclusive quasi-elastic electron scattering cross sections at high momentum transfer

We have measured inclusive electron-scattering cross sections for targets of ^(4)He, C, Al, Fe, and Au, for kinematics spanning the quasi-elastic peak, with squared, four­ momentum transfers (q^2) between 0.23 and 2.89 (GeV/c)^2. Additional data were measured for Fe with q^2's up to 3.69 (GeV/c)^2 These cross sections were analyzed for the y-scaling behavior expected from a simple, impulse-approximation model, and are found to approach a scaling limit at the highest q^2's. The q^2 approach to scaling is compared with a calculation for infinite nuclear matter, and relationships between the scaling function and nucleon momentum distributions are discussed. Deviations from perfect scaling are used to set limits on possible changes in the size of nucleons inside the nucleus.

A measurement of the proton elastic form factors for 1 ≤ Q^2 ≤ 3 (GeV/c)^2

We report measurements of the proton form factors, G^p_E and G^p_M, extracted from elastic electron scattering in the range 1 ≤ Q^2 ≤ 3 (GeV/c)^2 with uncertainties of <15% in G^p_E and <3% in G^p_M. The results for G^p_E are somewhat larger than indicated by most theoretical parameterizations. The ratio of Pauli and Dirac form factors, Q^2(F^p_2/F^p_1), is lower in value and demonstrates less Q^2 dependence than these parameterizations have indicated. Comparisons are made to theoretical models, including those based on perturbative QCD, vector-meson dominance, QCD sum rules, and diquark constituents to the proton. A global extraction of the form factors, including previous elastic scattering measurements, is also presented.

Measurement of the band bending and surface dipole at chemically functionalized Si(111)/vacuum interfaces

The core-level energy shifts observed using X-ray photoelectron spectroscopy (XPS) have been used to determine the band bending at Si(111) surfaces terminated with Si-Br, Si-H, and Si-CH₃ groups, respectively. The surface termination influenced the band bending, with the Si 2p_3/2 binding energy affected more by the surface chemistry than by the dopant type. The highest binding energies were measured on Si(111)-Br (whose Fermi level was positioned near the conduction band at the surface), followed by Si(111)-H, followed by Si(111)-CH₃ (whose Fermi level was positioned near mid-gap at the surface). Si(111)-CH₃ surfaces exposed to Br₂(g) yielded the lowest binding energies, with the Fermi level positioned between mid-gap and the valence band. The Fermi level position of Br₂(g)-exposed Si(111)-CH₃ was consistent with the presence of negatively charged bromine-containing ions on such surfaces. The binding energies of all of the species detected on the surface (C, O, Br) shifted with the band bending, illustrating the importance of isolating the effects of band bending when measuring chemical shifts on semiconductor surfaces. The influence of band bending was confirmed by surface photovoltage (SPV) measurements, which showed that the core levels shifted toward their flat-band values upon illumination. Where applicable, the contribution from the X-ray source to the SPV was isolated and quantified. Work functions were measured by ultraviolet photoelectron spectroscopy (UPS), allowing for calculation of the sign and magnitude of the surface dipole in such systems. The values of the surface dipoles were in good agreement with previous measurements as well as with electronegativity considerations. The binding energies of the adventitious carbon signals were affected by band bending as well as by the surface dipole. A model of band bending in which charged surface states are located exterior to the surface dipole is consistent with the XPS and UPS behavior of the chemically functionalized Si(111) surfaces investigated herein.

Complex behavior and perception in Drosophila emerges from iterative feedback-regulated reflexes

For a hungry fruit fly, locating and landing on a fermenting fruit where it can feed, find mates, and lay eggs, is an essential and difficult task requiring the integration of both olfactory and visual cues. Understanding how flies accomplish this will help provide a comprehensive ethological context for the expanding knowledge of their neural circuits involved in processing olfaction and vision, as well as inspire novel engineering solutions for control and estimation in computationally limited robotic applications. In this thesis, I use novel high throughput methods to develop a detailed overview of how flies track odor plumes, land, and regulate flight speed. Finally, I provide an example of how these insights can be applied to robotic applications to simplify complicated estimation problems. To localize an odor source, flies exhibit three iterative, reflex-driven behaviors. Upon encountering an attractive plume, flies increase their flight speed and turn upwind using visual cues. After losing the plume, flies begin zigzagging crosswind, again using visual cues to control their heading. After sensing an attractive odor, flies become more attracted to small visual features, which increases their chances of finding the plume source. Their changes in heading are largely controlled by open-loop maneuvers called saccades, which they direct towards and away from visual features. If a fly decides to land on an object, it begins to decelerate so as to maintain a stereotypical ratio of expansion to retinal size. Once they reach a stereotypical distance from the target, flies extend their legs in preparation for touchdown. Although it is unclear what cues they use to trigger this behavior, previous studies have indicated that it is likely under visual control. In Chapter 3, I use a nonlinear control theoretic analysis and robotic testbed to propose a novel and putative mechanism for how a fly might visually estimate distance by actively decelerating according to a visual control law. Throughout these behaviors, a common theme is the visual control of flight speed. Using genetic tools I show that the neuromodulator octopamine plays an important role in regulating flight speed, and propose a neural circuit for how this controller might be implemented in the flies brain. Two general biological and engineering principles are evident across my experiments: (1) complex behaviors, such as foraging, can emerge from the interactions of simple independent sensory-motor modules; (2) flies control their behavior in such a way that simplifies complex estimation problems.

Techniques for strength measurement at high pressures and strain-rates using transverse waves

The study of the strength of a material is relevant to a variety of applications including automobile collisions, armor penetration and inertial confinement fusion. Although dynamic behavior of materials at high pressures and strain-rates has been studied extensively using plate impact experiments, the results provide measurements in one direction only. Material behavior that is dependent on strength is unaccounted for. The research in this study proposes two novel configurations to mitigate this problem.

The first configuration introduced is the oblique wedge experiment, which is comprised of a driver material, an angled target of interest and a backing material used to measure in-situ velocities. Upon impact, a shock wave is generated in the driver material. As the shock encounters the angled target, it is reflected back into the driver and transmitted into the target. Due to the angle of obliquity of the incident wave, a transverse wave is generated that allows the target to be subjected to shear while being compressed by the initial longitudinal shock such that the material does not slip. Using numerical simulations, this study shows that a variety of oblique wedge configurations can be used to study the shear response of materials and this can be extended to strength measurement as well. Experiments were performed on an oblique wedge setup with a copper impactor, polymethylmethacrylate driver, aluminum 6061-t6 target, and a lithium fluoride window. Particle velocities were measured using laser interferometry and results agree well with the simulations.

The second novel configuration is the y-cut quartz sandwich design, which uses the anisotropic properties of y-cut quartz to generate a shear wave that is transmitted into a thin sample. By using an anvil material to back the thin sample, particle velocities measured at the rear surface of the backing plate can be implemented to calculate the shear stress in the material and subsequently the strength. Numerical simulations were conducted to show that this configuration has the ability to measure the strength for a variety of materials.

Measurement of the neutron beta decay asymmetry using ultracold neutrons

The free neutron beta decay correlation A₀ between neutron polarization and electron emission direction provides the strongest constraint on the ratio λ = g_A/g_V of the Axial-vector to Vector coupling constants in Weak decay. In conjunction with the CKM Matrix element V_ud and the neutron lifetime τ_n, λ provides a test of Standard Model assumptions for the Weak interaction. Leading high-precision measurements of A₀ and τ_n in the 1995-2005 time period showed discrepancies with prior measurements and Standard Model predictions for the relationship between λ, τ_n, and V_ud. The UCNA experiment was developed to measure A₀ from decay of polarized ultracold neutrons (UCN), providing a complementary determination of λ with different systematic uncertainties from prior cold neutron beam experiments. This dissertation describes analysis of the dataset collected by UCNA in 2010, with emphasis on detector response calibrations and systematics. The UCNA measurement is placed in the context of the most recent τ_n results and cold neutron A₀ experiments.

Measurement of the neutron (^3He) spin structure function at low Q^2 : a connection between the Bjorken and Drell-Hearn-Gerasimov sum rules

The spin dependent cross sections, σT_1/2 and σT_3/2 , and asymmetries, A_∥ and A_⊥ for ³He have been measured at the Jefferson Lab's Hall A facility. The inclusive scattering process ³He(e,e)X was performed for initial beam energies ranging from 0.86 to 5.1 GeV, at a scattering angle of 15.5°. Data includes measurements from the quasielastic peak, resonance region, and the deep inelastic regime. An approximation for the extended Gerasimov-Drell-Hearn integral is presented at a 4-momentum transfer Q² of 0.2-1.0 GeV².

Also presented are results on the performance of the polarized ³He target. Polarization of ³He was achieved by the process of spin-exchange collisions with optically pumped rubidium vapor. The ³He polarization was monitored using the NMR technique of adiabatic fast passage (AFP). The average target polarization was approximately 35% and was determined to have a systematic uncertainty of roughly ±4% relative.

Magnetic trapping of atomic tritium for neutrino mass measurement

Improved measurement of the neutrino mass via β decay spectroscopy requires the development of new energy measurement techniques and a new β decay source. A promising proposal is to measure the β energy by the frequency of the cyclotron radiation emitted in a magnetic field and to use a high purity atomic tritium source. This thesis examines the feasibility of using a magnetic trap to create and maintain such a source. We demonstrate that the loss rate due to β decay heating is not a limiting factor for the design. We also calculate the loss rate due to evaporative cooling and propose that the tritium can be cooled sufficiently during trap loading as to render this negligible. We further demonstrate a design for the magnetic field which produces a highly uniform field over a large fraction of the trap volume as needed for cyclotron frequency spectroscopy while still providing effective trapping.

Macroscopically Dissipative Systems with Underlying Microscopic Dynamics : Properties and Limits of Measurement

While some of the deepest results in nature are those that give explicit bounds between important physical quantities, some of the most intriguing and celebrated of such bounds come from fields where there is still a great deal of disagreement and confusion regarding even the most fundamental aspects of the theories. For example, in quantum mechanics, there is still no complete consensus as to whether the limitations associated with Heisenberg's Uncertainty Principle derive from an inherent randomness in physics, or rather from limitations in the measurement process itself, resulting from phenomena like back action. Likewise, the second law of thermodynamics makes a statement regarding the increase in entropy of closed systems, yet the theory itself has neither a universally-accepted definition of equilibrium, nor an adequate explanation of how a system with underlying microscopically Hamiltonian dynamics (reversible) settles into a fixed distribution.

Motivated by these physical theories, and perhaps their inconsistencies, in this thesis we use dynamical systems theory to investigate how the very simplest of systems, even with no physical constraints, are characterized by bounds that give limits to the ability to make measurements on them. Using an existing interpretation, we start by examining how dissipative systems can be viewed as high-dimensional lossless systems, and how taking this view necessarily implies the existence of a noise process that results from the uncertainty in the initial system state. This fluctuation-dissipation result plays a central role in a measurement model that we examine, in particular describing how noise is inevitably injected into a system during a measurement, noise that can be viewed as originating either from the randomness of the many degrees of freedom of the measurement device, or of the environment. This noise constitutes one component of measurement back action, and ultimately imposes limits on measurement uncertainty. Depending on the assumptions we make about active devices, and their limitations, this back action can be offset to varying degrees via control. It turns out that using active devices to reduce measurement back action leads to estimation problems that have non-zero uncertainty lower bounds, the most interesting of which arise when the observed system is lossless. One such lower bound, a main contribution of this work, can be viewed as a classical version of a Heisenberg uncertainty relation between the system's position and momentum. We finally also revisit the murky question of how macroscopic dissipation appears from lossless dynamics, and propose alternative approaches for framing the question using existing systematic methods of model reduction.

Measurement of the galactic cosmic ray antiproton flux from 0.25 gev to 3.11 gev with the isotope matter antimatter experiment (imax)

The intensities and relative abundances of galactic cosmic ray protons and antiprotons have been measured with the Isotope Matter Antimatter Experiment (IMAX), a balloon-borne magnet spectrometer. The IMAX payload had a successful flight from Lynn Lake, Manitoba, Canada on July 16, 1992. Particles detected by IMAX were identified by mass and charge via the Cherenkov-Rigidity and TOP-Rigidity techniques, with measured rms mass resolution ≤0.2 amu for Z=1 particles.

Cosmic ray antiprotons are of interest because they can be produced by the interactions of high energy protons and heavier nuclei with the interstellar medium as well as by more exotic sources. Previous cosmic ray antiproton experiments have reported an excess of antiprotons over that expected solely from cosmic ray interactions.

Analysis of the flight data has yielded 124405 protons and 3 antiprotons in the energy range 0.19-0.97 GeV at the instrument, 140617 protons and 8 antiprotons in the energy range 0.97-2.58 GeV, and 22524 protons and 5 antiprotons in the energy range 2.58-3.08 GeV. These measurements are a statistical improvement over previous antiproton measurements, and they demonstrate improved separation of antiprotons from the more abundant fluxes of protons, electrons, and other cosmic ray species.

When these results are corrected for instrumental and atmospheric background and losses, the ratios at the top of the atmosphere are p/p=3.21(+3.49, -1.97)x10^(-5) in the energy range 0.25-1.00 GeV, p/p=5.38(+3.48, -2.45) x10^(-5) in the energy range 1.00-2.61 GeV, and p/p=2.05(+1.79, -1.15) x10^(-4) in the energy range 2.61-3.11 GeV. The corresponding antiproton intensities, also corrected to the top of the atmosphere, are 2.3(+2.5, -1.4) x10^(-2) (m^2 s sr GeV)^(-1), 2.1(+1.4, -1.0) x10^(-2) (m^2 s sr GeV)^(-1), and 4.3(+3.7, -2.4) x10^(-2) (m^2 s sr GeV)^(-1) for the same energy ranges.

The IMAX antiproton fluxes and antiproton/proton ratios are compared with recent Standard Leaky Box Model (SLBM) calculations of the cosmic ray antiproton abundance. According to this model, cosmic ray antiprotons are secondary cosmic rays arising solely from the interaction of high energy cosmic rays with the interstellar medium. The effects of solar modulation of protons and antiprotons are also calculated, showing that the antiproton/proton ratio can vary by as much as an order of magnitude over the solar cycle. When solar modulation is taken into account, the IMAX antiproton measurements are found to be consistent with the most recent calculations of the SLBM. No evidence is found in the IMAX data for excess antiprotons arising from the decay of galactic dark matter, which had been suggested as an interpretation of earlier measurements. Furthermore, the consistency of the current results with the SLBM calculations suggests that the mean antiproton lifetime is at least as large as the cosmic ray storage time in the galaxy (~10^7 yr, based on measurements of cosmic ray ^(10)Be). Recent measurements by two other experiments are consistent with this interpretation of the IMAX antiproton results.

An investigation of techniques for the measurement and interpretation of cosmic ray isotopic abundances

An instrument, the Caltech High Energy Isotope Spectrometer Telescope (HEIST), has been developed to measure isotopic abundances of cosmic ray nuclei in the charge range 3 ≤ Z ≤ 28 and the energy range between 30 and 800 MeV/nuc by employing an energy loss -- residual energy technique. Measurements of particle trajectories and energy losses are made using a multiwire proportional counter hodoscope and a stack of CsI(TI) crystal scintillators, respectively. A detailed analysis has been made of the mass resolution capabilities of this instrument.

Landau fluctuations set a fundamental limit on the attainable mass resolution, which for this instrument ranges between ~.07 AMU for z~3 and ~.2 AMU for z~2b. Contributions to the mass resolution due to uncertainties in measuring the path-length and energy losses of the detected particles are shown to degrade the overall mass resolution to between ~.1 AMU (z~3) and ~.3 AMU (z~2b).

A formalism, based on the leaky box model of cosmic ray propagation, is developed for obtaining isotopic abundance ratios at the cosmic ray sources from abundances measured in local interstellar space for elements having three or more stable isotopes, one of which is believed to be absent at the cosmic ray sources. This purely secondary isotope is used as a tracer of secondary production during propagation. This technique is illustrated for the isotopes of the elements O, Ne, S, Ar and Ca.

The uncertainties in the derived source ratios due to errors in fragmentation and total inelastic cross sections, in observed spectral shapes, and in measured abundances are evaluated. It is shown that the dominant sources of uncertainty are uncorrelated errors in the fragmentation cross sections and statistical uncertainties in measuring local interstellar abundances.

These results are applied to estimate the extent to which uncertainties must be reduced in order to distinguish between cosmic ray production in a solar-like environment and in various environments with greater neutron enrichments.

A balloon measurement of the isotopic composition of galactic cosmic ray boron, carbon, and nitrogen

The isotopic compositions of galactic cosmic ray boron, carbon, and nitrogen have been measured at energies near 300 MeV amu^-1, using a balloon-borne instrument at an atmospheric depth of ~5 g cm^-2. The calibrations of the detectors comprising the instrument are described. The saturation properties of the cesium iodide scintilla tors used for measurement of particle energy are studied in the context of analyzing the data for mass. The achieved rms mass resolution varies from ~ 0.3 amu at boron to ~ 0.5 amu at nitrogen, consistent with a theoretical analysis of the contributing factors. Corrected for detector interactions and the effects of the residual atmosphere, the results are ^(10)B/B = 0.33^(+0.17)_(-0.11), ^(13)C/C = 0.06^(+0.13)_(-0.01), and ^(15)N/N = 0.42 (+0.19)_(-0.17). A model of galactic propagation and solar modulation is described. Assuming a cosmic ray source composition of solar-like isotopic abundances, the model predicts abundances near earth consistent with the measurements.

A measurement of B0-B0 mixing in e+e- annihilation at 29 GeV

This thesis describes a measurement of B⁰- B⁰ mixing in events produced by electron-positron annihilation at a center of mass energy of 29 GeV. The data were taken by the Mark II detector in the PEP storage ring at the Stanford Linear Accelerator Center between 1981 and 1987, and correspond to a total integrated luminosity of 224pb^-1.

We used a new method, based on the kinematics of hadronic events containing two leptons, to provide a measurement of the probability, x, that a hadron, initially containing a b (b) quark decays to a positive (negative) lepton to be X = 0.17^+0.15_-0.08, with 90% confidence level upper and lower limits of 0.38 and 0.06, respectively, including all estimated systematic errors. Because of the good separation of signal and background, this result is relatively insensitive to various systematic effects which have complicated previous measurements.

We interpret this result as evidence for the mixing of neutral B mesons. Based on existing B⁰_d mixing rate measurements, and some assumptions about the fractions of B⁰_d and B⁰_s mesons present in the data, this result favors maximal mixing of B⁰_s mesons, although it cannot rule out zero B⁰_s mixing at the 90% confidence level.