Variational inverse methods for transport problems

Variational inverse data assimilation schemes are developed for three types of parameter identification problems in transport models: (1) the tracer inverse for the Lagrangian mean transport velocity in a long-term advection-diffusion transport model; (2) determination of inflow salinity open boundary condition in an intra-tidal salinity transport model; and (3) determination of settling velocity and resuspension rate for a cohesive sediment transport model. The gradient of the cost function with respect to the control variables is obtained by the adjoint model. A series of twin experiments are conducted to test the inverse models for the three types of problems. Results show that variational data assimilation can successfully retrieve poorly known parameters in transport models. The first problem is associated with the long-term advective transport, represented by the Lagrangian mean transport velocity which can be decomposed into two parts: the Eulerian transport velocity and the curl of a 3-D vector potential A. The optimal long-term advective transport field is obtained through adjusting the vector potential using a variational data assimilation method. Experiments are performed in an idealized estuary. Results show that the variational data assimilation method can successfully retrieve the effective Lagrangian mean transport velocity in a long-term transport model. Results also show that the smooth best fit model state can still be retrieved using a penalty method when observations are too sparse or contain noisy signals. A variational inverse model for optimally determining open boundary condition is developed and tested in a 3-D intra-tidal salinity transport model. The maximum inflow salinity open boundary value and its recovery time from outflow condition are treated as control variables. Effects of scaling, preconditioning, and penalty are investigated. It is shown that proper scaling and preconditioning can greatly speed up the convergence rate of the minimization process. The spatial oscillations in the recovery time of the inflow boundary condition can be effectively eliminated by an penalty technique. A variational inverse model is developed to estimate the settling velocity and resuspension constant. The settling velocity &w\sb{lcub}s{rcub}& and resuspension constant &M\sb{lcub}o{rcub}& are assumed to be constant in the whole model domain. The inverse model is tested in an idealized 3-D estuary and the James River, a tributary of the Chesapeake Bay. Experimental results demonstrate that the variational inverse model can be used to identify the poorly known parameters in cohesive sediment transport modeling

Characterizing Tidal Stream Energy Resource in the Salish Sea

The Salish Sea has been identified as one of the top hotspots in the US for tidal stream energy development because of the presence of strong tidal currents in many tidal channels. To characterize the tidal stream energy resource, high-resolution and accurate current data are required. This presentation describes the development of a high-resolution tidal hydrodynamic model to support tidal stream energy development in the Salish Sea. The numerical model was based on the Finite Volume Community Ocean Model using the unstructured-grid framework. The model was validated using data derived from 10 real-time tidal gauges and 132 historical ADCP stations. A total of 16 tidal channels with strong currents were identified as hotspots for potential tidal energy development in the Salish Sea. Probability distributions and exceedance of the cross-channel average velocity were calculated at all 16 channels based on international standards for tidal energy resource characterization. The tidal energy resource at the 16 hotspots was also characterized using power density distributions and kinetic energy fluxes. The ranking of the kinetic energy fluxes suggested that Admiralty Inlet, Rosario Strait, and Middle Channel are the top three tidal energy hotspots in the Salish Sea. Because of the model covers the entire Salish Sea with extensive model validation, results from this modeling effort can also be used to support other estuarine applications such as effect of sea level rise, climate change and coastal community resilience

Mapping Waves and Storm Surge for Coastal Resilience in the Salish Sea

Pacific Northwest coasts are exposed to coastal inundation as a result of storm surge and large waves induced by extreme weather events. Accurate coastal risk projections depend on detailed and accurate information on sea level rise, including waves and storm surge under extreme weather events. This paper presents a modeling study simulating the wave climate and storm surge distribution in the Salish Sea. The Salish Sea wave model is configured with the SWAN model, driven by spectral open boundary conditions from the nested regional WaveWatch3 models and sea surface winds from a 6-km resolution Weather Research and Forecasting simulation. A series of historical storm surge events were identified for model simulations based on observed water levels at a number of NOAA tide gauges. Model simulations corresponding to selected storm surge events were conducted. Sensitivity analysis on the effect of local wind forcing was conducted. Both wave and storm surge models were validated with observed data at NOAA buoys and tide gauges. Wave climate and storm surge height in the major basins of the Salish Sea are analyzed. The maximum wave height and storm surge magnitude are mapped in the Salish Sea and areas exposed to large waves and high storm surge are identified based on model results. Results how that surge is remarkably uniform across Puget Sound, with the exception of a few locations, such as Sinclair Inlet, Liberty Bay and Oakland Bay that experience above-average surge because of the unique geometries of the bays. Waves in the Strait of Juan de Fuca are dominated by long swells, which dissipate significantly as propagating into Puget Sound. waves in Puget Sound are small and primarily contributed by wind-sea; peak periods are generally less than 5 s and maximum significant wave heights are less than 2.0 m

Special issue:Wave and tidal resource characterization

The papers that were initially presented in the Marine Renewable Energy: Resource Characterization, Environmental Impacts, and Societal Interactions session at the 2016 AGU/ASLO/TOS Ocean Sciences Meeting in New Orleans, USA, on 2/21-26/2016, are highlighted.The wave and tidal resource of Scotland, a nation that has been instrumental in the progress of the industry due to its energetic resource, and the foundation of the European Marine Energy Centre that has become a template for other test centers throughout the world, are discussed. Country-scale wave and tidal resource assessments from two contrasting continents, the Uruguayan shelf seas and within the context of post-Fukushima, Japan, are considered. A number of tidal stream resource assessments, discussing the tidal resource of the Bosphorus, Puget Sound, the Massachusetts coast, Rathlin Sound in Northern Ireland, and the famous Pentland Firth is provided

A review of tidal energy - Resource, feedbacks, and environmental interactions

International audienceThe ocean contains a variety of renewable energy resources, little of which has been exploited. Here, we review both tidal range and tidal stream energy, with a focus on the resource, feedbacks, and environmental interactions. The review covers a wide range of timescales of relevance to tidal energy, from fortnightly (spring-neap) and semi-diurnal variability, down to array, and device-scale turbulence. When simulating the regional tidal energy resource, and to assess environmental impacts, it is necessary to account for feedbacks between the tidal array and the resource itself. We critically review various methods for simulating energy extraction, from insights gained through theoretical studies of “tidal fences” in idealized channels, to realistic three-dimensional model studies with complex geometry and arrays of turbines represented by momentum sinks and additional turbulence due to the presence of rotors and support structures. We discuss how variability can be reduced by developing multiple (aggregated) sites with a consideration of the enhanced phase diversity offered by exploiting less energetic tidal currents. This leads to future research questions that have not yet been explored in depth at first-generation tidal sites in relatively sheltered channels (e.g., the interaction of waves with currents). Such enhanced understanding of real sea conditions, including the effects of wind and waves, leads to our other identified primary future research direction—reduced uncertainties in turbulence predictions, including the development of realistic models that simulate the interaction between ambient turbulence and the turbulence resulting from multiple wakes, and changes to system-wide hydrodynamics, water quality, and sedimentation

A modeling study of storm surge in the Salish Sea

The Pacific Northwest coasts are subject to the threat of coastal inundation as a result of storm surge. This snapshot presentation provides an overview of a modeling study of storm surge in the Salish Sea using a high resolution coastal hydrodynamic model. A series of historical storm surge events were identified based on non-tidal residual (NTR) water levels observed at Seattle tide gage. Model simulations corresponding to selected storm surge events were conducted. The Salish Sea storm surge model was validated with both observed tidal and NTR data at NOAA tide gauges in the Salish Sea. Sensitivity analysis on the effects of wind forcing and the open boundary conditions are investigated. Model results indicated that storm surge within Salish Sea is dominated by the open boundary conditions at the entrance of the Strait of Juan de Fuca and wind forcing plays a secondary role. Distributions of storm surge heights corresponding to the sub-basins of Salish Sea are analyzed. The result is a map showing coastal areas at higher risk of storm surge versus those that are less exposed. Note: this submission is for oral snapshot presentation

Plasmodium vivax populations revisited: mitochondrial genomes of temperate strains in Asia suggest ancient population expansion

<p>Abstract</p> <p>Background</p> <p><it>Plasmodium vivax </it>is the most widely distributed human malaria parasite outside of Africa, and its range extends well into the temperate zones. Previous studies provided evidence for vivax population differentiation, but temperate vivax parasites were not well represented in these analyses. Here we address this deficit by using complete mitochondrial (mt) genome sequences to elucidate the broad genetic diversity and population structure of <it>P. vivax </it>from temperate regions in East and Southeast Asia.</p> <p>Results</p> <p>From the complete mtDNA sequences of 99 clinical samples collected in China, Myanmar and Korea, a total of 30 different haplotypes were identified from 26 polymorphic sites. Significant differentiation between different East and Southeast Asian parasite populations was observed except for the comparison between populations from Korea and southern China. Haplotype patterns and structure diversity analysis showed coexistence of two different groups in East Asia, which were genetically related to the Southeast Asian population and Myanmar population, respectively. The demographic history of <it>P. vivax</it>, examined using neutrality tests and mismatch distribution analyses, revealed population expansion events across the entire <it>P. vivax </it>range and the Myanmar population. Bayesian skyline analysis further supported the occurrence of ancient <it>P. vivax </it>population expansion.</p> <p>Conclusions</p> <p>This study provided further resolution of the population structure and evolution of <it>P. vivax</it>, especially in temperate/warm-temperate endemic areas of Asia. The results revealed divergence of the <it>P. vivax </it>populations in temperate regions of China and Korea from other populations. Multiple analyses confirmed ancient population expansion of this parasite. The extensive genetic diversity of the <it>P. vivax </it>populations is consistent with phenotypic plasticity of the parasites, which has implications for malaria control.</p

Modeling water exchange and transport timescales in a multi-inlet bay system of Puget Sound, Washington

In this study, an integrated modeling framework consisting of the watershed model HSPF and the hydrodynamic model FVCOM is used to simulate the watershed hydrology and hydrodynamic circulations in a multi-inlet bay system of Puget Sound, which includes Liberty Bay, Port Orchard Bay, Dyes Inlet, and Sinclair Inlet. These interconnected inlets and bays form a unique subsystem that is connected to the Central Basin of Puget Sound through two narrow passages, namely Agate Passage and Rich Passage. Due to residential and industrial development in the watershed, degraded water quality has been observed in the system and manifests as bacteria contamination, low dissolved oxygen and harmful algal blooms. All these water quality issues require a good understanding of the pollutant sources from the watershed and the transport pathways in the receiving waters, and thus call for an integrated modeling approach based on watershed, hydrodynamic and water quality models. In this presentation, the high-resolution FVCOM model is used to simulate the general hydrodynamic circulation in the subsystem and quantify its physical transport timescales (e.g., residence time) with both neutral-buoyance tracers and Lagrangian particles under various hydrological conditions simulated by the HSPF model. The results demonstrate that hydrodynamic circulation plays an important role in explaining some of the water quality issues in the system. The transport timescales under various hydrological conditions provide useful indicators on how physical processes modulate pollutant transport and water quality in the subsystem

FOXO3a (Forkhead Transcription Factor O Subfamily Member 3a) Links Vascular Smooth Muscle Cell Apoptosis, Matrix Breakdown, Atherosclerosis, and Vascular Remodeling Through a Novel Pathway Involving MMP13 (Matrix Metalloproteinase 13).

OBJECTIVE: Vascular smooth muscle cell (VSMC) apoptosis accelerates atherosclerosis and promotes breakdown of the extracellular matrix, but the mechanistic links between these 2 processes are unknown. The forkhead protein FOXO3a (forkhead transcription factor O subfamily member 3a) is activated in human atherosclerosis and induces a range of proapoptotic and other transcriptional targets. We, therefore, determined the mechanisms and consequences of FOXO3a activation in atherosclerosis and arterial remodeling after injury. APPROACH AND RESULTS: Expression of a conditional FOXO3a allele (FOXO3aA3ER) potently induced VSMC apoptosis, expression and activation of MMP13 (matrix metalloproteinase 13), and downregulation of endogenous TIMPs (tissue inhibitors of MMPs). mmp13 and mmp2 were direct FOXO3a transcriptional targets in VSMCs. Activation of endogenous FOXO3a also induced MMP13, extracellular matrix degradation, and apoptosis, and MMP13-specific inhibitors and fibronectin reduced FOXO3a-mediated apoptosis. FOXO3a activation in mice with VSMC-restricted FOXO3aA3ER induced MMP13 expression and activity and medial VSMC apoptosis. FOXO3a activation in FOXO3aA3ER/ApoE-/- (apolipoprotein E deficient) mice increased atherosclerosis, increased necrotic core and reduced fibrous cap areas, and induced features of medial degeneration. After carotid artery ligation, FOXO3a activation increased VSMC apoptosis, VSMC proliferation, and neointima formation, all of which were reduced by MMP13 inhibition. CONCLUSIONS: FOXO3a activation induces VSMC apoptosis and extracellular matrix breakdown, in part, because of transcriptional activation of MMP13. FOXO3a activation promotes atherosclerosis and medial degeneration and increases neointima after injury that is partly dependent on MMP13. FOXO3a-induced MMP activation represents a direct mechanistic link between VSMC apoptosis and matrix breakdown in vascular disease