Nonexistence of looping trajectories in hydromagnetic waves of finite amplitude. Breaking of waves in a cold collision-free plasma in a magnetic field. On stabilities of periodic waves in a cold collision-free plasma in a magnetic field.

This dissertation consists of three parts. In Part I, it is shown that looping trajectories cannot exist in finite amplitude stationary hydromagnetic waves propagating across a magnetic field in a quasi-neutral cold collision-free plasma. In Part II, time-dependent solutions in series expansion are presented for the magnetic piston problem, which describes waves propagating into a quasi-neutral cold collision-free plasma, ensuing from magnetic disturbances on the boundary of the plasma. The expansion is equivalent to Picard's successive approximations. It is then shown that orbit crossings of plasma particles occur on the boundary for strong disturbances and inside the plasma for weak disturbances. In Part III, the existence of periodic waves propagating at an arbitrary angle to the magnetic field in a plasma is demonstrated by Stokes expansions in amplitude. Then stability analysis is made for such periodic waves with respect to side-band frequency disturbances. It is shown that waves of slow mode are unstable whereas waves of fast mode are stable if the frequency is below the cutoff frequency. The cutoff frequency depends on the propagation angle. For longitudinal propagation the cutoff frequency is equal to one-fourth of the electron's gyrofrequency. For transverse propagation the cutoff frequency is so high that waves of all frequencies are stable.

Analysis of temporal structure in spike trains of visual cortical area MT

The temporal structure of neuronal spike trains in the visual cortex can provide detailed information about the stimulus and about the neuronal implementation of visual processing. Spike trains recorded from the macaque motion area MT in previous studies (Newsome et al., 1989a; Britten et al., 1992; Zohary et al., 1994) are analyzed here in the context of the dynamic random dot stimulus which was used to evoke them. If the stimulus is incoherent, the spike trains can be highly modulated and precisely locked in time to the stimulus. In contrast, the coherent motion stimulus creates little or no temporal modulation and allows us to study patterns in the spike train that may be intrinsic to the cortical circuitry in area MT. Long gaps in the spike train evoked by the preferred direction motion stimulus are found, and they appear to be symmetrical to bursts in the response to the anti-preferred direction of motion. A novel cross-correlation technique is used to establish that the gaps are correlated between pairs of neurons. Temporal modulation is also found in psychophysical experiments using a modified stimulus. A model is made that can account for the temporal modulation in terms of the computational theory of biological image motion processing. A frequency domain analysis of the stimulus reveals that it contains a repeated power spectrum that may account for psychophysical and electrophysiological observations.

Some neurons tend to fire bursts of action potentials while others avoid burst firing. Using numerical and analytical models of spike trains as Poisson processes with the addition of refractory periods and bursting, we are able to account for peaks in the power spectrum near 40 Hz without assuming the existence of an underlying oscillatory signal. A preliminary examination of the local field potential reveals that stimulus-locked oscillation appears briefly at the beginning of the trial.

Identifying and interpreting stratification in sedimentary rocks on Mars : insight from Rover and orbital observations and terrestrial field analogs

Sedimentary rocks on Mars provide insight into past aqueous and atmospheric processes, climate regimes, and potential habitability. The stratigraphic architecture of sedimentary rocks on Mars is similar to that of Earth, indicating that the processes that govern deposition and erosion on Mars can be reasonably inferred through reference to analogous terrestrial systems. This dissertation aims to understand Martian surface processes through the use of (1) ground-based observations from the Mars Exploration Rovers, (2) orbital data from the High Resolution Imaging Science Experiment onboard the Mars Reconnaissance Orbiter, and (3) the use of terrestrial field analogs to understand bedforms and sediment transport on Mars. Chapters 1 and 2 trace the history of aqueous activity at Meridiani Planum, through the reconstruction of eolian bedforms at Victoria crater, and the identification of a potential mudstone facies at Santa Maria crater. Chapter 3 uses Terrestrial Laser Scanning to study cross-bedding in pyroclastic surge deposits on Earth in order to understand sediment transport in these events and to establish criteria for their identification on Mars. The final chapter analyzes stratal geometries in the Martian North Polar Layered Deposits using tools for sequence stratigraphic analysis, to better constrain past surface processes and past climate conditions on Mars.

Teleseismic array analysis of upper mantle compressional velocity structure

Large quantities of teleseismic short-period seismograms recorded at SCARLET provide travel time, apparent velocity and waveform data for study of upper mantle compressional velocity structure. Relative array analysis of arrival times from distant (30° < Δ < 95°) earthquakes at all azimuths constrains lateral velocity variations beneath southern California. We compare dT/dΔ back azimuth and averaged arrival time estimates from the entire network for 154 events to the same parameters derived from small subsets of SCARLET. Patterns of mislocation vectors for over 100 overlapping subarrays delimit the spatial extent of an east-west striking, high-velocity anomaly beneath the Transverse Ranges. Thin lens analysis of the averaged arrival time differences, called 'net delay' data, requires the mean depth of the corresponding lens to be more than 100 km. Our results are consistent with the PKP-delay times of Hadley and Kanamori (1977), who first proposed the high-velocity feature, but we place the anomalous material at substantially greater depths than their 40-100 km estimate.

Detailed analysis of travel time, ray parameter and waveform data from 29 events occurring in the distance range 9° to 40° reveals the upper mantle structure beneath an oceanic ridge to depths of over 900 km. More than 1400 digital seismograms from earthquakes in Mexico and Central America yield 1753 travel times and 58 dT/dΔ measurements as well as high-quality, stable waveforms for investigation of the deep structure of the Gulf of California. The result of a travel time inversion with the tau method (Bessonova et al., 1976) is adjusted to fit the p(Δ) data, then further refined by incorporation of relative amplitude information through synthetic seismogram modeling. The application of a modified wave field continuation method (Clayton and McMechan, 1981) to the data with the final model confirms that GCA is consistent with the entire data set and also provides an estimate of the data resolution in velocity-depth space. We discover that the upper mantle under this spreading center has anomalously slow velocities to depths of 350 km, and place new constraints on the shape of the 660 km discontinuity.

Seismograms from 22 earthquakes along the northeast Pacific rim recorded in southern California form the data set for a comparative investigation of the upper mantle beneath the Cascade Ranges-Juan de Fuca region, an ocean-continent transit ion. These data consist of 853 seismograms (6° < Δ < 42°) which produce 1068 travel times and 40 ray parameter estimates. We use the spreading center model initially in synthetic seismogram modeling, and perturb GCA until the Cascade Ranges data are matched. Wave field continuation of both data sets with a common reference model confirms that real differences exist between the two suites of seismograms, implying lateral variation in the upper mantle. The ocean-continent transition model, CJF, features velocities from 200 and 350 km that are intermediate between GCA and T7 (Burdick and Helmberger, 1978), a model for the inland western United States. Models of continental shield regions (e.g., King and Calcagnile, 1976) have higher velocities in this depth range, but all four model types are similar below 400 km. This variation in rate of velocity increase with tectonic regime suggests an inverse relationship between velocity gradient and lithospheric age above 400 km depth.

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

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

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

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

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

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

Wide Field-of-view Microscopes and Endoscopes for Time-lapse Imaging and High-throughput Screening

Wide field-of-view (FOV) microscopy is of high importance to biological research and clinical diagnosis where a high-throughput screening of samples is needed. This thesis presents the development of several novel wide FOV imaging technologies and demonstrates their capabilities in longitudinal imaging of living organisms, on the scale of viral plaques to live cells and tissues.

The ePetri Dish is a wide FOV on-chip bright-field microscope. Here we applied an ePetri platform for plaque analysis of murine norovirus 1 (MNV-1). The ePetri offers the ability to dynamically track plaques at the individual cell death event level over a wide FOV of 6 mm × 4 mm at 30 min intervals. A density-based clustering algorithm is used to analyze the spatial-temporal distribution of cell death events to identify plaques at their earliest stages. We also demonstrate the capabilities of the ePetri in viral titer count and dynamically monitoring plaque formation, growth, and the influence of antiviral drugs.

We developed another wide FOV imaging technique, the Talbot microscope, for the fluorescence imaging of live cells. The Talbot microscope takes advantage of the Talbot effect and can generate a focal spot array to scan the fluorescence samples directly on-chip. It has a resolution of 1.2 μm and a FOV of ~13 mm². We further upgraded the Talbot microscope for the long-term time-lapse fluorescence imaging of live cell cultures, and analyzed the cells’ dynamic response to an anticancer drug.

We present two wide FOV endoscopes for tissue imaging, named the AnCam and the PanCam. The AnCam is based on the contact image sensor (CIS) technology, and can scan the whole anal canal within 10 seconds with a resolution of 89 μm, a maximum FOV of 100 mm × 120 mm, and a depth-of-field (DOF) of 0.65 mm. We also demonstrate the performance of the AnCam in whole anal canal imaging in both animal models and real patients. In addition to this, the PanCam is based on a smartphone platform integrated with a panoramic annular lens (PAL), and can capture a FOV of 18 mm × 120 mm in a single shot with a resolution of 100─140 μm. In this work we demonstrate the PanCam’s performance in imaging a stained tissue sample.

Development of Microfluidic Devices with the Use of Nanotechnology to Aid in the Analysis of Biological Systems Including Membrane Protein Separation, Single Cell Analysis, and Genetic Markers

Computation technology has dramatically changed the world around us; you can hardly find an area where cell phones have not saturated the market, yet there is a significant lack of breakthroughs in the development to integrate the computer with biological environments. This is largely the result of the incompatibility of the materials used in both environments; biological environments and experiments tend to need aqueous environments. To help aid in these development chemists, engineers, physicists and biologists have begun to develop microfluidics to help bridge this divide. Unfortunately, the microfluidic devices required large external support equipment to run the device. This thesis presents a series of several microfluidic methods that can help integrate engineering and biology by exploiting nanotechnology to help push the field of microfluidics back to its intended purpose, small integrated biological and electrical devices. I demonstrate this goal by developing different methods and devices to (1) separate membrane bound proteins with the use of microfluidics, (2) use optical technology to make fiber optic cables into protein sensors, (3) generate new fluidic devices using semiconductor material to manipulate single cells, and (4) develop a new genetic microfluidic based diagnostic assay that works with current PCR methodology to provide faster and cheaper results. All of these methods and systems can be used as components to build a self-contained biomedical device.

Magnetic field and pressure effects in a saturated gas laser amplifier

Theoretical and experimental studies of a gas laser amplifier are presented, assuming the amplifier is operating with a saturating optical frequency signal. The analysis is primarily concerned with the effects of the gas pressure and the presence of an axial magnetic field on the characteristics of the amplifying medium. Semiclassical radiation theory is used, along with a density matrix description of the atomic medium which relates the motion of single atoms to the macroscopic observables. A two-level description of the atom, using phenomenological source rates and decay rates, forms the basis of our analysis of the gas laser medium. Pressure effects are taken into account to a large extent through suitable choices of decay rate parameters.

Two methods for calculating the induced polarization of the atomic medium are used. The first method utilizes a perturbation expansion which is valid for signal intensities which barely reach saturation strength, and it is quite general in applicability. The second method is valid for arbitrarily strong signals, but it yields tractable solutions only for zero magnetic field or for axial magnetic fields large enough such that the Zeeman splitting is much larger than the power broadened homogeneous linewidth of the laser transition. The effects of pressure broadening of the homogeneous spectral linewidth are included in both the weak-signal and strong-signal theories; however the effects of Zeeman sublevel-mixing collisions are taken into account only in the weak-signal theory.

The behavior of a He-Ne gas laser amplifier in the presence of an axial magnetic field has been studied experimentally by measuring gain and Faraday rotation of linearly polarized resonant laser signals for various values of input signal intensity, and by measuring nonlinearity - induced anisotropy for elliptically polarized resonant laser signals of various input intensities. Two high-gain transitions in the 3.39-μ region were used for study: a J = 1 to J = 2 (3s₂ → 3p₄) transition and a J = 1 to J = 1 (3s₂ → 3p₂) transition. The input signals were tuned to the centers of their respective resonant gain lines.

The experimental results agree quite well with corresponding theoretical expressions which have been developed to include the nonlinear effects of saturation strength signals. The experimental results clearly show saturation of Faraday rotation, and for the J = 1 t o J = 1 transition a Faraday rotation reversal and a traveling wave gain dip are seen for small values of axial magnetic field. The nonlinearity induced anisotropy shows a marked dependence on the gas pressure in the amplifier tube for the J = 1 to J = 2 transition; this dependence agrees with the predictions of the general perturbational or weak signal theory when allowances are made for the effects of Zeeman sublevel-mixing collisions. The results provide a method for measuring the upper (neon 3s₂) level quadrupole moment decay rate, the dipole moment decay rates for the 3s₂ → 3p₄ and 3s₂ → 3p₂ transitions, and the effects of various types of collision processes on these decay rates.

Field and Laboratory Studies of Atmospheric Organic Aerosol

This thesis is the culmination of field and laboratory studies aimed at assessing processes that affect the composition and distribution of atmospheric organic aerosol. An emphasis is placed on measurements conducted using compact and high-resolution Aerodyne Aerosol Mass Spectrometers (AMS). The first three chapters summarize results from aircraft campaigns designed to evaluate anthropogenic and biogenic impacts on marine aerosol and clouds off the coast of California. Subsequent chapters describe laboratory studies intended to evaluate gas and particle-phase mechanisms of organic aerosol oxidation.

The 2013 Nucleation in California Experiment (NiCE) was a campaign designed to study environments impacted by nucleated and/or freshly formed aerosol particles. Terrestrial biogenic aerosol with > 85% organic mass was observed to reside in the free troposphere above marine stratocumulus. This biogenic organic aerosol (BOA) originated from the Northwestern United States and was transported to the marine atmosphere during periodic cloud-clearing events. Spectra recorded by a cloud condensation nuclei counter demonstrated that BOA is CCN active. BOA enhancements at latitudes north of San Francisco, CA coincided with enhanced cloud water concentrations of organic species such as acetate and formate.

Airborne measurements conducted during the 2011 Eastern Pacific Emitted Aerosol Cloud Experiment (E-PEACE) were aimed at evaluating the contribution of ship emissions to the properties of marine aerosol and clouds off the coast of central California. In one study, analysis of organic aerosol mass spectra during periods of enhanced shipping activity yielded unique tracers indicative of cloud-processed ship emissions (m/z 42 and 99). The variation of their organic fraction (f₄₂ and f₉₉) was found to coincide with periods of heavy (f₄₂ > 0.15; f₉₉ > 0.04), moderate (0.05 < f₄₂ < 0.15; 0.01 < f₉₉ < 0.04), and negligible (f₄₂ < 0.05; f₉₉ < 0.01) ship influence. Application of these conditions to all measurements conducted during E-PEACE demonstrated that a large fraction of cloud droplet (72%) and dry aerosol mass (12%) sampled in the California coastal study region was heavily or moderately influenced by ship emissions. Another study investigated the chemical and physical evolution of a controlled organic plume emitted from the R/V Point Sur. Under sunny conditions, nucleated particles composed of oxidized organic compounds contributed nearly an order of magnitude more cloud condensation nuclei (CCN) than less oxidized particles formed under cloudy conditions. The processing time necessary for particles to become CCN active was short ( < 1 hr) compared to the time needed for particles to become hygroscopic at sub-saturated humidity ( > 4 hr).

Laboratory chamber experiments were also conducted to evaluate particle-phase processes influencing aerosol phase and composition. In one study, ammonium sulfate seed was coated with a layer of secondary organic aerosol (SOA) from toluene oxidation followed by a layer of SOA from α-pinene oxidation. The system exhibited different evaporative properties than ammonium sulfate seed initially coated with α-pinene SOA followed by a layer of toluene SOA. This behavior is consistent with a shell-and-core model and suggests limited mixing among different SOA types. Another study investigated the reactive uptake of isoprene epoxy diols (IEPOX) onto non-acidified aerosol. It was demonstrated that particle acidity has limited influence on organic aerosol formation onto ammonium sulfate seed, and that the chemical system is limited by the availability of nucleophiles such as sulfate.

Flow tube experiments were conducted to examine the role of iron in the reactive uptake and chemical oxidation of glycolaldehyde. Aerosol particles doped with iron and hydrogen peroxide were mixed with gas-phase glycolaldehyde and photochemically aged in a custom-built flow reactor. Compared to particles free of iron, iron-doped aerosols significantly enhanced the oxygen to carbon (O/C) ratio of accumulated organic mass. The primary oxidation mechanism is suggested to be a combination of Fenton and photo-Fenton reactions which enhance particle-phase OH radical concentrations.

Understanding Micro- and Macro-Mechanics of Soil Liquefaction: A Necessary Step for Field-Scale Assessment

Liquefaction is a devastating instability associated with saturated, loose, and cohesionless soils. It poses a significant risk to distributed infrastructure systems that are vital for the security, economy, safety, health, and welfare of societies. In order to make our cities resilient to the effects of liquefaction, it is important to be able to identify areas that are most susceptible. Some of the prevalent methodologies employed to identify susceptible areas include conventional slope stability analysis and the use of so-called liquefaction charts. However, these methodologies have some limitations, which motivate our research objectives. In this dissertation, we investigate the mechanics of origin of liquefaction in a laboratory test using grain-scale simulations, which helps (i) understand why certain soils liquefy under certain conditions, and (ii) identify a necessary precursor for onset of flow liquefaction. Furthermore, we investigate the mechanics of liquefaction charts using a continuum plasticity model; this can help in modeling the surface hazards of liquefaction following an earthquake. Finally, we also investigate the microscopic definition of soil shear wave velocity, a soil property that is used as an index to quantify liquefaction resistance of soil. We show that anisotropy in fabric, or grain arrangement can be correlated with anisotropy in shear wave velocity. This has the potential to quantify the effects of sample disturbance when a soil specimen is extracted from the field. In conclusion, by developing a more fundamental understanding of soil liquefaction, this dissertation takes necessary steps for a more physical assessment of liquefaction susceptibility at the field-scale.