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.

Did galaxies reionize the universe?

The epoch of reionization remains one of the last uncharted eras of cosmic history, yet this time is of crucial importance, encompassing the formation of both the first galaxies and the first metals in the universe. In this thesis, I present four related projects that both characterize the abundance and properties of these first galaxies and uses follow-up observations of these galaxies to achieve one of the first observations of the neutral fraction of the intergalactic medium during the heart of the reionization era.

First, we present the results of a spectroscopic survey using the Keck telescopes targeting 6.3 < z < 8.8 star-forming galaxies. We secured observations of 19 candidates, initially selected by applying the Lyman break technique to infrared imaging data from the Wide Field Camera 3 (WFC3) onboard the Hubble Space Telescope (HST). This survey builds upon earlier work from Stark et al. (2010, 2011), which showed that star-forming galaxies at 3 < z < 6, when the universe was highly ionized, displayed a significant increase in strong Lyman alpha emission with redshift. Our work uses the LRIS and NIRSPEC instruments to search for Lyman alpha emission in candidates at a greater redshift in the observed near-infrared, in order to discern if this evolution continues, or is quenched by an increase in the neutral fraction of the intergalactic medium. Our spectroscopic observations typically reach a 5-sigma limiting sensitivity of < 50 AA. Despite expecting to detect Lyman alpha at 5-sigma in 7-8 galaxies based on our Monte Carlo simulations, we only achieve secure detections in two of 19 sources. Combining these results with a similar sample of 7 galaxies from Fontana et al. (2010), we determine that these few detections would only occur in < 1% of simulations if the intrinsic distribution was the same as that at z ~ 6. We consider other explanations for this decline, but find the most convincing explanation to be an increase in the neutral fraction of the intergalactic medium. Using theoretical models, we infer a neutral fraction of X_HI ~ 0.44 at z = 7.

Second, we characterize the abundance of star-forming galaxies at z > 6.5 again using WFC3 onboard the HST. This project conducted a detailed search for candidates both in the Hubble Ultra Deep Field as well as a number of additional wider Hubble Space Telescope surveys to construct luminosity functions at both z ~ 7 and 8, reaching 0.65 and 0.25 mag fainter than any previous surveys, respectively. With this increased depth, we achieve some of the most robust constraints on the Schechter function faint end slopes at these redshifts, finding very steep values of alpha_{z~7} = -1.87 +/- 0.18 and alpha_{z~8} = -1.94 +/- 0.23. We discuss these results in the context of cosmic reionization, and show that given reasonable assumptions about the ionizing spectra and escape fraction of ionizing photons, only half the photons needed to maintain reionization are provided by currently observable galaxies at z ~ 7-8. We show that an extension of the luminosity function down to M_{UV} = -13.0, coupled with a low level of star-formation out to higher redshift, can fit all available constraints on the ionization history of the universe.

Third, we investigate the strength of nebular emission in 3 < z < 5 star-forming galaxies. We begin by using the Infrared Array Camera (IRAC) onboard the Spitzer Space Telescope to investigate the strength of H alpha emission in a sample of 3.8 < z < 5.0 spectroscopically confirmed galaxies. We then conduct near-infrared observations of star-forming galaxies at 3 < z < 3.8 to investigate the strength of the [OIII] 4959/5007 and H beta emission lines from the ground using MOSFIRE. In both cases, we uncover near-ubiquitous strong nebular emission, and find excellent agreement between the fluxes derived using the separate methods. For a subset of 9 objects in our MOSFIRE sample that have secure Spitzer IRAC detections, we compare the emission line flux derived from the excess in the K_s band photometry to that derived from direct spectroscopy and find 7 to agree within a factor of 1.6, with only one catastrophic outlier. Finally, for a different subset for which we also have DEIMOS rest-UV spectroscopy, we compare the relative velocities of Lyman alpha and the rest-optical nebular lines which should trace the cites of star-formation. We find a median velocity offset of only v_{Ly alpha} = 149 km/s, significantly less than the 400 km/s observed for star-forming galaxies with weaker Lyman alpha emission at z = 2-3 (Steidel et al. 2010), and show that this decrease can be explained by a decrease in the neutral hydrogen column density covering the galaxy. We discuss how this will imply a lower neutral fraction for a given observed extinction of Lyman alpha when its visibility is used to probe the ionization state of the intergalactic medium.

Finally, we utilize the recent CANDELS wide-field, infra-red photometry over the GOODS-N and S fields to re-analyze the use of Lyman alpha emission to evaluate the neutrality of the intergalactic medium. With this new data, we derive accurate ultraviolet spectral slopes for a sample of 468 3 < z < 6 star-forming galaxies, already observed in the rest-UV with the Keck spectroscopic survey (Stark et al. 2010). We use a Bayesian fitting method which accurately accounts for contamination and obscuration by skylines to derive a relationship between the UV-slope of a galaxy and its intrinsic Lyman alpha equivalent width probability distribution. We then apply this data to spectroscopic surveys during the reionization era, including our own, to accurately interpret the drop in observed Lyman alpha emission. From our most recent such MOSFIRE survey, we also present evidence for the most distant galaxy confirmed through emission line spectroscopy at z = 7.62, as well as a first detection of the CIII]1907/1909 doublet at z > 7.

We conclude the thesis by exploring future prospects and summarizing the results of Robertson et al. (2013). This work synthesizes many of the measurements in this thesis, along with external constraints, to create a model of reionization that fits nearly all available constraints.

Nuclear structure effects in internal conversion

Experimental studies of nuclear effects in internal conversion in Ta¹⁸¹ and Lu¹⁷⁵ have been performed. Nuclear structure effects (“penetration” effects), in internal conversion are described in general. Calculation of theoretical conversion coefficients are outlined. Comparisons with the theoretical conversion coefficient tables of Rose and Sliv and Band are made. Discrepancies between our results and those of Rose and Sliv are noted. The theoretical conversion coefficients of Sliv and Band are in substantially better agreement with our results than are those of Rose. The ratio of the M1 penetration matrix element to the M1 gamma-ray matrix element, called λ, is equal to + 175 ± 25 for the 482 keV transition in Ta¹⁸¹ . The results for the 343 keV transition in Lu¹⁷⁵ indicate that λ may be as large as – 8 ± 5. These transitions are discussed in terms of the unified collective model. Precision L subshell measurements in Tm¹⁶⁹ (130keV), W¹⁸² (100 keV), and Ta¹⁸¹ (133 keV) show definite systematic deviations from the theoretical conversion coefficients. The possibility of explaining these deviations by penetration effects is investigated and is shown to be excluded. Other explanations of these anomalies are discussed.

Sputtering of insulators in the electronic stopping region

Using track detectors we have measured sputtering yields induced by MeV light ions incident on a uranium containing glass, UO₂ and UF₄. No deviation from the behavior predicted by the Sigmund theory was detected in the glass or the UO₂. The same was true for UF₄ bombarded with ⁴He at 1 MeV and with ¹⁶O and ²⁰Ne at 100 keV. In contrast to this, 4.75 MeV ¹⁹F(+2) sputters uranium from UF₄ with a yield of 5.6 ± 1.0, which is about 3 orders of magnitude larger than expected from the Sigmund theory. The energy dependence of the yield indicates that it is generated by electronic rather than nuclear stopping processes. The yield depends on the charge state of the incident fluorine but not on the target temperature. We have also measured the energy spectrum of the uranium sputtered from the UF₄. Ion explosions, thermal spikes, chemical rearrangement and induced desorption are considered as possible explanations for the anomalous yields.

Solar flare particle propagation--comparison of a new analytic solution with spacecraft measurements

A new analytic solution has been obtained to the complete Fokker-Planck equation for solar flare particle propagation including the effects of convection, energy-change, corotation, and diffusion with ĸ_r = constant and ĸ_Ɵ ∝ r². It is assumed that the particles are injected impulsively at a single point in space, and that a boundary exists beyond which the particles are free to escape. Several solar flare particle events have been observed with the Caltech Solar and Galactic Cosmic Ray Experiment aboard OGO-6. Detailed comparisons of the predictions of the new solution with these observations of 1-70 MeV protons show that the model adequately describes both the rise and decay times, indicating that ĸ_r = constant is a better description of conditions inside 1 AU than is ĸ_r ∝ r. With an outer boundary at 2.7 AU, a solar wind velocity of 400 km/sec, and a radial diffusion coefficient ĸ_r ≈ 2-8 x 10²⁰ cm²/sec, the model gives reasonable fits to the time-profile of 1-10 MeV protons from "classical" flare-associated events. It is not necessary to invoke a scatter-free region near the sun in order to reproduce the fast rise times observed for directly-connected events. The new solution also yields a time-evolution for the vector anisotropy which agrees well with previously reported observations.

In addition, the new solution predicts that, during the decay phase, a typical convex spectral feature initially at energy T_o will move to lower energies at an exponential rate given by T_KINK = T_oexp(-t/Ƭ_KINK). Assuming adiabatic deceleration and a boundary at 2.7 AU, the solution yields Ƭ_KINK ≈ 100h, which is faster than the measured ~200h time constant and slower than the adiabatic rate of ~78h at 1 AU. Two possible explanations are that the boundary is at ~5 AU or that some other energy-change process is operative.