Developing Efficient High-Order Transport Schemes for Cross-Scale Coupled Estuary-Ocean Modeling

Geophysical fluid dynamics (GFD) models have progressed greatly in simulating the world’s oceans and estuaries in the past three decades, thanks to the development of novel numerical algorithms and the advent of massively parallel high-performance computing platforms. Study of inter-related processes on multi-scales (e.g., between large-scale (remote) processes and small-scale (local) processes) has always been an important theme for GFD modeling. For this purpose, models based on unstructured-grid (UG) have shown great potential because of their superior abilities in enabling multi-resolution and in fitting geometry and boundary. Despite UG models’ successful applications on coastal systems, significant obstacles still exist that have so far prevented UG models from realizing their full cross-scale capability. The pressing issues include the computation overhead resulting from large contrasts in the spatial resolutions, and the relative lack of skill for UG model in the eddying regime. Specifically for our own implicit UG model (SCHISM), the transport solver often emerges as a major bottleneck for both accuracy and efficiency. The overall goal of this dissertation is two-fold. The first goal is to address the challenges in tracer transport by developing efficient high-order schemes for the transport processes and test them in the framework of a community supported modeling system (SCHISM: Semi-implicit Cross-scale Hydroscience Integrated System Model) for cross-scale processes. The second goal is to utilize the new schemes developed in this dissertation and elsewhere to build a bona fide cross-scale Chesapeake Bay model and use it to address some key knowledge gaps in the physical processes in this system and to better assist decision makers of coastal resource management. The work on numerical scheme development has resulted in two new high-order transport solvers. The first solver tackles the vertical transport that often imposes the most stringent constraint on model efficiency (Chapter 2). With an implicit method and two flux limiters in both space and time, the new TVD2 solver leads to a speed-up of 1.6-6.0 in various cross-scale applications as compared to traditional explicit methods, while achieving 2nd-order accuracy in both space and time. Together with a flexible vertical gridding system, the flow over steep slopes can be faithfully simulated efficiently and accurately without altering the underlying bathymetry. The second scheme aims at improving the model skill in the eddying ocean (Chapter 4). UG coastal models tend to under-resolve features like meso-scale eddies and meanders, and this issue is partially attributed to the numerical diffusion in the transport schemes that are originally developed for estuarine applications. to address this issue, a 3rd-order transport scheme based on WENO formulation is developed, and is demonstrated to improve the meso-scale features. The new solvers are then tested in the Chesapeake Bay and adjacent Atlantic Ocean on small, medium and large domains respectively, corresponding to the three main chapters of this dissertation (Chapter 2-4), with an ultimate goal of achieving a seamless cross-scale model from the Gulf Stream to the shallow regions in the Bay tributaries and sub-tributaries. We highlight the dominant role played by the bathymetry in nearshore systems and the detrimental effects of bathymetric smoothing commonly used in many coastal models (Chapter 3). With the new methods developed in this dissertation and elsewhere, the model has enabled the analyses on some important processes that are hard to quantify with traditional techniques, e.g., the effect of channel-shoal contrast on lateral circulation and salinity distribution, hypoxia volume, the influence of realistic bathymetry on the freshwater plume etc. Potential topics for future research are also discussed at the end. In addition, the new solvers have also been successfully exported to many other oceanic and nearshore systems around the world via user groups of our community modeling system (cf. ‘Publications’ under ‘schism.wiki’)

U.S. Law of the Sea Cruise to Map and Sample the US Arctic Ocean Margin

U.S. Law of the Sea cruise to map and sample the US Arctic Ocean margin CRUISE HEALY 1202 August 25 to September 27, 2012 Barrow, AK to Dutch Harbor, A

Environmental Information: Placing Biodiversity Phenomena in an Ecological and Environmental Context

Environmental models are increasingly being used as surrogates to determine plant and animal species’ distributions for a range of uses. This use of models has become an important part of the recent science that has become known as biodiversity informatics. Because of the nature of species data, considerable effort has often been spent in managing the quality of those species data, but less time has generally been spent on determining the quality and efficacy of the environmental data against which the species data are being modeled. This paper examines a range of environmental data being used in species distribution modeling, and looks at how they are prepared, their quality and use, and some of the commonly encountered pitfalls and problems in using these data in species’ distribution modeling

Development and Extrapolation of a General Light Use Efficiency Model for the Gross Primary Production

The global carbon cycle is one of the large biogeochemical cycles spanning all living and non-living compartments of the Earth system. Against the background of accelerating global change, the scientific community is highly interested in analyzing and understanding the dynamics of the global carbon cycle and its complex feedback mechanism with the terrestrial biosphere. The international network FLUXNET was established to serve this aim with measurement towers around the globe. The overarching objective of this thesis is to exploit the powerful combination of carbon flux measurements and satellite remote sensing in order to develop a simple but robust model for the gross primary production (GPP) of vegetation stands. Measurement data from FLUXNET sites as well as remote sensing data from the NASA sensor MODIS are exploited in a data-based model development approach. The well-established concept of light use efficiency is chosen as modeling framework. As a result, a novel gross primary production model is established to quantify the carbon uptake of forests and grasslands across a broad range of climate zones. Furthermore, an extrapolation scheme is derived, with which the model parameters calibrated at FLUXNET sites can be regionalized to pave the way for spatially continuous model applications

Phenology-based land cover classification using Landsat 8 time series

This article describes the methodology and results of a new JRC phenology-based classification algorithm able to generate accurate land cover maps in a fully automatic manner from Landsat 8 (L8) remote sensed data available since 12th April 2013 at no charge throughout the USGS website. A preliminary study aiming to bypass the single date classification inaccuracy (mainly due to seasonality) using long term MODIS time series as a “driver” to fill gaps between high resolution data, has been carried out. The high global acquisition frequency (~16 days) and distribution policy are making Landsat 8 product extremely suitable for near real time land cover mapping and monitoring. Five national parks in east Africa have been selected as study areas (Mahale Mountains, Mana Pools, West Lunga, Gorongosa, Tsimanampetsotsa); they are covering diverse eco-regions and vegetation types, from evergreen to deciduous. A buffer of 20 km around each park has been considered as well. Selected single date images were first preprocessed in order to convert raw DN values to top of atmosphere (TOA) reflectance and minimizes spectral differences caused by different acquisition time, sun elevation, sun-earth distance, and after processed by the algorithm to generate a thematic raster map with land cover classes. Is worth noting that the single date classification accuracy is closely related to the acquisition date of the image, the status of the vegetation and weather conditions such as cloud and shadows often present in tropical regions; here the need of developing a phenology based algorithm that considers the vegetation evolution and generates a more accurate land cover map including evergreen and deciduous discrimination on the basis of “frequency” rules. Land cover maps have been created for all parks and an exhaustive accuracy assessment has been carried out on Mahale Mountains and Tsimanampetsotsa. The combined overall accuracy of 82.8% demonstrates the high potentiality of this method and makes it usable at either local or regional scale.JRC.H.3-Forest Resources and Climat

Modelling global pyrogeography using data derived from satellite imagery

Doutoramento em Engenharia Florestal e dos Recursos Naturais - Instituto Superior de Agronomia - ULVegetation burning has an important impact on the global atmosphere and vegetated land surface. Deforestation fires, peatland fires, and ecosystems with shortening fire return interval contribute substantially to the build-up of atmospheric greenhouse gases affecting environmental quality and the climate system at local and regional scales. Recognition of the role of fire in the Earth system led to its designation as an Essential Climate Variable (ECV), a physical, chemical, or biological variable that has a crucial contribution towards characterization of Earth’s climate. The central task of this thesis was the development of a new global classification and map of fire regimes, using multiple correspondence analysis and hierarchical clustering, and relying on active fire data from the Moderate Resolution Imaging Spectroradiometer (MODIS) MCD14ML product. That work was preceded by study dedicated to a thorough screening and exploratory spatial analysis of the dataset, and led to the development of an improved algorithm for identifying individual active fire clusters, and to global analysis of size inequality in their statistical distributions. In addition to this core research, other continental-global pyrogeography studies were developed, and are presented, dealing with: the time lag between the timing of optimal fire weather conditions and peak fire season dates as a diagnostic of anthropogenic vegetation burning; the spatial non-stationarity in the parameters of the relationship between population density and area burned; and the modulation of weekly cycles of vegetation burning in African croplands by regionally dominant religious affiliation. We hope that this set of studies may constitute a useful contribution to the burgeoning topic of global pyrogeograph

Leaf Area Index (LAI) monitoring at global scale (improved definition, continuity and consistency of LAI estimates from kilometric satellite observations)

Le suivi des variables biophysiques à l échelle globale sur de longues périodes de temps est essentiellepour répondre aux nouveaux enjeux que constituent le changement climatique et la sécurité alimentaire. L indice foliaire (LAI) est une variable de structure définissant la surface d interception du rayonnement incident et d échanges gazeux avec l atmosphère. Le LAI est donc une variable importante des modèles d écosystèmes et a d ailleurs été reconnue comme variable climatique essentielle (ECV). Cette thèse a pour objectif de fournir des estimations globales et continues de LAI à partir d observations satellitaires en temps quasi-réel en réponse aux besoins des utilisateurs pour fournir des diagnostiques et pronostiques de l état et du fonctionnement de la végétation. Quelques produits LAI sont déjà disponibles mais montrent des désaccords et des limitations en termes de cohérence et de continuité. Cette thèse a pour objectif de lever ces limitations. Dans un premier temps, on essaiera de mieux définir la nature des estimations de LAI à partir d observations satellitaires. Puis, différentes méthodes de lissage te bouchage des séries temporelles ont été analysées pour réduire le bruit et les discontinuités principalement liées à la couverture nuageuse. Finalement quelques méthodes d estimation temps quasi réel ont été évaluées en considérant le niveau de bruit et les données manquantes.Les résultats obtenus dans la première partie de cette thèse montrent que la LAI effectif et bien mieux estimé que la valeur réelle de LAI du fait de l agrégation des feuilles observée au niveau du couvert. L utilisation d observations multidirectionnelles n améliore que marginalement les performances d estimation. L étude montre également que les performances d estimation optimales sont obtenues quand les solutions sont recherchées à l intérieur d une enveloppe définie par l incertitude associée aux mesures radiométriques. Dans la deuxième partie consacrée à l amélioration de la continuité et la cohérence des séries temporelles, les méthodes basées sur une fenêtre temporelle locale mais de largeur dépendant du nombre d observations présentes, et utilisant la climatologie comme information a priori s avèrent les plus intéressantes autorisant également l estimation en temps quasi réel.Monitoring biophysical variables at a global scale over long time periods is vital to address the climatechange and food security challenges. Leaf Area Index (LAI) is a structure variable giving a measure of the canopysurface for radiation interception and canopy-atmosphere interactions. LAI is an important variable in manyecosystem models and it has been recognized as an Essential Climate Variable. This thesis aims to provide globaland continuous estimates of LAI from satellite observations in near-real time according to user requirements to beused for diagnostic and prognostic evaluations of vegetation state and functioning. There are already someavailable LAI products which show however some important discrepancies in terms of magnitude and somelimitations in terms of continuity and consistency. This thesis addresses these important issues. First, the nature ofthe LAI estimated from these satellite observations was investigated to address the existing differences in thedefinition of products. Then, different temporal smoothing and gap filling methods were analyzed to reduce noiseand discontinuities in the time series mainly due to cloud cover. Finally, different methods for near real timeestimation of LAI were evaluated. Such comparison assessment as a function of the level of noise and gaps werelacking for LAI.Results achieved within the first part of the thesis show that the effective LAI is more accurately retrievedfrom satellite data than the actual LAI due to leaf clumping in the canopies. Further, the study has demonstratedthat multi-view observations provide only marginal improvements on LAI retrieval. The study also found that foroptimal retrievals the size of the uncertainty envelope over a set of possible solutions to be approximately equal tothat in the reflectance measurements. The results achieved in the second part of the thesis found the method withlocally adaptive temporal window, depending on amount of available observations and Climatology as backgroundestimation to be more robust to noise and missing data for smoothing, gap-filling and near real time estimationswith satellite time series.AVIGNON-Bib. numérique (840079901) / SudocSudocFranceF