Dynamics of vector rogue waves in a fiber laser with a ring cavity

A pulse–pulse interaction that leads to rogue wave (RW) generation in lasers was previously attributed either to soliton–soliton or soliton–dispersive-wave interaction. The beating between polarization modes in the absence of a saturable absorber causes similar effects. Accounting for these polarization modes in a laser resonator is the purpose of the distributed vector model of laser resonators. Furthermore, high pump power, high amplitude, and short pulse duration are not necessary conditions to observe pulse attraction, repulsion, and collisions and the resonance exchange of energy between among them. The regimes of interest can be tuned just by changing the birefringence in the cavity with the pump power slightly higher than the laser threshold. This allows the observation of a wide range of RW patterns in the same experiment, as well as to classify them. The dynamics of the interaction between pulses leads us to the conclusion that all of these effects occur due to nonlinearity induced by the inverse population in the active fiber as well as an intrinsic nonlinearity in the passive part of the cavity. Most of the mechanisms of pulse–pulse interaction were found to be mutually exclusive. This means that all the observed RW patterns, namely, the “lonely,” “twins,” “three sisters,” and “cross,” are probably different cases of the same process.

Near-field coupling and resonant cavity modes in plasmonic nanorod metamaterials

Plasmonic resonant cavities are capable of confining light at the nanoscale, resulting in both enhanced local electromagnetic fields and lower mode volumes. However, conventional plasmonic resonant cavities possess large Ohmic losses at metal-dielectric interfaces. Plasmonic near-field coupling plays a key role in a design of photonic components based on the resonant cavities because of the possibility to reduce losses. Here, we study the plasmonic near-field coupling in the silver nanorod metamaterials treated as resonant nanostructured optical cavities. Reflectance measurements reveal the existence of multiple resonance modes of the nanorod metamaterials, which is consistent with our theoretical analysis. Furthermore, our numerical simulations show that the electric field at the longitudinal resonances forms standing waves in the nanocavities due to the near-field coupling between the adjacent nanorods, and a new hybrid mode emerges due to a coupling between nanorods and a gold-film substrate. We demonstrate that this coupling can be controlled by changing the gap between the silver nanorod array and gold substrate.

Micro-Fabricated Surface Trap and Cavity Integration for Trapped Ion Quantum Computing

Atomic ions trapped in micro-fabricated surface traps can be utilized as a physical platform with which to build a quantum computer. They possess many of the desirable qualities of such a device, including high fidelity state preparation and readout, universal logic gates, long coherence times, and can be readily entangled with each other through photonic interconnects. The use of optical cavities integrated with trapped ion qubits as a photonic interface presents the possibility for order of magnitude improvements in performance in several key areas of their use in quantum computation. The first part of this thesis describes the design and fabrication of a novel surface trap for integration with an optical cavity. The trap is custom made on a highly reflective mirror surface and includes the capability of moving the ion trap location along all three trap axes with nanometer scale precision. The second part of this thesis demonstrates the suitability of small micro-cavities formed from laser ablated fused silica substrates with radii of curvature in the 300-500 micron range for use with the mirror trap as part of an integrated ion trap cavity system. Quantum computing applications for such a system include dramatic improvements in the photonic entanglement rate up to 10 kHz, the qubit measurement time down to 1 microsecond, and the measurement error rates down to the 10e-5 range. The final part of this thesis details a performance simulator for exploring the physical resource requirements and performance demands to scale such a quantum computer to sizes capable of performing quantum algorithms beyond the limits of classical computation.

Ultrahigh Purcell factor in low-threshold nanolaser based on asymmetric hybrid plasmonic cavity

A low-threshold nanolaser with all three dimensions at the subwavelength scale is proposed and investigated. The nanolaser is constructed based on an asymmetric hybrid plasmonic F-P cavity with Ag-coated end facets. Lasing characteristics are calculated using finite element method at the wavelength of 1550 nm. The results show that owing to the low modal loss, large modal confinement factor of the asymmetric plasmonic cavity structure, in conjunction with the high reflectivity of the Ag reflectors, a minimum threshold gain of 240 cm−1 is predicted. Furthermore, the Purcell factor as large as 2518 is obtained with optimized structure parameters to enhance rates of spontaneous and stimulated emission.

Antarctic ice sheet topography, cavity geometry, and global bathymetry (RTopo 1.0.5-beta)

Sub-ice shelf circulation and freezing/melting rates in ocean general circulation models depend critically on an accurate and consistent representation of cavity geometry. Existing global or pan-Antarctic data sets have turned out to contain various inconsistencies and inaccuracies. The goal of this work is to compile independent regional fields into a global data set. We use the S-2004 global 1-minute bathymetry as the backbone and add an improved version of the BEDMAP topography for an area that roughly coincides with the Antarctic continental shelf. Locations of the merging line have been carefully adjusted in order to get the best out of each data set. High-resolution gridded data for upper and lower ice surface topography and cavity geometry of the Amery, Fimbul, Filchner-Ronne, Larsen C and George VI Ice Shelves, and for Pine Island Glacier have been carefully merged into the ambient ice and ocean topographies. Multibeam survey data for bathymetry in the former Larsen B cavity and the southeastern Bellingshausen Sea have been obtained from the data centers of Alfred Wegener Institute (AWI), British Antarctic Survey (BAS) and Lamont-Doherty Earth Observatory (LDEO), gridded, and again carefully merged into the existing bathymetry map. The global 1-minute dataset (RTopo-1 Version 1.0.5) has been split into two netCDF files. The first contains digital maps for global bedrock topography, ice bottom topography, and surface elevation. The second contains the auxiliary maps for data sources and the surface type mask. A regional subset that covers all variables for the region south of 50 deg S is also available in netCDF format. Datasets for the locations of grounding and coast lines are provided in ASCII format.

Tight-Binding Approximations in 1D and 2D Coupled-Cavity Photonic Crystal Structures

Light confinement and controlling an optical field has numerous applications in the field of telecommunications for optical signals processing. When the wavelength of the electromagnetic field is on the order of the period of a photonic microstructure, the field undergoes reflection, refraction, and coherent scattering. This produces photonic bandgaps, forbidden frequency regions or spectral stop bands where light cannot exist. Dielectric perturbations that break the perfect periodicity of these structures produce what is analogous to an impurity state in the bandgap of a semiconductor. The defect modes that exist at discrete frequencies within the photonic bandgap are spatially localized about the cavity-defects in the photonic crystal. In this thesis the properties of two tight-binding approximations (TBAs) are investigated in one-dimensional and two-dimensional coupled-cavity photonic crystal structures We require an efficient and simple approach that ensures the continuity of the electromagnetic field across dielectric interfaces in complex structures. In this thesis we develop \textrm{E} -- and \textrm{D} --TBAs to calculate the modes in finite 1D and 2D two-defect coupled-cavity photonic crystal structures. In the \textrm{E} -- and \textrm{D} --TBAs we expand the coupled-cavity \overrightarrow{E} --modes in terms of the individual \overrightarrow{E} -- and \overrightarrow{D} --modes, respectively. We investigate the dependence of the defect modes, their frequencies and quality factors on the relative placement of the defects in the photonic crystal structures. We then elucidate the differences between the two TBA formulations, and describe the conditions under which these formulations may be more robust when encountering a dielectric perturbation. Our 1D analysis showed that the 1D modes were sensitive to the structure geometry. The antisymmetric \textrm{D} mode amplitudes show that the \textrm{D} --TBA did not capture the correct (tangential \overrightarrow{E} --field) boundary conditions. However, the \textrm{D} --TBA did not yield significantly poorer results compared to the \textrm{E} --TBA. Our 2D analysis reveals that the \textrm{E} -- and \textrm{D} --TBAs produced nearly identical mode profiles for every structure. Plots of the relative difference between the \textrm{E} and \textrm{D} mode amplitudes show that the \textrm{D} --TBA did capture the correct (normal \overrightarrow{E} --field) boundary conditions. We found that the 2D TBA CC mode calculations were 125-150 times faster than an FDTD calculation for the same two-defect PCS. Notwithstanding this efficiency, the appropriateness of either TBA was found to depend on the geometry of the structure and the mode(s), i.e. whether or not the mode has a large normal or tangential component.

Characterisation of a secretory serine protease inhibitor (SjB6) from Schistosoma japonicum

BACKGROUND: Proteins belonging to the serine protease inhibitor (serpin) superfamily play essential physiological roles in many organisms. In pathogens, serpins are thought to have evolved specifically to limit host immune responses by interfering with the host immune-stimulatory signals. Serpins are less well characterised in parasitic helminths, although some are thought to be involved in mechanisms associated with host immune modulation. In this study, we cloned and partially characterised a secretory serpin from Schistosoma japonicum termed SjB6, these findings provide the basis for possible functional roles.

METHODS: SjB6 gene was identified through database mining of our previously published microarray data, cloned and detailed sequence and structural analysis and comparative modelling carried out using various bioinformatics and proteomics tools. Gene transcriptional profiling was determined by real-time PCR and the expression of native protein determined by immunoblotting. An immunological profile of the recombinant protein produced in insect cells was determined by ELISA.

RESULTS: SjB6 contains an open reading frame of 1160 base pairs that encodes a protein of 387 amino acid residues. Detailed sequence analysis, comparative modelling and structural-based alignment revealed that SjB6 contains the essential structural motifs and consensus secondary structures typical of inhibitory serpins. The presence of an N-terminal signal sequence indicated that SjB6 is a secretory protein. Real-time data indicated that SjB6 is expressed exclusively in the intra-mammalian stage of the parasite life cycle with its highest expression levels in the egg stage (p < 0.0001). The native protein is approximately 60 kDa in size and recombinant SjB6 (rSjB6) was recognised strongly by sera from rats experimentally infected with S. japonicum.

CONCLUSIONS: The significantly high expression of SjB6 in schistosome eggs, when compared to other life cycle stages, suggests a possible association with disease pathology, while the strong reactivity of sera from experimentally infected rats against rSjB6 suggests that native SjB6 is released into host tissue and induces an immune response. This study presents a comprehensive demonstration of sequence and structural-based analysis of a secretory serpin from a trematode and suggests SjB6 may be associated with important functional roles in S. japonicum, particularly in parasite modulation of the host microenvironment.

Design and Fabrication of Perovskite Micro-Cavity Lasers

Thesis (Master's)--University of Washington, 2016-08

Secretory breast cancer. Case report

Secretory carcinoma of the breast is a rare tumor initially described in children but occurring equally in adult population. This unusual breast cancer subtype has a generally favorable prognosis, although several cases have been described in adults with increased aggressiveness and a risk of metastases. However, surgery is still considered the most appropriate treatment for this pathology. We describe the case of a 50 –year-old woman who has undergone a breast conservative surgery for a little tumor, preoperatively diagnosticated by a fine needle aspiration biopsy (FNAB) as a well differentiated infiltrating carcinoma.

Abdominal hyperalgesia in secretory phospholipase A(2)-induced rat pancreatitis: Distinct roles of NK1 receptors

We investigated the potential of secretory phospholipase A(2) (sPLA(2))-induced pancreatitis to promote abdominal hyperalgesia, as well as to depolarize sensory fibres in vitro using a grease-gap technique. Pancreatitis was induced by the injection of sPLA(2) from Crotalus durissus terrificus (sPLA(2) Cdt, 300 mu g kg(-1)) venom into the common bile duct of rats. Pancreatic inflammatory signs, serum amylase levels and abdominal hyperalgesia were evaluated in rats treated or not with SR140333, a tachykinin NK1 receptor antagonist. Injection of sPLA(2) Cdt caused pancreatic oedema formation and increased pancreatic neutrophil infiltration and serum amylase at 4 h, which returned to normality by 24 h, except for the neutrophil infiltration, which was still increased at this time point. Animals injected with sPLA(2) exhibited a lower withdrawal threshold to electronic von Frey stimulation in the upper abdominal region at 4 h, but not 24 h, post-injection when compared with saline-injected rats. Pre-treatment of animals with SR140333 significantly reduced the sPLA(2) Cdt-induced abdominal hyperalgesia, without affecting the other parameters. Neither sPLA(2) Cdt nor sPLA(2) from Naja mocambique mocambique venom depolarized capsaicin-sensitive sensory fibres from rat vagus nerve, but they decreased the propagated compound action potentials in both A and C fibres. These data show for the first time that NK1 receptors play an important role in the early abdominal hyperalgesia in a rat model of sPLA(2)-induced pancreatitis, suggesting that these receptors are of importance in the development of pain in the pancreatitis condition. We also provide evidence that sPLA(2)s do not directly depolarize sensory fibres in vitro. (C) 2011 European Federation of International Association for the Study of Pain Chapters. Published by Elsevier Ltd. All rights reserved.

Effect of umbelliferone (7-hydroxycoumarin, 7-HOC) on the enzymatic, edematogenic and necrotic activities of secretory phospholipase A2 (sPLA2) isolated from Crotalus durissus collilineatus venom

Flavonoids, coumarins and other polyphenolic compounds are powerful antioxiants both in hydrophilic and lipophylic environments with diverse pharmacological properties including anti-inflammatory activity. Despite being widely used as powerful therapeutic agents for blood coagulation disorders, more specifically to control some serine protease enzymes, the mechanism of anti-inflammatory activity of coumarins is unknown, unlike that of flavonoids. Although their controlling effect on serine proteases is well acknowledged, their action on secretory phospholipase A2 (sPLA2) remains obscure. The present study describes the interaction between umbelliferone (7-HOC) and the sPLA2 from Crotalus durissus collilineatus venom. In vitro inhibition of sPLA2 enzymatic activity by 7-HOC was estimated using 4N3OBA as substrate, resulting in an irreversible decrease in such activity proportional to 7-HOC concentration. The biophysical interaction between 7-HOC and sPLA2 was examined by fluorescent spectral analysis and circular dichroism studies. Results from both techniques clearly showed that 7-HOC strongly modified the secondary structure of this enzyme and CD spectra revealed that it strongly decreased sPLA2 alphahelical conformation. In addition, two-dimensional electrophoresis indicated an evident difference between HPLC-purified native and 7-HOC-treated sPLA2s, which were used in pharmacological experiments to compare their biological activities. In vivo anti-inflammatory activity was assessed by the sPLA2-induced mouse paw edema model, in which 7-HOC presented an effect similar to those of dexamethasone and cyproheptacline against the pro-inflammatory effect induced by native sPLA2 on the mouse paw edema, mast cell degranulation and skin edema. on the other hand, 7-HOC exhibited a more potent inhibitory effect on sPUL2 than that of p-bromophenacyl bromide (p-BPB). Our data suggest that 7-HOC interacts with sPLA2 and causes some structural modifications that lead to a sharp decrease or inhibition of the edematogenic and myotoxic activities of this enzyme, indicating its potential use to suppress inflammation induced by sPLA2 from the snake venom. (C) 2008 Published by Elsevier Ltd.

Inhibition of Neurotoxic Secretory Phospholipases A(2) Enzymatic, Edematogenic, and Myotoxic Activities by Harpalycin 2, an Isoflavone Isolated from Harpalyce brasiliana Benth

Secretory phospholipases A(2) (sPLA(2)) exert proinflammatory actions through lipid mediators. These enzymes have been found to be elevated in many inflammatory disorders such as rheumatoid arthritis, sepsis, and atherosclerosis. The aim of this study was to evaluate the effect of harpalycin 2 (Har2), an isoflavone isolated from Harpalyce brasiliana Benth., in the enzymatic, edematogenic, and myotoxic activities of sPLA2 from Bothrops pirajai, Crotalus durissus terrificus, Apis mellifera, and Naja naja venoms. Har2 inhibits all sPLA(2) tested. PrTX-III (B. pirajai venom) was inhibited at about 58.7%, Cdt F15 (C. d. terrificus venom) at 78.8%, Apis (from bee venom) at 87.7%, and Naja (N. naja venom) at 88.1%. Edema induced by exogenous sPLA(2) administration performed in mice paws showed significant inhibition by Har2 at the initial step. In addition, Har2 also inhibited the myotoxic activity of these sPLA(2)s. In order to understand how Har2 interacts with these enzymes, docking calculations were made, indicating that the residues His48 and Asp49 in the active site of these enzymes interacted powerfully with Har2 through hydrogen bonds. These data pointed to a possible anti-inflammatory activity of Har2 through sPLA(2) inhibition.

Quercetin as an inhibitor of snake venom secretory phospholipase A2

As polyphenolic compounds isolated from plants extracts, flavonoids have been applied to various pharmaceutical uses in recent decades due to their anti-inflammatory, cancer preventive, and cardiovascular protective activities. In this study, we evaluated the effects of the flavonoid quercetin on Crotalus durissus terrificus secretory phospholipase A2 (sPLA2), an important protein involved in the release of arachidonic acid from phospholipid membranes. The protein was chemically modified by treatment with quercetin, which resulted in modifications in the secondary structure as evidenced through circular dichroism. In addition, quercetin was able to inhibit the enzymatic activity and some pharmacological activities of sPLA2, including its antibacterial activity, its ability to induce platelet aggregation, and its myotoxicity by approximately 40%, but was not able to reduce the inflammatory and neurotoxic activities of sPLA2. These results suggest the existence of two pharmacological sites in the protein, one that is correlated with the enzymatic site and another that is distinct from it. We also performed molecular docking to better understand the possible interactions between quercetin and sPLA2. Our docking data showed the existence of hydrogen-bonded, polar interactions and hydrophobic interactions, suggesting that other flavonoids with similar structures could bind to sPLA2. Further research is warranted to investigate the potential use of flavonoids as sPLA2 inhibitors. (C) 2010 Elsevier B.V. All rights reserved.