Nanophotonics is finding myriad applications in information technology, health care, lighting and sensing. Plasmonics, as one of the most rapidly growing fields in nanophotonics, has great potential to revolutionize many applications in nanophotonics, including bio-sensing, imaging, lighting, photolithography and magnetic recording. In this dissertation, we explore the electrodynamics of plasmonic fields on different structured metallic chips and demonstrate how to manipulate light from nano to micro scale on the structure plasmonic chips. It is highly desired to excite and control propagation of surface plasmon polariton fields in a systematic fashion as it is possible with optical fields both in free space and dielectric waveguides. To accomplish this goal, we developed the design methodology compatible with the conventional Fourier optical devices, investigated on-chip plasmonic metamaterials with novel material response and functionalities, as well as constructed sophisticated chip-scale integration of different optical element. We begin by discussing the fundamentals of plasmonic fields and modal propagation properties. We next investigate a metallic metamaterial showing form-birefringence by engineering the inherent metal properties on nanoscale, and experimentally characterized their supported plasmonic index ellipsoids. We present novel experimental and analytic results of plasmonic nano metamaterials allowing excitation of plasmonic fields by transverse electric polarized incidence, complementing so far demonstrated transverse magnetic polarized excitation. We further construct a plasmonic photonic crystal to manipulate the propagating plasmonic field on a micro scale. On a lager sub- millimeter scale, we experimentally validated the feasibility of Fourier plasmonics, demonstrating possibilities of miniaturizing the conventional bulky optical devices on small plasmonic chips. We ultimately integrate various photonic components on different scales and provide an approach for efficiently using resonant plasmonic phenomena to achieve nanoscale optical field localization

The ability to control light propagation in photonic integrated circuits is at the foundation of modern light-based communication. However, the inherent crosstalk in densely packed waveguides and the lack of robust control of the coupling are a major roadblock toward ultra-high density photonic integrated circuits. As a result, the diffraction limit is often considered as the lower bound for ultra-dense silicon photonics circuits. Here we experimentally demonstrate an active control of the coupling between two closely packed waveguides via the interaction with a decoupled waveguide. This control scheme is analogous to the adiabatic elimination, a well-known procedure in atomic physics. This approach offers an attractive solution for ultra-dense integrated nanophotonics for light-based communications and integrated quantum computing.

"Strain engineering" in functional materials has been widely explored to tailor the physical properties of electronic materials and improve their electrical and/or optical properties. Here, we exploit both in plane and out of plane uniaxial tensile strains in MoS2 to modulate its band gap and engineer its optical properties. We utilize X-ray diffraction and cross-sectional transmission electron microscopy to quantify the strains in the as-synthesized MoS2 nanosheets and apply measured shifts of Raman-active modes to confirm lattice strain modification of both the out-of-plane and in-plane phonon vibrations of the MoS2 nanosheets. The induced band gap evolution due to in-plane and out-of-plane tensile stresses is validated by photoluminescence (PL) measurements, promising a potential route for unprecedented manipulation of the physical, electrical and optical properties of MoS2.

Nickel ditelluride (NiTe2), a recently discovered Type-II Dirac semimetal with topological Dirac fermions near the Fermi energy, is expected to exhibit strong thickness-mediated electronic tunability and intrinsic two-gap superconductivity in the single-layer limit. Realizing such intriguing phenomena requires the fabrication of ultrathin NiTe2 films and an understanding of the underlying physics that is still under debate. By conducting experimental band mappings of ultrathin films prepared with molecular beam epitaxy, we reveal spectroscopic evidence for the dimensionality crossover of single-crystalline ultrathin NiTe2 films as a function of film thickness. As the film thickness increases from one to five layers, the gap in the conical topological surface states closes. Comparisons of experimental to first-principles results also highlight difficulties in fabricating atomically smooth single-layer NiTe2 films. Our results not only provide further impetus for studying emergent phenomena in NiTe2 but also underscore the limitations of fabricating NiTe2 films for device applications.

Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER) protein that can be secreted and protects dopamine neurons and cardiomyocytes from ER stress and apoptosis. The mechanism of action of extracellular MANF has long been elusive. From a genetic screen for mutants with abnormal ER stress response, we identified the gene Y54G2A.23 as the evolutionarily conserved C. elegans MANF orthologue. We find that MANF binds to the lipid sulfatide, also known as 3-O-sulfogalactosylceramide present in serum and outer-cell membrane leaflets, directly in isolated forms and in reconstituted lipid micelles. Sulfatide binding promotes cellular MANF uptake and cytoprotection from hypoxia-induced cell death. Heightened ER stress responses of MANF-null C. elegans mutants and mammalian cells are alleviated by human MANF in a sulfatide-dependent manner. Our results demonstrate conserved roles of MANF in sulfatide binding and ER stress response, supporting sulfatide as a long-sought lipid mediator of MANF's cytoprotection.

Lysosomal amino acid efflux by proton-driven transporters is essential for lysosomal homeostasis, amino acid recycling, mTOR signaling, and maintaining lysosomal pH. To unravel the mechanisms of these transporters, we focus on cystinosin, a prototypical lysosomal amino acid transporter that exports cystine to the cytosol, where its reduction to cysteine supplies this limiting amino acid for diverse fundamental processes and controlling nutrient adaptation. Cystinosin mutations cause cystinosis, a devastating lysosomal storage disease. Here, we present structures of human cystinosin in lumen-open, cytosol-open, and cystine-bound states, which uncover the cystine recognition mechanism and capture the key conformational states of the transport cycle. Our structures, along with functional studies and double electron-electron resonance spectroscopic investigations, reveal the molecular basis for the transporters conformational transitions and protonation switch, show conformation-dependent Ragulator-Rag complex engagement, and demonstrate an unexpected activation mechanism. These findings provide molecular insights into lysosomal amino acid efflux and a potential therapeutic strategy.

During the 2015–2016 El Niño, the Amazon basin released almost one gigaton of carbon (GtC) into the atmosphere due to extreme temperatures and drought. The link between the drought impact and recovery of the total carbon pools and its biogeochemical drivers is still unknown. With satellite-constrained net carbon exchange and its component fluxes including gross primary production and fire emissions, we show that the total carbon loss caused by the 2015–2016 El Niño had not recovered by the end of 2018. Forest ecosystems over the Northeastern (NE) Amazon suffered a cumulative total carbon loss of ∼0.6 GtC through December 2018, driven primarily by a suppression of photosynthesis whereas southeastern savannah carbon loss was driven in part by fire. We attribute the slow recovery to the unexpected large carbon loss caused by the severe atmospheric aridity coupled with a water storage deficit during drought. We show the attenuation of carbon uptake is three times higher than expected from the pre-drought sensitivity to atmospheric aridity and ground water supply. Our study fills an important knowledge gap in our understanding of the unexpectedly enhanced response of carbon fluxes to atmospheric aridity and water storage deficit and its impact on regional post-drought recovery as a function of the vegetation types and climate perturbations. Our results suggest that the disproportionate impact of water supply and demand could compromise resiliency of the Amazonian carbon balance to future increases in extreme events.

Methane is an important greenhouse gas, responsible for about 20% of the warming induced by long-lived greenhouse gases since pre-industrial times. By reacting with hydroxyl radicals, methane reduces the oxidizing capacity of the atmosphere and generates ozone in the troposphere. Although most sources and sinks of methane have been identified, their relative contributions to atmospheric methane levels are highly uncertain. As such, the factors responsible for the observed stabilization of atmospheric methane levels in the early 2000s, and the renewed rise after 2006, remain unclear. Here, we construct decadal budgets for methane sources and sinks between 1980 and 2010, using a combination of atmospheric measurements and results from chemical transport models, ecosystem models, climate chemistry models and inventories of anthropogenic emissions. The resultant budgets suggest that data-driven approaches and ecosystem models overestimate total natural emissions. We build three contrasting emission scenarios-which differ in fossil fuel and microbial emissions-to explain the decadal variability in atmospheric methane levels detected, here and in previous studies, since 1985. Although uncertainties in emission trends do not allow definitive conclusions to be drawn, we show that the observed stabilization of methane levels between 1999 and 2006 can potentially be explained by decreasing-to-stable fossil fuel emissions, combined with stable-to-increasing microbial emissions. We show that a rise in natural wetland emissions and fossil fuel emissions probably accounts for the renewed increase in global methane levels after 2006, although the relative contribution of these two sources remains uncertain. © 2013 Macmillan Publishers Limited.

Background:Previous findings suggest that apathy symptoms independently of depressive symptoms measured using the Geriatric Depression Scale (GDS) are associated with cardiovascular disease (CVD) in older individuals. Aims:To study whether apathy and depressive symptoms in older people are associated with future CVD, stroke, and mortality using individual patient-data meta-analysis. Methods:Medline, Embase, and PsycInfo databases up to September 3, 2013, were systematically searched without language restrictions. We sought prospective studies with older (mean age ≥65 years) community-dwelling populations in which the GDS was employed and subsequent stroke and/or CVD were recorded to provide individual participant data. Apathy symptoms were defined as the three apathy-related subitems of the GDS, with depressive symptoms the remaining items. We used myocardial infarction (MI), stroke, and all-cause mortality as main outcomes. Analyses were adjusted for age, sex, and MI/stroke history. An adaptation of the Newcastle-Ottawa scale was used to evaluate bias. Hazard ratios were calculated using one-stage random-effect Cox regression models. Results:Of the 52 eligible studies, 21 (40.4%) were included, comprising 47,625 older people (mean age [standard deviation] 74 [7.4] years), over a median follow-up of 8.8 years. Participants with apathy symptoms had a 21% higher risk of MI (95% confidence interval [CI] 1.08-1.36), a 37% higher risk of stroke (95% CI 1.18-1.59), and a 47% higher risk of all-cause mortality (95% CI 1.38-1.56). Participants with depressive symptoms had a comparably higher risk of stroke (HR 1.36, 95% CI 1.18-1.56) and all-cause mortality (HR 1.44, 95% CI 1.35-1.53), but not of MI (HR 1.08, 95% CI 0.91-1.29). Associations for isolated apathy and isolated depressive symptoms were comparable. Sensitivity analyses according to risk of bias yielded similar results. Conclusion:Our findings stress the clinical importance of recognizing apathy independently of depressive symptoms, and could help physicians identify persons at increased risk of vascular disease.