Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1989

Description: This thesis studies mixing and convection in a rectangular basin driven by a specified heat flux at the surface. A numerical model is constructed for this purpose. The main focus of the study is on the density and circulation structure resulting from the thermal forcing. In chapter two, a simple vertical one-dimensional model is developed to examine the mixing processes under a given surface heat flux. In order to simulate strong vertical mixing in the region where stratification is unstable, turbulent processes are modeled by a convective overturning parameterization of eddy viscosity and diffusivity. The results show that the density structure is strongly affected by the convective overturning adjustment as surface cooling prevails, and the resulting density field is nearly depth independent. In chapter three, a more complicated two-dimensional model is constructed to simulate mixing and circulation in a vertical rectangular basin with rigid boundaries. The aspect ratio of the basin ranges from 1 to 0.001 and Rayleigh number from 104 to 2 x 1012. It is found that the circulation pattern is dominated by these two important numbers. The roles of density overturning and density-momentum overturning mixing are further investigated. The results show that the convective overturning not only homogenizes the density field in the unstably stratified region but also contributes to increase the circulation. A crude scale analysis of the system shows that the characteristics of the density and momentum fields from the analysis agree well with the numerical results.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1992

Description: This study concerns the barotropic interactions between a mesoscale eddy and a straight monotonic bottom topography. Through simple to relatively complicated modeling effort, some of the fundamental properties of the interaction are investigated. In chapter two, the fundamental aspects of the interaction are examined using a simple contour dynamics model. With the simplest model configuration of an ideal vortex and a step topography, the basic dynamical features of the observed oceanic eddy-topography interaction are qualitatively reproduced. The results consist of eddy-induced cross-topography exchange, formation of topographic eddies, eddy propagation and generation of topographic waves. In chapter three, a more complicated primitive equation model is used to investigate a mesoscale eddy interacting with an exponential continental shelf/slope topography on both f and β-planes. The f-plane model recasts the important features of chapter two. The roles of the eddy size and strength and the geometry of topography are studied. It is seen that the multiple anticyclonic eddy-slope interactions strongly affect the total cross-slope volume transport and the evolution of both the original anticyclone and the topographic eddy. Since a cyclone is trapped at the slope and eventually moves on to the slope, it is most effective in causing perturbation on the shelf and slope. The responses on the shelf and slope are mainly wavelike with dispersion relation obeying that of the free shelf-trapped wave modes. On the β-plane, the problem of an eddy colliding onto a continental shelf/slope from a distance with straight or oblique incident angles is investigated. It is found that the straight eddy incident is more effective in achieving large onslope eddy penetration distance than the oblique eddy incident. The formation of a dipole-like eddy pair consisting of the original anticyclone and the topographic cyclone acts to suppress the eddy decay due to long Rossby wave radiation. A weak along-slope current near the edge of the slope is found, which is part of a outer slope circulation cell originated from the Rossby wave wake trailing the propagating eddy. Model-observation comparisons in_chapter four show favorable qualitative agreement of the model results with some of the observed events in the eastern U.S. continental margins and in the Gulf of Mexico. The model results give dynamical interpretations to some observed features of the oceanic eddy-topography interactions and provide enlightening insight into the problem.

Description: Author(s): Ryan Stearrett, W. G. Wang, Xiaoming Kou, J. F. Feng, J. M. D. Coey, J. Q. Xiao, and E. R. Nowak The strength of the exchange bias field is found to influence the low-frequency magnetoresistive noise associated with the magnetic reference layer in sputtered-deposited and electron-beam-evaporated CoFeB/MgO/CoFeB tunnel junctions. The noise is due to magnetic losses arising in the reference layer... [Phys. Rev. B 86, 014415] Published Mon Jul 16, 2012

Description: [1]  One of the primary goals for the Visible Infrared Imaging Radiometer Suite (VIIRS) onboard the Suomi National Polar-orbiting Partnership (SNPP) is to provide the science and user communities with the data continuity of the Environmental Data Records (EDR) (or Level-2 products) over global oceanic waters for various research and applications, including assessment of climatic and environmental variations. The ocean color EDR is one of the most important products derived from VIIRS. Since ocean color EDR is processed from the upstream Sensor Data Records (SDR) (or Level-1B data), the objective of this study is to evaluate the impact of the SDR on the VIIRS ocean color EDR. The quality of the SDR relies on pre-launch sensor characterizations as well as on-orbit radiometric calibrations, which are used to develop the sensor F-factor lookup tables (F-LUTs). VIIRS F-LUTs derived from solar and lunar calibrations have been used in processing data from the VIIRS Raw Data Records (RDR) (or Level-0 data) to SDR. In this study, three sets of F-LUTs with different generation schemes have been used to reprocess the SDR and then the ocean color EDR for product evaluations. VIIRS ocean color products are compared with in situ data from the Marine Optical Buoy (MOBY) and products from the Moderate Resolution Imaging Spectroradiometer (MODIS) on the satellite Aqua. It is found that the data quality of VIIRS operational ocean color products before 6 February 2012 is poor due to the inappropriate use of the at-launch F-LUTs for the SDR calibration, and that the recently updated VIIRS F-LUTs have significantly improved the SDR and ocean color EDR. Using reprocessed SDR with updated F-LUTs and including vicarious calibration, VIIRS ocean color EDR products are consistent with those from MODIS-Aqua in global deep waters. Although there are still some significant issues with VIIRS ocean color EDR, e.g., poor data quality over coastal regions, our results demonstrate that VIIRS has great potential to provide the science and user communities with consistently high quality global ocean color data records that are established from heritage ocean color sensors such as MODIS-Aqua.

Description: Langmuir DOI: 10.1021/la500049w

Description: Purpose To investigate the diffusion abnormalities in the brain of children with idiopathic generalized epilepsy (IGE) with generalized tonic-clonic seizure (GTCS) by using diffusion kurtosis imaging (DKI). Materials and Methods Twenty-one IGE children with GTCS and 16 controls were recruited. DKI was performed and maps of radial diffusivity (λ ⊥ ), axial diffusivity (λ // ), mean diffusivity (MD), fractional anisotropy (FA), radial kurtosis (K ⊥ ), axial kurtosis (K // ) and mean kurtosis (MK) were calculated. Voxel-based analyses were employed to compare diffusion metrics in epilepsy versus the controls. Results In the case group, MD was found significantly higher in the right temporal lobe, the right occipital lobe, hippocampus, and some subcortical regions, while FA increased in bilateral supplementary motor area and the left superior frontal lobe (false discovery rate corrected P  〈 0.05). Analysis of λ ⊥ and λ // showed that the increased MD was mainly due to the elevated λ // . Significantly decreased MK was also detected in bilateral temporo-occipital regions, the right hippocampus, the left insula, the left post-central area, and some subcortical regions (false discovery rate corrected P  〈 0.05). In most regions the changed MK were due to the decreased K // . Conclusion The kurtosis parameters (K ⊥ , K // , and MK) reflect different microstructural information in the IGE children with GTCS, and this support the value of DKI in studying children GTCS. J. Magn. Reson. Imaging 2014 . © 2014 Wiley Periodicals, Inc .

Description: Nature Chemical Biology 9, 84 (2013). doi:10.1038/nchembio.1153 Authors: Gelin Wang, Xiaoming Wang, Hong Yu, Shuguang Wei, Noelle Williams, Daniel L Holmes, Randal Halfmann, Jacinth Naidoo, Lai Wang, Lin Li, She Chen, Patrick Harran, Xiaoguang Lei & Xiaodong Wang

Description: AmyP is a raw-starch-degrading α-amylase newly identified from a marine metagenome library. It shares low sequence similarity with characterized glycoside hydrolases and was classified into a new subfamily of GH13. In particular, it showed preferential degradation to raw rice starch. Full-length AmyP was cloned and overexpressed in Escherichia coli , then purified and crystallized in the presence of its substrate analogue β-cyclodextrin. X-ray diffraction data were collected to a resolution of 2.1 Å. The crystal belonged to space group P 2 1 2 1 2, with unit-cell parameters a = 129.824, b = 215.534, c = 79.699 Å, α = β = γ = 90°, and was estimated to contain two molecules in one asymmetric unit.

Description: A large number of half-Heusler compounds have been recently proposed as three-dimensional (3D) topological insulators (TIs) with tunable physical properties. However, no transport measurements associated with the topological surface states have been observed in these half-Heusler candidates due to the dominating contribution from bulk electrical conductance. Here we show that, by reducing the mobility of bulk carriers, a two-dimensional (2D) weak antilocalization (WAL) effect, one of the hallmarks of topological surface states, was experimentally revealed from the tilted magnetic field dependence of magnetoconductance in a topologically nontrivial semimetal LuPdBi. Besides the observation of a 2D WAL effect, a superconducting transition was revealed at Tc ~ 1.7 K in the same bulk LuPdBi. Quantitative analysis within the framework of a generalized BCS theory leads to the conclusion that the noncentrosymmetric superconductivity of LuPdBi is fully gapped with a possibly unconventional pairing character. The co-existence of superconductivity and the transport signature of topological surface states in the same bulk alloy suggests that LuPdBi represents a very promising candidate as a topological superconductor. Scientific Reports 4 doi: 10.1038/srep05709

Description: Cases of convergent evolution, particularly within ecomorphological contexts, are instructive in identifying universally adaptive morphological features across clades. Tracing of evolutionary pathways by which ecomorphological convergence takes place can further reveal mechanisms of adaptation, which may be strongly influenced by phylogeny. Ecomorphologies of carnivorous mammals represent some of the most outstanding cases of convergent evolution in the Cenozoic radiation of mammals. This study examined patterns of cranial shape change in the dog (Canidae) and hyena (Hyaenidae) families, in order to compare the evolutionary pathways that led to the independent specialization of bone-cracking hypercarnivores within each clade. Geometric morphometrics analyses of cranial shape in fossil hyaenids and borophagine canids provided evidence for deep-time convergence in morphological pathways toward the independent evolution of derived bone-crackers. Both clades contained stem members with plesiomorphic generalist/omnivore cranial shapes, which evolved into doglike species along parallel pathways of shape change. The evolution of specialized bone-crackers from these doglike forms, however, continued under the constraint of a full cheek dentition and restriction on rostrum length reduction in canids, but not hyaenids. Functionally, phylogenetic constraint may have limited borophagine canids to crack bones principally with their carnassial instead of the third premolar as in hyaenids, but other cranial shape changes associated with durophagy nevertheless evolved in parallel in the two lineages. Size allometry was not a major factor in cranial shape evolution in either lineage, supporting the interpretation of functional demands as drivers for the observed convergence. The comparison between borophagines and hyaenids showed that differential effects of alternative functional "solutions" that arise during morphological evolution may be multiplied with processes of the "macroevolutionary ratchet" already in place to further limit the evolutionary pathways available to specialized lineages.