Physical Sciences and Mathematics Commons^™

Associated Dataset: Modeling The Seasonal Cycle Of Iron And Carbon Fluxes In The Amundsen Sea Polynya, Antarctica, Pierre St-Laurent

Data

This dataset features the results from the numerical simulation described in the associated publication (St-Laurent et al.). The simulation results are in the standard, self-documented NetCDF format (extension .nc); see https://www.unidata.ucar.edu/software/netcdf/ for more information. Files in this format can be manipulated and displayed by a wide range of freely available software. The results from the simulation are divided into monthly files (ocean_avg_0001.nc to ocean_avg_0098.nc). Each file holds 30 days worth of time-averaged daily model fields, from January 2006 to December 2013. The dataset also includes the forcings used in the model calculation (in the same format as above). Detailed information …

Estimating Relative Abundance Of Young-Of-The-Year American Eel, Anguilla Rostrata, In The Virginia Tributaries Of Chesapeake Bay, Spring 2018, Troy D. Tuckey, Mary C. Fabrizio

Reports

American Eel (Anguilla rostrata) is a valuable commercial species along the Atlantic coast of North America from New Brunswick to Florida. In the U.S., harvests have declined, with similar patterns occurring in the Canadian Maritime Provinces (Meister and Flagg 1997). An average of 62% of the annual landings of U.S. commercial harvest since 1993 have come from the Chesapeake Bay (personal communication from the National Marine Fisheries Service, Fisheries Statistics Division, 9 February 2015). In 2013, Virginia commercial landings were approximately 100,298 lbs; since mandatory reporting began in 1993, average annual landings in Virginia have been 193,200 lbs or 19% …

Water Quality In Southern Accomack County Watersheds, Richard A. Snyder, Paige G. Ross

Reports

Expansion of poultry grow out houses in Accomack County, VA has raised concerns for water quality impacts both seaside and bayside where harvesting marine resources and aquaculture operations may be affected. The dust and litter from the poultry houses are potential sources of nitrogen, phosphorous, and fecal contamination to watersheds and receiving waters. Siting regulations, storm water controls, and management of litter storage and handling are designed to limit these impacts, yet no analysis has been implemented to verify the efficacy of these protective measures. This investigation sampled watersheds after a 2 week dry period prior to a storm event …

Modeling The Seasonal Cycle Of Iron And Carbon Fluxes In The Amundsen Sea Polynya, Antarctica, P. St-Laurent, Pl Yager, Rm Sherrell, H. Oliver, Ms Dinniman, Se Stammerjohn

VIMS Articles

The Amundsen Sea Polynya (ASP) is distinguished by having the highest net primary production per unit area in the coastal Antarctic. Recent studies have related this high productivity to the presence of fast-melting ice shelves, but the mechanisms involved are not well understood. In this study we describe the first numerical model of the ASP to represent explicitly the ocean-ice interactions, nitrogen and iron cycles, and the coastal circulation at high resolution. The study focuses on the seasonal cycle of iron and carbon, and the results are broadly consistent with field observations collected during the summer of 2010–2011. The simulated …

Ocean Circulation Causes Strong Variability In The Mid-Atlantic Bight Nitrogen Budget, Marjorie A.M. Friedrichs, Pierre St-Laurent, Yongjin Xiao, Et Al

VIMS Articles

Portions of the ocean adjacent to land masses play a particularly important role in global nutrient cycling; however, strong spatial and temporal variability in these shallow regions of the ocean make it difficult to quantify nitrogen fluxes from observations alone. Here we use a computer simulation to estimate the fluxes and transformations of inorganic and organic nitrogen in Mid-Atlantic U.S. coastal waters. The coastal circulation flows southward providing roughly two thirds of the inorganic nitrogen to this region, with the remaining third entering from rivers and estuaries. Nitrogen transport across the continental slope is highly variable, directed into the system …

Impacts Of Physical Transport On Estuarine Phytoplankton Dynamics And Harmful Algal Blooms, Qubin Qin

Dissertations, Theses, and Masters Projects

The spatial and temporal variability of phytoplankton biomass in estuaries is determined by both local processes and transport processes. Local processes include biological processes (e.g., photosynthesis, respiration/excretion, and grazing) and settling, whereas transport processes include advective and diffusive transports. Transport processes have been demonstrated to regulate phytoplankton dynamics significantly by distributing both phytoplankton and other dissolved and particulate substances (e.g., nutrients, salts, sediments, and chromophoric dissolved organic matter). Yet, these transport properties lack a framework that unifies the pieced description of their various effects, and quantification of their importance under various environmental conditions. This dissertation highlights the role of horizontal …

2019 Wachapreague Station Tide Prediction Calendars, Virginia Institute Of Marine Science

Miscellaneous

No abstract provided.

2019 Hampton Roads Station Tide Prediction Calendars, Virginia Institute Of Marine Science

Miscellaneous

No abstract provided.

2019 Chesapeake Bay Bridge Tunnel Station Tide Prediction Calendars, Virginia Institute Of Marine Science

Miscellaneous

No abstract provided.

2019 Gloucester Point Station Tide Prediction Calendars, Virginia Institute Of Marine Science

Miscellaneous

No abstract provided.

Gis Data: King & Queen County Tidal Marsh Inventory, Marcia Berman, Karinna Nunez, Sharon Killeen, Tamia Rudnicky, Julie G. Bradshaw, Carl Hershner, Evan Hill

Data

The Virginia Institute of Marine Science published the first Tidal marsh Inventories using data collected in the early 1970's. Using high resolution color infra-red imagery from 2009 a new Tidal Marsh Inventory has been developed for the York River Watershed in 2010. Marsh boundaries were generated using heads-up digitizing techniques at a scale of 1:1,000. Each marsh polygon was classified by morphologic type: fringe, extensive, embayed, or marsh island. Marshes were ground-truthed in the field where a community type index was assigned to each marsh based on plant community make-up. Each marsh was also coded with a marsh number which …

King William County, Virginia Shoreline Inventory Data 2019, Marcia Berman, Karinna Nunez, Sharon Killeen, Tamia Rudnicky, Julie Bradshaw, Jessica Hendricks, Carl Hershner, Evan Hill

Data

The 2019 Inventory for King William County was generated using on-screen, digitizing techniques in ArcGIS® -ArcMap v10.4.1 while viewing conditions observed in 2017 imagery from the Virginia Base Mapping Program (VBMP), Google Earth, and Bing high resolution oblique imagery. Five GIS shapefiles are developed. The first describes land use and bank conditions (KingWilliam_lubc_2019). The second portrays the presence of beaches (KingWilliam_beach_2019). The third reports shoreline structures that are described as arcs or lines (e.g. riprap) (KingWilliam_sstru_2019). The fourth shapefile includes all structures that are represented as points (e.g. piers) (KingWilliam_astru_2019). The Tidal Marsh Inventory is included as the fifth file …

Embracing Dynamic Design For Climate-Resilient Living Shorelines, Molly Mitchell, Donna M. Bilkovic

VIMS Articles

As natural marshes are lost to erosion, sea level rise, and human activity, small created marshes, (sometimes with ancillary stabilization structures, and frequently called living shorelines) have gained interest as a replacement habitat; providing both shoreline stabilization and restoration of important ecological functions. These living shorelines enhance ecological function while reducing erosion through the use of marsh plants (Table 1). In all but the lowest energy settings, oyster reefs, low rock structures, or other stabilizing material are frequently used to enhance marsh establishment. Due to their ability to stabilize the shoreline with minimal impact to the ecology, living shorelines are …

Pattern And Scale: Evaluating Generalities In Crab Distributions And Marsh Dynamics From Small Plots To A National Scale, K Wasson, K Raposa, Et Al, David S. Johnson, Scott Lerberg, Et Al

VIMS Articles

The generality of ecological patterns depends inextricably on the scale at which they are examined. We investigated patterns of crab distribution and the relationship between crabs and vegetation in salt marshes at multiple scales. By using consistent monitoring protocols across 15 U.S. National Estuarine Research Reserves, we were able to synthesize patterns from the scale of quadrats to the entire marsh landscape to regional and national scales. Some generalities emerged across marshes from our overall models, and these are useful for informing broad coastal management policy. We found that crab burrow distribution within a marsh could be predicted by marsh …

High-Frequency Co2-System Variability Over The Winter-To-Spring Transition In A Large Coastal Plain Estuary, Elizabeth H. Shadwick, Marjorie A.M. Friedrichs, Raymond G. Najjar, Olivia A. De Meo, Jaclyn R. Friedman, Fei Da, W. G. Reay

VIMS Articles

Understanding the vulnerability of estuarine ecosystems to anthropogenic impacts requires a quantitative assessment of the dynamic drivers of change to the carbonate (CO₂) system. Here we present new high‐frequency pH data from a moored sensor. These data are combined with discrete observations to create continuous time series of total dissolved inorganic carbon (TCO₂), CO₂ partial pressure (pCO₂), and carbonate saturation state. We present two deployments over the winter‐to‐spring transition in the lower York River (where it meets the Chesapeake Bay mainstem) in 2016/2017 and 2017/2018. TCO₂ budgets with daily resolution are constructed, …

Projections Of Atmospheric Nitrogen Deposition To The Chesapeake Bay Watershed, Patrick C. Campbell, Jesse O. Bash, Christopher G. Nolte, Tanya L. Spero, Ellen J. Cooter, Kyle Hinson, Lewis C. Linker

VIMS Articles

Atmospheric deposition is among the largest pathways of nitrogen loading to the Chesapeake Bay Watershed (CBW). The interplay between future climate and emission changes in and around the CBW will likely shift the future nutrient deposition abundance and chemical regime (e.g., oxidized vs. reduced nitrogen). In this work, a Representative Concentration Pathway from the Community Earth System Model is dynamically downscaled using a recently updated Weather Research and Forecasting model that subsequently drives the Community Multiscale Air Quality model coupled to the agroeconomic Environmental Policy Integrated Climate model. The relative impacts of emission and climate changes on atmospheric nutrient deposition …

The Future Of Coastal And Estuarine Modeling: Findings From A Workshop, Oliver B. Fringer, Clint N. Dawson, Ruoying He, David K. Ralston, Yinglong J. Zhang

VIMS Articles

This paper summarizes the findings of a workshop convened in the United States in 2018 to discuss methods in coastal and estuarine modeling and to propose key areas of research and development needed to improve their accuracy and reliability. The focus of this paper is on physical processes, and we provide an overview of the current state-of-the-art based on presentations and discussions at the meeting, which revolved around the four primary themes of parameterizations, numerical methods, in-situ and remote-sensing measurements,and high-performance computing. A primary outcome of the workshop was agreement on the need to reduce subjectivity and improve reproducibility in …

High-Frequency Co2-System Observations From A Moored Sensor In The York River, Elizabeth H. Shadwick, Olivia A. De Meo

Data

These are CO₂-system data from a moored sensor in the York River, a tributary of the Chesapeake Bay. Temperature, salinity and pH were acquired hourly over two deployments lasting several months. Sensor data were then averaged to 24-hour resolution. Data were calibrated with discrete dissolved inorganic carbon (TCO₂) and alkalinity samples analyzed at the Virginia Institute of Marine Science, following standard procedures. The pH sensor data were then combined with salinity data, and a relationship between alkalinity and salinity, to compute the remaining CO₂-system parameters (TCO₂, CO₂ partial pressure (pCO_{2 …}

Seasonal Variability Of The Co2-System Throughout The Chesapeake Bay Mainstem, Jaclyn Rain Friedman

Dissertations, Theses, and Masters Projects

Declining water quality, in addition to hypoxia and eutrophication, may have a significant impact on the seasonality of biogeochemical parameters throughout the mainstem of the Chesapeake Bay. The carbonate (CO2) system in the Chesapeake Bay experiences seasonal and spatial complexities and is influenced by both natural and anthropogenic variability. Although site-specific studies investigating CO2-system variability exist within the Chesapeake Bay, few studies have investigated the seasonality of the CO2-system throughout the entire mainstem. Additionally, recent comprehensive studies investigating over 50 estuaries along the East Coast of the United States suggest that estuarine systems are heterotrophic and act as sources of …

Summer Carbonate Chemistry In The Dalton Polynya, East Antarctica, Mc Arroyo, Eh Shadwick, B Tilbrook

VIMS Articles

The carbonate chemistry in the Dalton Polynya in East Antarctica (115°–123°E) was investigated in summer 2014/2015 using high‐frequency underway measurements of CO2 fugacity (fCO2) and discrete water column measurements of total dissolved inorganic carbon (TCO2) and total alkalinity. Air‐sea CO2 fluxes indicate this region was a weak net source of CO2 to the atmosphere (0.7 ± 0.9 mmol C m−2 day−1) during the period of observation, with the largest degree of surface water supersaturation (ΔfCO2 = +45 μatm) in ice‐covered waters near the Totten Ice Shelf (TIS) as compared to the ice‐free surface waters in the Dalton Polynya. The seasonal …

Alkalinity In Tidal Tributaries Of The Chesapeake Bay, R. G. Najjar, M. Herrmann, S. M. Cintrón Del Valle, Jaclyn R. Friedman, Marjorie A.M. Friedrichs, Et Al

VIMS Articles

Despite the important role of alkalinity in estuarine carbon cycling, the seasonal and decadal variability of alkalinity, particularly within multiple tidal tributaries of the same estuary, is poorly understood. Here we analyze more than 25,000 alkalinity measurements, mostly from the 1980s and 1990s,in the major tidal tributaries of the Chesapeake Bay, a large, coastal‐plain estuary of eastern North America.The long‐term means of alkalinity in tidal‐fresh waters vary by a factor of 6 among seven tidal tributaries,reflecting the alkalinity of nontidal rivers draining to these estuaries. At 25 stations, mostly in the Potomac River Estuary, wefind significant long‐term increasing trends that …

Ocean Change Within Shoreline Communities: From Biomechanics To Behaviour And Beyond, Brian Gaylord, Kristina M. Barclay, Brittany M. Jellison, Laura L. Jurgens, Aaron T. Ninokawa, Emily B. Rivest, Lindsey R. Leighton

VIMS Articles

Humans are changing the physical properties of Earth. In marine systems, elevated carbon dioxide concentrations are driving notable shifts in temperature and seawater chemistry. Here, we consider consequences of such perturbations for organism biomechanics and linkages amongst species within communities.In particular,we examine case examples of altered morphologies and material properties, disrupted consumer–prey behaviours, and the potential for modulated positive (i.e. facilitative) interactions amongst taxa, as incurred through increasing ocean acidity and rising temperatures. We focus on intertidal rocky shores of temperate seas as model systems, acknowledging the longstanding role of these communities in deciphering ecological principles. Our survey illustrates the …

Simulating Storm Surge And Compound Flooding Events With A Creek-To-Ocean Model: Importance Of Baroclinic Effects : Model Files, Fei Ye, Yinglong J. Zhang, Haocheng Yu, Weiling Sun, Saeed Moghimi, Edward Myers, Karinna Nunez, Ruoyin Zhang, Harry V. Wang, Aron Roland, Kevin Martins, Xavier Bertin, Jiabi Du, Zhou Liu

Data

The supplemental material contains the input files for setting up a 3D baroclinic model based on the Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM), supplementing the description of model setup in Ye et al. (2019; associated publication).

The SCHISM version used for the simulation was r5082 in the SCHISM svn repository. A compressed file (setup.tar.gz) is provided, which can be extracted with common zip/unzip software on Unix/Windows/Mac (such as gzip, winzip, 7-zip, etc.). Since the dataset is intended for conducting a SCHISM simulation, readers/users should familiarize themselves with the SCHISM model system first.

The SCHISM manual is at: http://ccrm.vims.edu/schismweb/schism_manual.html; …

A Model Archive For Simulations In A Partially-Mixed Idealized Estuary Using The Coawst System: Model Code And Output, Danielle R.N. Tarpley, Courtney K. Harris, Carl Friedrichs

Data

This dataset includes model input, code and output used in the publication Tarpley et al. (2019, Journal of Marine Science and Engineering), which used a coupled hydrodynamic-sediment transport model to investigate the roles of flocculation, bed consolidation and sediment-induced stratification on changes in fine-grained sediment distribution in an idealized estuarine model. The modeling system used in the development was the Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) framework.

Gpgpu Reliability Analysis: From Applications To Large Scale Systems, Bin Nie

Dissertations, Theses, and Masters Projects

Over the past decade, GPUs have become an integral part of mainstream high-performance computing (HPC) facilities. Since applications running on HPC systems are usually long-running, any error or failure could result in significant loss in scientific productivity and system resources. Even worse, since HPC systems face severe resilience challenges as progressing towards exascale computing, it is imperative to develop a better understanding of the reliability of GPUs. This dissertation fills this gap by providing an understanding of the effects of soft errors on the entire system and on specific applications. To understand system-level reliability, a large-scale study on GPU soft …

Learning Code Transformations Via Neural Machine Translation, Michele Tufano

Dissertations, Theses, and Masters Projects

Source code evolves – inevitably – to remain useful, secure, correct, readable, and efficient. Developers perform software evolution and maintenance activities by transforming existing source code via corrective, adaptive, perfective, and preventive changes. These code changes are usually managed and stored by a variety of tools and infrastructures such as version control, issue trackers, and code review systems. Software Evolution and Maintenance researchers have been mining these code archives in order to distill useful insights on the nature of such developers’ activities. One of the long-lasting goal of Software Engineering research is to better support and automate different types of …

Topics In Proton Structure: Bsm Answers To Its Radius Puzzle And Lattice Subtleties Within Its Momentum Distribution, Michael Chaim Freid

Dissertations, Theses, and Masters Projects

This thesis covers two subjects, briefly outlined below, of hadronic physics. The proton radius puzzle and the muon anomalous magnetic moment discrepancy point to possible signs of lepton-universality violation. We introduce the context and background necessary to understand these two problems. And we analyze two suitable beyond-the-standard-model solutions, one vector-based and one scalar-based, which simultaneously solves both issues. Furthermore, we demonstrate that the parameter space of the respective solutions can be chosen so as to not be completely forbidden by considered experimental constraints. Specifically, we show that certain violations, analyzed by other authors in the context of similar solutions to …

Evolution Of The Genome-Wide Distribution Of Genes And Transposons, Ronald Dutilh Smith

Dissertations, Theses, and Masters Projects

Genomes exhibit a striking amount of complexity across a broad range of scales. This includes variation in the spatial distribution of features such as genes and transposable elements (TEs), which is observed both between species and among individuals in natural and artificial populations. Additionally, all eukaryotes studied to date have had gene duplications occur in their evolutionary history. In this dissertation, we develop a statistical method for analyzing relative changes in the expression of duplicated genes. We show that this method performs better than could otherwise be achieved using traditional methods of differential gene expression analysis. We apply this method …

Scattering A Bose-Einstein Condensate Off A Modulated Barrier, Andrew James Pyle

Dissertations, Theses, and Masters Projects

A quantum pump is a device that transports particles through a circuit with localized time-varying potentials, and without the need for an external applied voltage or chemical potential. Quantum pumping was originally proposed in the context of electron transport in nanowires, but has proven difficult to implement. The ultracold atom approach represents a possible route around the current experimental bottleneck. We present an experiment to study 1D quantum mechanical scattering by an amplitude-modulated barrier. This experiment represents a first step toward implementing a quantum pump for ultracold atoms based on two such barriers modulated out of phase with one another. …

Complex Mixtures: Identifying And Characterizing Secondary Organic Aerosols, Emma Quinn Walhout

Dissertations, Theses, and Masters Projects

Complex organic mixtures in the environment can contain hundreds to thousands of different organic molecules, and their composition and reactivity can have important environmental implications. In addition to gases, the atmosphere is made of a variety of small liquids and solids called aerosols. These aerosols have large impacts on human health, climate, and atmospheric chemical reactions. Here, secondary organic aerosol (SOA) from the ozonolysis of α-pinene is characterized. The atmospheric lifetime of SOA is very uncertain, but recent laboratory and modeling studies have demonstrated that photolysis is potentially an important process for organic mass loss from aerosol particles.1-5 Photolysis modifies …