Studies of ambient and chamber aerosol composition using the aerosol mass spectrometer

This thesis presents composition measurements for atmospherically relevant inorganic and organic aerosol from laboratory and ambient measurements using the Aerodyne aerosol mass spectrometer. Studies include the oxidation of dodecane in the Caltech environmental chambers, and several aircraft- and ground-based field studies, which include the quantification of wildfire emissions off the coast of California, and Los Angeles urban emissions.

The oxidation of dodecane by OH under low NO conditions and the formation of secondary organic aerosol (SOA) was explored using a gas-phase chemical model, gas-phase CIMS measurements, and high molecular weight ion traces from particle- phase HR-TOF-AMS mass spectra. The combination of these measurements support the hypothesis that particle-phase chemistry leading to peroxyhemiacetal formation is important. Positive matrix factorization (PMF) was applied to the AMS mass spectra which revealed three factors representing a combination of gas-particle partitioning, chemical conversion in the aerosol, and wall deposition.

Airborne measurements of biomass burning emissions from a chaparral fire on the central Californian coast were carried out in November 2009. Physical and chemical changes were reported for smoke ages 0 – 4 h old. CO₂ normalized ammonium, nitrate, and sulfate increased, whereas the normalized OA decreased sharply in the first 1.5 - 2 h, and then slowly increased for the remaining 2 h (net decrease in normalized OA). Comparison to wildfire samples from the Yucatan revealed that factors such as relative humidity, incident UV radiation, age of smoke, and concentration of emissions are important for wildfire evolution.

Ground-based aerosol composition is reported for Pasadena, CA during the summer of 2009. The OA component, which dominated the submicron aerosol mass, was deconvolved into hydrocarbon-like organic aerosol (HOA), semi-volatile oxidized organic aerosol (SVOOA), and low-volatility oxidized organic aerosol (LVOOA). The HOA/OA was only 0.08–0.23, indicating that most of Pasadena OA in the summer months is dominated by oxidized OA resulting from transported emissions that have undergone photochemistry and/or moisture-influenced processing, as apposed to only primary organic aerosol emissions. Airborne measurements and model predictions of aerosol composition are reported for the 2010 CalNex field campaign.

Deep tissue fluorescence imaging with time-reversed light

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

Tissue engineering active biological machines : bio-inspired design, directed self-assembly, and characterization of muscular pumps simulating the embryonic heart

Biological machines are active devices that are comprised of cells and other biological components. These functional devices are best suited for physiological environments that support cellular function and survival. Biological machines have the potential to revolutionize the engineering of biomedical devices intended for implantation, where the human body can provide the required physiological environment. For engineering such cell-based machines, bio-inspired design can serve as a guiding platform as it provides functionally proven designs that are attainable by living cells. In the present work, a systematic approach was used to tissue engineer one such machine by exclusively using biological building blocks and by employing a bio-inspired design. Valveless impedance pumps were constructed based on the working principles of the embryonic vertebrate heart and by using cells and tissue derived from rats. The function of these tissue-engineered muscular pumps was characterized by exploring their spatiotemporal and flow behavior in order to better understand the capabilities and limitations of cells when used as the engines of biological machines.

Influence of composition on the structure and properties of Fe-Pd-P and Ni-Pd-P amorphous alloys

Ternary alloys of nickel-palladium-phosphorus and iron-palladium- phosphorus containing 20 atomic % phosphorus were rapidly quenched from the liquid state. The structure of the quenched alloys was investigated by X-ray diffraction. Broad maxima in the diffraction patterns, indicative of a glass-like structure, were obtained for 13 to 73 atomic % nickel and 13 to 44 atomic % iron, with palladium adding up to 80%.

Radial distribution functions were computed from the diffraction data and yielded average interatomic distances and coordination numbers. The structure of the amorphous alloys could be explained in terms of structural units analogous to those existing in the crystalline Pd₃P, Ni₃P and Fe₃P phases, with iron or nickel substituting for palladium. A linear relationship between interatomic distances and composition, similar to Vegard's law, was shown for these metallic glasses.

Electrical resistivity measurements showed that the quenched alloys were metallic. Measurements were performed from liquid helium temperatures (4.2°K) up to the vicinity of the melting points (900°K- 1000°K). The temperature coefficient in the glassy state was very low, of the order of 10^-4/°K. A resistivity minimum was found at low temperature, varying between 9°K and 14°K for Ni_x-Pd_80-x -P₂₀ and between 17°K and 96°K for Fe_x-Pd_80-x -P₂₀, indicating the presence of a Kondo effect. Resistivity measurements, with a constant heating rate of about 1.5°C/min,showed progressive crystallization above approximately 600°K.

The magnetic moments of the amorphous Fe-Pd-P alloys were measured as a function of magnetic field and temperature. True ferromagnetism was found for the alloys Fe₃₂-Pd₄₈-P₂₀ and Fe₄₄-Pd₃₆-P₂₀ with Curie points at 165° K and 380° K respectively. Extrapolated values of the saturation magnetic moments to 0° K were 1.70 µ_B and 2.10 µ_B respectively. The amorphous alloy Fe₂₃-Pd₅₇-P₂₀ was assumed to be superparamagnetic. The experimental data indicate that phosphorus contributes to the decrease of moments by electron transfer, whereas palladium atoms probably have a small magnetic moment. A preliminary investigation of the Ni-Pd-P amorphous alloys showed that these alloys are weakly paramagnetic.

Designing conformational control of human tissue transglutaminase

Understanding the mechanisms of enzymes is crucial for our understanding of their role in biology and for designing methods to perturb or harness their activities for medical treatments, industrial processes, or biological engineering. One aspect of enzymes that makes them difficult to fully understand is that they are in constant motion, and these motions and the conformations adopted throughout these transitions often play a role in their function.

Traditionally, it has been difficult to isolate a protein in a particular conformation to determine what role each form plays in the reaction or biology of that enzyme. A new technology, computational protein design, makes the isolation of various conformations possible, and therefore is an extremely powerful tool in enabling a fuller understanding of the role a protein conformation plays in various biological processes.

One such protein that undergoes large structural shifts during different activities is human type II transglutaminase (TG2). TG2 is an enzyme that exists in two dramatically different conformational states: (1) an open, extended form, which is adopted upon the binding of calcium, and (2) a closed, compact form, which is adopted upon the binding of GTP or GDP. TG2 possess two separate active sites, each with a radically different activity. This open, calcium-bound form of TG2 is believed to act as a transglutaminse, where it catalyzes the formation of an isopeptide bond between the sidechain of a peptide-bound glutamine and a primary amine. The closed, GTP-bound conformation is believed to act as a GTPase. TG2 is also implicated in a variety of biological and pathological processes.

To better understand the effects of TG2’s conformations on its activities and pathological processes, we set out to design variants of TG2 isolated in either the closed or open conformations. We were able to design open-locked and closed-biased TG2 variants, and use these designs to unseat the current understanding of the activities and their concurrent conformations of TG2 and explore each conformation’s role in celiac disease models. This work also enabled us to help explain older confusing results in regards to this enzyme and its activities. The new model for TG2 activity has immense implications for our understanding of its functional capabilities in various environments, and for our ability to understand which conformations need to be inhibited in the design of new drugs for diseases in which TG2’s activities are believed to elicit pathological effects.

Influence of composition on the structure, electric and magnetic properties of Pd-Mn-P and Pd-Co-P amorphous alloys

The influence of composition on the structure and on the electric and magnetic properties of amorphous Pd-Mn-P and Pd-Co-P prepared by rapid quenching techniques were investigated in terms of (1) the 3d band filling of the first transition metal group, (2) the phosphorus concentration effect which acts as an electron donor and (3) the transition metal concentration.

The structure is essentially characterized by a set of polyhedra subunits essentially inverse to the packing of hard spheres in real space. Examination of computer generated distribution functions using Monte Carlo random statistical distribution of these polyhedra entities demonstrated tile reproducibility of the experimentally calculated atomic distribution function. As a result, several possible "structural parameters" are proposed such as: the number of nearest neighbors, the metal-to-metal distance, the degree of short-range order and the affinity between metal-metal and metal-metalloid. It is shown that the degree of disorder increases from Ni to Mn. Similar behavior is observed with increase in the phosphorus concentration.

The magnetic properties of Pd-Co-P alloys show that they are ferromagnetic with a Curie temperature between 272 and 399°K as the cobalt concentration increases from 15 to 50 at.%. Below 20 at.% Co the short-range exchange interactions which produce the ferromagnetism are unable to establish a long-range magnetic order and a peak in the magnetization shows up at the lowest temperature range . The electric resistivity measurements were performed from liquid helium temperatures up to the vicinity of the melting point (900°K). The thermomagnetic analysis was carried out under an applied field of 6.0 kOe. The electrical resistivity of Pd-Co-P shows the coexistence of a Kondo-like minimum with ferromagnetism. The minimum becomes less important as the transition metal concentration increases and the coefficients of ℓn T and T^2 become smaller and strongly temperature dependent. The negative magnetoresistivity is a strong indication of the existence of localized moment.

The temperature coefficient of resistivity which is positive for Pd- Fe-P, Pd-Ni-P, and Pd-Co-P becomes negative for Pd-Mn-P. It is possible to account for the negative temperature dependence by the localized spin fluctuation model and the high density of states at the Fermi energy which becomes maximum between Mn and Cr. The magnetization curves for Pd-Mn-P are typical of those resulting from the interplay of different exchange forces. The established relationship between susceptibility and resistivity confirms the localized spin fluctuation model. The magnetoresistivity of Pd-Mn-P could be interpreted in tenns of a short-range magnetic ordering that could arise from the Rudennan-Kittel type interactions.

Elemental composition of solar energetic particles

The Low Energy Telescopes on the Voyager spacecraft are used to measure the elemental composition (2 ≤ Z ≤ 28) and energy spectra (5 to 15 MeV /nucleon) of solar energetic particles (SEPs) in seven large flare events. Four flare events are selected which have SEP abundance ratios approximately independent of energy/nucleon. The abundances for these events are compared from flare to flare and are compared to solar abundances from other sources: spectroscopy of the photosphere and corona, and solar wind measurements.

The selected SEP composition results may be described by an average composition plus a systematic flare-to-flare deviation about the average. For each of the four events, the ratios of the SEP abundances to the four-flare average SEP abundances are approximately monotonic functions of nuclear charge Z in the range 6 ≤ Z ≤ 28. An exception to this Z-dependent trend occurs for He, whose abundance relative to Si is nearly the same in all four events.

The four-flare average SEP composition is significantly different from the solar composition determined by photospheric spectroscopy: The elements C, N and O are depleted in SEPs by a factor of about five relative to the elements Na, Mg, Al, Si, Ca, Cr, Fe and Ni. For some elemental abundance ratios (e.g. Mg/O), the difference between SEP and photospheric results is persistent from flare to flare and is apparently not due to a systematic difference in SEP energy/nucleon spectra between the elements, nor to propagation effects which would result in a time-dependent abundance ratio in individual flare events.

The four-flare average SEP composition is in agreement with solar wind abundance results and with a number of recent coronal abundance measurements. The evidence for a common depletion of oxygen in SEPs, the corona and the solar wind relative to the photosphere suggests that the SEPs originate in the corona and that both the SEPs and solar wind sample a coronal composition which is significantly and persistently different from that of the photosphere.

The isotopic composition of energetic particles emitted from a large solar flare

We report measurements of isotope abundance ratios for 5-50 MeV/nuc nuclei from a large solar flare that occurred on September 23, 1978. The measurements were made by the Heavy Isotope Spectrometer Telescope (HIST) on the ISEE-3 satellite orbiting the Sun near an Earth-Sun libration point approximately one million miles sunward of the Earth. We report finite values for the isotope abundance ratios ¹³C/¹²C, ¹⁵N/¹⁴N, ¹⁸O/¹⁶O, ²²Ne/ ²⁰Ne, ²⁵Mg/²⁴Mg, and ²⁶Mg/²⁴Mg, and upper limits for the isotope abundance ratios ³He/⁴He, ¹⁴C/¹²C, ¹⁷O/¹⁶O, and ²¹Ne/²⁰Ne.

We measured element abundances and spectra to compare the September 23, 1978 flare with other flares reported in the literature. The flare is a typical large flare with "low" Fe/O abundance (≤ 0.1).

For ¹³C/¹²C, ¹⁵N/¹⁴N, ¹⁸O/¹⁶O, ²⁵Mg/ ²⁴Mg, and ²⁶Mg/²⁴Mg, our measured isotope abundance ratios agree with the solar system abundance ratios of Cameron (1981). For neon we measure ²²Ne/²⁰Ne = 0.109 + 0.026 - 0.019, a value that is different with confidence 97.5% from the abundance measured in the solar wind by Geiss at al. (1972) of ²²Ne/²⁰Ne = 0.073 ± 0.001. Our measurement for ²²Ne/²⁰Ne agrees with the isotopic composition of the meteoritic component neon-A.

Separate arguments appear to rule out simple mass fractionation in the solar wind and in our solar energetic particle measurements as the cause of the discrepancy in the comparison of the apparent compositions of these two sources of solar material.

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.

Secondary Organic Aerosol Composition Studies Using Mass Spectrometry

Trace volatile organic compounds emitted by biogenic and anthropogenic sources into the atmosphere can undergo extensive photooxidation to form species with lower volatility. By equilibrium partitioning or reactive uptake, these compounds can nucleate into new aerosol particles or deposit onto already-existing particles to form secondary organic aerosol (SOA). SOA and other atmospheric particulate matter have measurable effects on global climate and public health, making understanding SOA formation a needed field of scientific inquiry. SOA formation can be done in a laboratory setting, using an environmental chamber; under these controlled conditions it is possible to generate SOA from a single parent compound and study the chemical composition of the gas and particle phases. By studying the SOA composition, it is possible to gain understanding of the chemical reactions that occur in the gas phase and particle phase, and identify potential heterogeneous processes that occur at the surface of SOA particles. In this thesis, mass spectrometric methods are used to identify qualitatively and qualitatively the chemical components of SOA derived from the photooxidation of important anthropogenic volatile organic compounds that are associated with gasoline and diesel fuels and industrial activity (C12 alkanes, toluene, and o-, m-, and p-cresols). The conditions under which SOA was generated in each system were varied to explore the effect of NO_x and inorganic seed composition on SOA chemical composition. The structure of the parent alkane was varied to investigate the effect on the functionalization and fragmentation of the resulting oxidation products. Relative humidity was varied in the alkane system as well to measure the effect of increased particle-phase water on condensed-phase reactions. In all systems, oligomeric species, resulting potentially from particle-phase and heterogeneous processes, were identified. Imines produced by reactions between (NH₄)₂SO₄ seed and carbonyl compounds were identified in all systems. Multigenerational photochemistry producing low- and extremely low-volatility organic compounds (LVOC and ELVOC) was reflected strongly in the particle-phase composition as well.