Self-doping in graphene has been studied by examining single-layer epitaxially grown graphene samples with differing characteristic lateral terrace widths. Low energy electron microscopy was used to gain real-space information about the graphene surface morphology, which was compared with data obtained by angle-resolved photoemission spectroscopy to study the effect of the monolayer graphene terrace width on the low energy dispersions. By altering the graphene terrace width, we report significant changes in the electronic structure and quasiparticle relaxation time of the material, in addition to a terrace width-dependent doping effect.

Gravitational sinking of particles is a key pathway for the transport of particulate organic carbon (POC) into the deep ocean. The sinking of POC and its remineralization directly impact ocean carbon storage on climatologically relevant timescales. Particle size, density and composition influence particle sinking velocity and the remineralization length scale i.e., the depth where POC is converted to suspended organic carbon or inorganic carbon. However, the factors affecting this relationship and their spatiotemporal variability are not well understood. Here, we use data collected from Marine Snow Catchers to characterize profiles of both suspended and sinking particles. Particle size, biogeochemical composition, and microbial activity are used to understand the controls and fate of suspended and sinking POC in the upper ocean. My first chapter shows that during the late summer in the subarctic Pacific POC fluxes were low, marine snow-sized aggregates (d > 0.5 mm) were rare and small, suspended particles differed from small sinking particles by their higher TEP (transparent exopolymer particles) content. This work provides the first in situ data to support the hypothesis by Xavier et al. (2017) that the ratio between TEP-C and POC determines, at least partially, the efficiency of the biological carbon pump (i.e., POC flux 100 m below reference depth/flux at reference depth).My second chapter focuses on the decline of the spring diatom bloom in the NE Atlantic and shows that turbulent disaggregation and changes in the mixed layer depth due to four strong storms delayed the formation and sinking of POC-rich marine snow-sized aggregates (d > 0.1 mm) while small, slow-sinking silica-rich particles sank from the mixed layer, creating an inefficient POC export event. After the last storm passed, we observed the sinking of marine snow aggregates, which resulted in vertical flux of a mixed post-bloom plankton community out of the euphotic zone. My third chapter focuses on a study conducted in the Labrador Sea, where microbial degradation of total organic carbon (TOC) differed between suspended and sinking particles and across different stages of a spring Phaeocystis bloom. Carbon removal rates for fast-sinking and slow-sinking particles were similar but were on average one order of magnitude larger than those found for the suspended fraction. However, at the station characterized by abundant free-floating Phaeocystis colonies, the suspended fraction sustained a TOC removal rate similar to the ones for sinking particles. This observation suggests that the presence of Phaeocystis colonies may have enhanced the rate of microbial degradation of TOC. Overall, this work highlights the importance of investigating characteristics and dynamics of suspended and sinking particles to understand which factors affect the efficiency of the biological carbon pump in different open ocean systems.

Quantifying and determining the oceanographic and climate forcings of variability in phytoplankton community composition (PCC) represents a critical step in understanding and predicting marine ecosystem structure and function. In this dissertation, I analyzed samples and data from an extensive oceanographic time series from the highly productive Santa Barbara Channel, CA (SBC). The goals of this work were to (1) determine the “best-case scenario” for retrieving PCC from remotely sensible hyperspectral bio-optical observations; (2) characterize the dominant oceanographic and climate forcings of PCC variations in the SBC; and (3) integrate HPLC pigment and amplicon sequencing observations of PCC to assess the agreement between methods and the potential to gain novel insights into phytoplankton physiology and ecology and ecosystem function. In Chapter 2, we considered nearly a decade of concurrent HPLC phytoplankton pigment and spectrophotometric phytoplankton absorption coefficient observations. We implemented covariance-based analyses to identify 3-5 phytoplankton pigment communities from the HPLC pigment data, and spectral derivative analysis of phytoplankton absorption to identify phytoplankton absorption features. We then developed a bio-optical modeling approach to retrieve phytoplankton pigment concentrations and PCC indices from phytoplankton absorption derivative spectra with high skill. Notably, we found that absorption features from across the visible spectrum are useful in modeling PCC. In Chapter 3, we applied the bio-optical models from Chapter 2 to the PnB archive of phytoplankton absorption observations to double the length of the PnB HPLC phytoplankton biomarker pigment time series to 20+ years of observations. We then characterized the dominant oceanographic and climate forcings of five phytoplankton groups resolved from HPLC pigment data. Despite the widely documented dominant response of diatoms to seasonal upwelling, our analysis revealed that prymnesiophytes and chlorophytes are the typical “first responders” to seasonal upwelling in the SBC. On multi-decadal time scales, we identified an association between anomalous SBC dinoflagellate blooms and surface ocean advection patterns likely forced by a dominant mode of decadal climate variability, the North Pacific Gyre Oscillation. Finally, Chapter 4 focused on integrating HPLC pigment and amplicon sequencing observations to assess PCC in the coastal ocean. High uncertainty in estimates of biomass contributions of specific phytoplankton groups was often introduced by inter- and intra-group variability in biomarker pigment expression. However, we observed that distinct suites of biomarker pigments covary with unique communities of phytoplankton and other protistan groups. Integrating the two data sets thus provided novel insights into phytoplankton physiology and function, and suggested a path toward monitoring ecosystem structure and function on unprecedented spatiotemporal scales via ocean color remote sensing of phytoplankton biomarker pigment concentrations.

The ocean contains reservoirs of carbon that influence atmospheric CO2, impact climate, fuel deep-sea metabolism, and sustain fisheries worldwide. Despite the ocean’s substantial role in the global carbon cycle, much remains to be known about the fundamental influences for carbon transport over climatically relevant scales. These details remain elusive because 1) available data is sparse, 2) the collection of new data is expensive, time consuming, and logistically difficult, and 3) the system itself is complex and highly variable. Overall, this dissertation confronts sources of uncertainty for data and models associated with differences in technology, incongruous spatiotemporal sampling schemes, and model complexity in order to extract as much as possible given what is currently available to use.

The chapter specific objectives are as follows:

(1) Examine how intrinsic and extrinsic sources of variability affect model calibration through a compilation of data sets spanning method, space and time,

(2) Assess mechanisms of the biological pump given available data products, and diagnose mechanistic parameter sensitivities as they relate to experimental/observational work,

(3) Test and recalibrate parameters to predict the flux of carbon from a rapidly growing technology (Underwater Vision Profiler data) from the surface to depth.

In Chapter 1 carbon export predictions from a mechanistic model are compared with observations of particulate organic carbon (POC) fluxes from several datasets compiled from the literature spanning different space, time, and depth scales as well as using different observational methodologies. Model parameters are optimized to provide the best match between model-predicted and observed POC fluxes, explicitly accounting for sources of error associated with each dataset. Model-predicted globally integrated values of POC flux at the base of the euphotic layer range from 3.8 to 5.5 Pg C yr-1, depending on the dataset used to optimize the model. Results from Chapter 2 reveal that modeled carbon export pathways also vary depending on the dataset used to optimize the model, and depending on the processes explicitly represented within a quite of nested models. Chapter 3 tests the relationship between the particle size distribution and flux in the global ocean using abundant observations of particle size spectra in tandem with high-resolution model outputs. Results motivate the need for improved parameterizations that link particle size to flux based on depth and/or surface ecosystem characteristics. Altogether these findings highlight the importance of collecting field data that average over the substantial natural temporal and spatial variability in carbon export fluxes, and of advancing satellite algorithms for ocean NPP, in order to improve predictions of biological carbon export.

Phytoplankton are microscopic protists that are ubiquitous in the sunlit global ocean. These organisms form the base of the marine food web and are essential to biogeochemical cycling as sources and sinks of elemental compounds and nutrients. Carbon sequestration from the atmosphere to ocean sediments is facilitated through biological production by phytoplankton, and phytoplankton produce half of the oxygen in Earth’s atmosphere. Distinct phytoplankton taxa differentially impact these essential ecosystem processes. Thus, a complete understanding of the role of phytoplankton in the Earth system can only be achieved through a complete description of the distribution and abundance of phytoplankton communities in the global ocean. Existing methods to characterize phytoplankton community composition (PCC) using in situ measurements are limited by the scales of observation. However, satellites provide unprecedented coverage of the global surface ocean. While existing global ocean color sensors are limited to multi-spectral sampling resolution, future satellites (such as NASA’s Plankton, Aerosol, Cloud, ocean Ecosystem [PACE] sensor) will have hyperspectral resolution, providing observations across the visible spectrum of light at wavelengths sensitive to absorption and scattering by phytoplankton. Satellite ocean color approaches can therefore be leveraged to distinguish between phytoplankton groups. The major goal of this thesis is to characterize patterns of PCC in the global surface ocean using a combination of existing chemotaxonomic, molecular, and imaging methods with newly-developed remote sensing approaches. In chapter 1, I used quality-controlled, consistent measurements of high performance liquid chromatography (HPLC) phytoplankton pigments collected across the global surface ocean to characterize the distributions of phytoplankton groups from co-variability in phytoplankton pigment concentrations. In both the global dataset and regional time series datasets, the number of phytoplankton groups that could be separated from HPLC pigments was limited across statistical methods to maximum 4-6 distinct pigment-based groups. In chapter 2, the statistical methods employed in chapter 1 were applied to a dataset of HPLC pigments and flow cytometry collected as part of the North Atlantic Aerosols and Marine Ecosystems Study (NAAMES) to describe the evolving surface ocean PCC in the western North Atlantic Ocean across distinct bloom phases. Pigment-based phytoplankton communities revealed a transition from diatoms and dinoflagellates in spring and early summer to haptophytes and cyanobacteria in early fall, followed by green algae and mixed pigment assemblages in early winter. In chapter 3, I modeled phytoplankton pigment concentrations in the global surface ocean from measured and modeled remote sensing reflectance spectra. The concentrations of thirteen pigments were retrieved by the model, and these results were validated with measured HPLC phytoplankton pigment concentrations. The relationships between and among groups of phytoplankton pigments remained consisted between measured and modeled pigment datasets, separating five distinct pigment communities. Finally, in chapter 4, multiple in situ methods were compared to better constrain and quantify the information content of HPLC pigment data using samples collected as part of NAAMES and the first EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) field campaign in the North Pacific Ocean. The eukaryotic phytoplankton community was compared from HPLC pigments, 18S rRNA metabarcoding, and quantitative cell imagery from the Imaging FlowCytobot. The prokaryotic and eukaryotic phytoplankton communities were both compared from HPLC pigments, 16S rRNA metabarcoding, and flow cytometry. While broad group-level trends were consistent between methods, inconsistencies between methods arose at higher taxonomic resolution and when environmental and physiological impacts were taken into account (e.g., sea surface temperature; mixotrophy). Taken together, these four chapters describe PCC from in situ and remote sensing approaches across the global surface ocean. Chapters 1 and 2 use HPLC pigments to describe broad trends in phytoplankton pigments across regions (chapter 1) and seasons (chapter 2). Chapter 3 demonstrates that pigments can be modeled with reasonable accuracy from hyperspectral ocean color data. Chapter 4 then describes the strengths and limitations of HPLC pigment data when compared to methods with higher taxonomic resolution and in the context of a changing ocean environment.

This dissertation examines the variability of physical and bio-optical properties in the Southern California Bight over various time and space scales. The research is divided into three chapters, and each chapter was written mostly as stand-alone pieces. An abstract is presented for each, and Tables, Figures and Appendices that support the text are shown at the end of each specific chapter. A list of all the references used in the text is shown at the end of the dissertation.

In Chapter One, “Assessing controls on cross-shelf phytoplankton and suspended particle distributions”, an underwater glider was used to “super-sample” the inner and mid-shelf Santa Barbara Channel (from 20 to 70m depth), providing data in detail never before observed. Highly resolved glider data in time and depth for a 4km long section perpendicular to the coast allowed answering questions such as: what is the space-time distribution of bio-optical properties (specifically phytoplankton and sediments) in the inner/mid-shelf SBC? And, what are the main controls on the variability of these properties? Six glider missions were completed, sampling a wide range of environmental conditions (e.g. upwelling, highly stratified, large blooms, small blooms, intense mixing). A storm event was also captured by the glider, providing a unique view of its evolution and effect on bio-optical properties. This confirmed the importance of instruments such as gliders in sampling events that are normally missed by ships and satellites. The data allowed characterizing the coastal zone in terms of surface, bottom and intermediate nepheloid layers of various compositions that evolve according to specific stratification conditions. Winds, precipitation, waves, and surface currents were used to infer some of the drivers of the variability. Waves were found as the main controls on sediment re-suspension during the storm mission, and advection processes were related to local changes in phytoplankton abundances. Unique examples of high-frequency events, such as the cross-shore propagation of a phytoplankton patch, the interaction between tides and sediment re-suspension and the co-evolution of phytoplankton and non-biogenic materials in similar portions of the water column – determining the complexity of the coastal ocean - are shown and discussed.

In Chapter Two, “Transport and Fate of heat, salt, oxygen and particles in the innershelf Santa Barbara Channel, CA”, the capabilities of the glider dataset are explored even further to ask questions that are in the very core of the studies in upwelling environments: How important is the cross-shelf exchange of materials to the health of nearshore ecosystems? Is the innershelf a source or a sink for particles/heat/salt? Is the nearshore zone net autotrophic or net heterotrophic? Do source/sink patterns change over time? Although the glider was not equipped with velocity meters, this study takes advantage of the Acoustic Doppler Current Profiler moored at the 10m isobath just North of the shallowest glider observations to provide depth-resolved velocity estimates for the calculations of biogeochemical fluxes across the innershelf. Despite large uncertainties, interesting patterns of the nearshore zone acting as a source or sink for phytoplankton, sediments and oxygen are observed for the different missions. Nonetheless, this study shows the feasibility of using depth-resolved instruments to assess cross-shore transport of biogeochemical properties, and provides insights into how an experiment should be designed to properly obtain those fluxes estimates in the future.

Chapter Three, “Satellite assessments of particulate matter and phytoplankton variations in the Santa Maria Basin and Southern California Bight”, takes a larger scale approach to determine what drives bio-optical variability in the Southern California Bight and Santa Maria Basin. This study took advantage of the now more than 13 years worth of quality optical imagery from SeaWiFS, MODIS and MERIS sensors, which were spectrally merged using a bio-optical algorithm to increase space-time coverage. 8-day composites and 2-km pixel sizes were used in the analysis, allowing the observation of weekly to seasonal and inter-annual changes in bio-optical properties, as well as long-term trends. Controls on chlorophyll distribution were different in different portions of the domain, indicating the importance of regional scale upwelling and larger scale changes in circulation patterns in determining productivity. Controls on backscatter far from shore mimicked the observed for chlorophyll. Near the coast, however, changes in backscatter were shown to be modulated by waves throughout the seasons and, episodically, by the large discharge events associated with El Niño conditions.

Single-layer graphene has been widely researched in recent years due to its perceived technological applicability and its scientific importance as a unique model system with relativistic Dirac Fermions. Because of its unique geometric and electronic structure, the properties of graphene can be tuned or manipulated in several ways. This tunability is important for technological applications in its own right, and it also allows us to study the fundamental properties of Dirac Fermions, including unique many-body interactions and the nature of the quasiparticles at half-filling. This thesis is a detailed examination of the electronic and structural properties of graphene, studied with angle-resolved photoemission spectroscopy (ARPES) and other surface science techniques like low-energy electron microscopy and diffraction.

This thesis is organized as follows. Chapter 1 gives an introduction to the electronic and structural properties of single-layer graphene. It provides a brief historical overview of major theoretical and experimental milestones and sets the stage for the important theoretical and experimental questions that this thesis addresses.

Chapters 2 and 3 describe the experimental setup. Chapter 2 discusses the experimental techniques used in this thesis with particular focus on the mechanics of ARPES. Chapter 3 discusses the different graphene growth techniques that were used to create our sample with particular focus on our characterization of epitaxial graphene on SiC(0001).

Chapters 4 and 5 form the meat of this thesis: they provide a thorough discussion of the electronic properties of graphene as studied by ARPES. Chapter 4 describes how various perturbations can result in the manipulation of the bare electronic band structure, including the deposition of atomic or molecular species on top of an epitaxial graphene sheet as well as the interactions between graphene and its substrate. Chapter 5 describes the many-body physics in single-layer graphene. It begins with a discussion of the electron-electron interaction in undoped graphene, demonstrating that these interactions qualitatively differ from ordinary metals and semiconductors and depart from the standard Fermi liquid picture for quasiparticles; it then continues by describing how screening the electron-electron and electron-impurity interactions can impact the electronic properties of graphene. Chapter 5 ends with a discussion of the doping-dependent coupling strength of the electron-phonon interaction.