Physical Sciences and Mathematics Commons^™

Soed Open Course: Seamless Modeling From Creek To Ocean On Unstructured Grids, Y. Joseph Zhang

Miscellaneous

This course explains the basic formulations used in the cross-scale SCHISM model, including the recent new developments. Hands-on tutorials will be conducted to familiarize the trainees with the basic tools useful for the modeling system. Although no formal pre-requisites are expected, trainees with prior UG model experience may find it easier to learn. Upon completion the trainees will have acquired basic knowledge on workflow in typical SCHISM simulations and be able to conduct simulations for cross-scale baroclinic processes as found in geophysical fluid dynamics (GFD)

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Chesterfield County And The Cities Of Colonial Heights, Petersburg, And Richmond, Virginia - Shoreline Inventory Report: Methods And Guidelines, Marcia Berman, Karinna Nunez, Sharon Killeen, Tamia Rudnicky, Julie G. Bradshaw, Karen A. Duhring, Kallie Brown, Jessica Hendricks, David Weiss, Carl Hershner

Reports

The 2017Inventory for Chesterfield County and the Cities of Colonial Heights, Petersburg, and Richmond was generated using on-screen, digitizing techniques in ArcGIS® -ArcMap v10.4.1while viewing conditions observed in Bing high resolution oblique imagery, Google Earth, and2013imagery from the Virginia Base Mapping Program (VBMP).Four GIS shapefiles are developed. The first describes land use and bank conditions (Chesterfield_lubc_2017). The second portrays the presence of beaches (Chesterfield_beaches_2017). The third reports shoreline structures that are described as arcs or lines(e.g. riprap)(Chesterfield_sstru_2017). The final shapefile includes all structures that are represented as points (e.g. piers)(Chesterfield_astru_2017).The metadata file accompanies the shapefiles and defines attribute accuracy, data …

Chesterfield County And The Cities Of Colonial Heights, Petersburg, And Richmond, Virginia - Shoreline Inventory Report: Summary Tables, Marcia Berman, Karinna Nunez, Sharon Killeen, Tamia Rudnicky, Julie Bradshaw, Karen Duhring, Kallie Brown, Jessica Hendricks, David Weiss, Carl Hershner

Reports

The Shoreline Inventory Summary Tables quantify observed conditions based on river systems, such as the combined length of linear features (e.g. shoreline miles surveyed, miles of bulkhead and revetment), the total number of point features (e.g. docks, boathouses, boat ramps) & total acres of polygon features (tidal marshes).

Spotsylvania County, Virginia Shoreline Inventory Report Summary Tables, Marcia Berman, Karinna Nunez, Tamia Rudnicky, Julie Bradshaw, Karen Duhring, Kallie Brown, Jessica Hendricks, David Weiss, Carl Hershner

Reports

The Shoreline Inventory Summary Tables quantify observed conditions based on river systems, such as the combined length of linear features (e.g. shoreline miles surveyed, miles of bulkhead and revetment), the total number of point features (e.g. docks, boathouses, boat ramps) & total acres of polygon features (tidal marshes).

Evaluation Of Striped Bass Stocks In Virginia: Monitoring And Tagging Studies, 2015-2019 Progress Report 1 September 2016 - 31 November 2017, Philip W. Sadler, Lydia M. Goins, John M. Hoenig, Savannah Michaelsen, Maya L. Groner, Robert E. Harris

Reports

This report presents the results of striped bass (Morone saxatilis) tagging and monitoring activities in Virginia during the period 1 September 2016 through 31 August 2017. It includes an assessment of the biological characteristics of striped bass taken from the 2017 spring spawning run and estimates of annual survival and fishing mortality based on annual spring tagging. Also included is an investigation on the potential use of close-kin analyses to determine the size of the spawning stock in the Rappahannock River and an evaluation of mortality rates associated with the bacterial dermal disease mycobacteriosis in relation to water …

Improving Modeled Light Attenuation (Kd) In A Land-Estuarine Ocean Biogeochemical Model For Chesapeake Bay, Jessica Turner, Carl T. Friedrichs, Marjorie A.M. Friedrichs

Presentations

No abstract provided.

Marsh Persistence Under Sea-Level Rise Is Controlled By Multiple, Geologically Variable Stressors, Molly Mitchell, Julie Herman, Donna M. Bilkovic, Carl Hershner

VIMS Articles

Introduction: Marshes contribute to habitat and water quality in estuaries and coastal bays. Their importance to continued ecosystem functioning has led to concerns about their persistence.

Outcomes: Concurrent with sea-level rise, marshes are eroding and appear to be disappearing through ponding in their interior; in addition, in many places, they are being replaced with shoreline stabilization structures. We examined the changes in marsh extent over the past 40 years within a subestuary of Chesapeake Bay, the largest estuary in the United States, to better understand the effects of sea-level rise and human pressure on marsh coverage.

Tetragonal Diiodotetrapyridinedicopper(I): Structure, Luminescence, And Computational Modeling, Andrew W. Kelly, Joseph V. Handy, Aaron D. Nicholas, Et Al., Robert D. Pike

Arts & Sciences Articles

We report on a new crystal modification of (CuIPy2) n (Py = pyridine), a compound first reported by White et al. In contrast to White’s orthorhombic structure, which is comprised of rhomboid iodide-bridged dimers, Cu2I2Py4, our new tetragonal crystal structure in space group P41212 is disordered and can be interpreted as either iodide-bridged dimers or helical chains. To determine the structure type, variable temperature X-ray diffraction and luminescence measurements were carried out. The photoluminescence spectrum shows a distinct cluster-centered transition at high excitation energies which is consistent with the dimer structure. DFT and TD-DFT calculations were performed to explain …

A Brief Guide To Striped Bass Ecology & Management In Chesapeake Bay, Mary C. Fabrizio, Troy D. Tuckey, Susanna Musick

Reports

Chesapeake Bay striped bass support important recreational fisheries along the US Atlantic coast; in the late 1970s, the population of striped bass collapsed as a result of overfishing and poor water quality in rivers used for spawning and rear-ing of young. Informed by stock assessments, strict management regulations were enacted in the mid-1980s and early 1990s; these highly effective regulations resulted in the recovery of the population in 1995. A key to the successful recov-ery of the Atlantic coast striped bass was the wide range of ages of spawning females and the associated differences in spawning behavior among ages. Age …

Tetraquark Operators In Lattice Qcd And Exotic Flavour States In The Charm Sector, Gavin K. C. Cheung, Christopher E. Thomas, Jozef J. Dudek, Robert G. Edwards

Arts & Sciences Articles

We present a general class of operators resembling compact tetraquarks which have a range of colour-flavour-spin structures, transform irreducibly under the symmetries of the lattice and respect other relevant symmetries. These constructions are demonstrated in lattice QCD calculations with light quarks corresponding to m(pi) = 391 MeV. Using the distillation framework, correlation functions involving large bases of meson-meson and tetraquark operators are computed in the isospin-1 hidden-charm and doubly-charmed sectors, and finite-volume spectra are extracted with the variational method. We find the spectra are insensitive to the addition of tetraquark operators to the bases of meson-meson operators. For the first …

Light-Induced Photochemical Changes In Copper(I) Thiocyanate Complexes Decorated With Halopyridines: Optical Memory Manifestation, Aaron D. Nicholas, Brooke M. Otten, Gerardo Ayala, Et Al., Robert D. Pike

Arts & Sciences Articles

We report on the photoluminescence of {CuSCN(3-XPy)2}n crystals (X = Br, Cl; Py = pyridine). Laser excitation at 266 nm for CuSCN(3-BrPy)2 at 78 K results in a decrease in the luminescence intensity with increasing irradiation time. Heating the sample to 298 K and recooling to 78 K results in recovery of the original luminescence intensity, hence manifesting an optical memory effect. Laser irradiation at longer or shorter wavelengths fails to produce a reduction in emission intensity. Interestingly, CuSCN(3-ClPy)2, despite being isomorphic, does not undergo emission intensity changes regardless of laser irradiation wavelength variation. Density functional theory (DFT) and …

Metal Substitution And Solvomorphism In Alkylthiolate-Bridged Zn3 And Hgzn2 Metal Clusters, Madeline R. Hallinger, Alison C. Gerhard, Mikhaila D. Ritz, Et Al., John C. Poutsma, Robert D. Pike

Arts & Sciences Articles

The impact of substituting Hg(II) for Zn(II) in a thiolate-bridged trinuclear cluster with parallels to a metallothionein metal cluster was investigated. A new solvomorph of [Zn(ZnL)2](ClO4)2 (1) (L = N-(2-pyridylmethyl)-N-(2-(ethylthiolato)-amine) and five solvomorphs of a new compound [Hg(ZnL)2](ClO4)2 (2) were characterized by single-crystal X-ray crystallography. The interplay of hydrogen bonding and aromatic-packing interactions in producing lamellar, 2D lamellar, and columnar arrangements of complex cations in the crystalline state is discussed. Both variable temperature proton nuclear magnetic resonance and electrospray ion-mass spectrometry (ESI-MS) suggest that the complex ions of 1 and 2 are the predominant solution species at …

Iodobismuthate(Iii) And Iodobismuthate(Iii)/Iodocuprate(I) Complexes With Organic Ligands, Andrew W. Kelly, Amelia M. Wheaton, Aaron D. Nicholas, Francis H. Barnes, Howard H. Patterson, Robert D. Pike

Arts & Sciences Articles

Iodobismuthate(III) and iodobismuthate(III)/cuprate(I) complexes with chelating and bridging organic ligands are structurally characterized, including the first iodobismuthate(III) metal–organic polymers. BiIII/CuI clusters show ligand binding at copper. Diffuse reflectance spectra show UV/Vis absorptions, and DFT calculations suggest MLCT and metal–halide centered transitions.

Numerical Simulations Of The Biogeochemical Impact Of Atmospheric Nitrogen Deposition On Surface Waters Of The Western North Atlantic, Pierre St-Laurent, Marjorie A.M. Friedrichs

Data

The impacts of atmospheric nitrogen deposition on the chlorophyll and nitrogen dynamics of surface waters in the western North Atlantic (25-45N, 65-80W) were examined with a biogeochemical ocean model forced with a regional atmospheric chemistry model. The model simulations cover the period 2004 to 2008 and are fully described in the following reference: St-Laurent, P., et al., Impacts of atmospheric nitrogen deposition on surface waters of the western North Atlantic mitigated by multiple feedbacks, J. Geophys. Res. Oceans, vol.122, doi:10.1002/2017jc013072.

Living Shoreline Design Guidelines For Shore Protection In Virginia’S Estuarine Environments, C. Scott Hardaway Jr., Donna A. Milligan, Christine A. Wilcox, Karen Duhring

Reports

The Chesapeake Bay has about 10 million people living along its shores (Chesapeake Bay Foundation, 2017) and about 150,000 new people move into the Bay watershed each year. For communities along the shore, the continual shore retreat may be a problem. When land along the shore shows signs of erosion, property owners tend to address it.

In the past, shore stabilization strategies generally were stone revetments or wood bulkheads. Though these strategies are effective at shore stabilization, they can create a disconnect between the upland and the water and typically provide few natural habitats along the shoreline. In the past …

Assessment Of Hydrodynamic And Water Quality Impacts For Channel Deepening In The Thimble Shoals, Norfolk Harbor, And Elizabeth River Channels : Final Report On The “Hydrodynamic Modeling”, Yinglong J. Zhang, Harry V. Wang, Fei Ye, Zhengui Wang

Reports

For over twenty years, the U. S. Army Corps of Engineers (USACE) and the Virginia Port Authority (VPA), representing the Commonwealth Secretary of Transportation, have collaborated on projects key to port development that also preserve the environmental integrity of both Hampton Roads and the Elizabeth River. The USACE and the VPA are working to investigate channel deepening in this region to provide access to a new generation of cargo ships (e.g., Panamax-class). The main goal of this project is to investigate the feasibility for Norfolk Harbor channel deepening in the lower James and Elizabeth Rivers and assess the environmental impact …

Incorporating Sea Level Change Scenarios Into Norfolk Harbor Channels Deepening And Elizabeth River Southern Branch Navigation Improvements Study : Final Report On The “Hydrodynamic Modeling”, Zhuo Liu, Harry V. Wang, Yinglong J. Zhang, Fei Ye

Reports

The Virginia Institute of Marine Science (VIMS) team has applied a 3D unstructured-grid hydrodynamic model SCHISM in the study of the impact of channel dredging on hydrodynamics in the lower Chesapeake Bay project area. This report is a companion report to that of Zhang et al. (2017; doi:10.21220/V5MF0F) and focuses on the impact of channel dredging specifically under the projected future sea-level change (SLC) of 1 meter rise by 2100. This is an average of the high end of semi-empirical, global sea-level rise (SLR) projections adopted by the Virginia Port Authority (VPA) and the Army Corps of Engineers, Norfolk District, …

Incorporation Of Sea Level Change Scenarios Into Norfolk Harbor And Channels Deepening Study & Elizabeth River Southern Branch Navigation Improvements Study : Final Report, Rico Wang, Jian Shen, Mac Sisson

Reports

Previously the VIMS modeling group has studied the impact of channel deepening on the water quality in lower James River, including Norfolk Harbor and Elizabeth River. A study of the response of the water quality to future Sea Level Change (SLC) is required by present USACE guidance (ER 1100-2-8162 and ETL 1100-2-1). ETL 1100-2-1 recommends analyzing the effects of SLC on the projects at three future time periods of post-construction, including 20 years, 50 years, and 100 years. The future change of sea level is mainly caused by the sea level rise (SLR) in this region. This document provides results …

Assessment Of Hydrodynamic And Water Quality Impacts For Channel Deepening In The Thimble Shoals, Norfolk Harbor, And Elizabeth River Channels, Jian Shen, Rico Wang, Mac Sisson

Reports

To investigate the feasibility for Norfolk Harbor channel deepening in the lower James and Elizabeth Rivers, one of the key services of the project is to evaluate the impacts of deepening the Atlantic Ocean Channel to 55 feet (from 50 feet), Thimble Shoal Channel to 55 feet (from 50 feet), Elizabeth River (north of Lambert Point) to 50 feet (from 45 feet) and the Southern Branch (north of the I64 Bridge) to 50/45/45 feet. In general, the shipping channel dredging will result in enhancement of estuarine gravitational circulation, accentuate the tidal and wind wave influence upstream, and affect the ecosystem …

Summary Tables: 2017 Henrico County, Virginia Shoreline Inventory, Marcia Berman, Karinna Nunez, Sharon Kileen, Tamia Rudnicky, Julie G. Bradshaw, Karen Duhring, Kallie Brown, Jessica Hendricks, David Weiss, Carl Hershner

Reports

The Shoreline Inventory Summary Tables quantify observed conditions based on river systems, such as the combined length of linear features (e.g. shoreline miles surveyed, miles of bulkhead and revetment), the total number of point features (e.g. docks, boathouses, boat ramps) & total acres of polygon features (tidal marshes).

Henrico County, Virginia - Shoreline Inventory Report: Methods And Guidelines, Marcia Berman, Karinna Nunez, Sharon Kileen, Tamia Rudnicky, Julie Bradshaw, Karen Duhring, Kallie Brown, Jessica Hendricks, David Weiss, Carl Hershner

Reports

No abstract provided.

Sea Level Rise May Increase Extinction Risk Of A Saltmarsh Ontogenetic Habitat Specialist, David S. Johnson, Bethany L. Williams

VIMS Articles

Specialist species are more vulnerable to environmental change than generalist species. For species with ontogenetic niche shifts, specialization may occur at a particular life stage making those stages more susceptible to environmental change. In the salt marshes in the northeast U.S., accelerated sea level rise is shifting vegetation patterns from flood-intolerant species such as Spartina patens to the flood-tolerant Spartina alterniflora. We tested the potential impact of this change on the coffee bean snail, Melampus bidentatus, a numerically dominant benthic invertebrate with an ontogenetic niche shift. From a survey of eight marshes throughout the northeast U.S., small snails …

First Measurement Of Proton's Charge Form Factor At Very Low Q(2) With Initial State Radiation, M. Mihovilovic, K. Griffioen, Et Al.

Arts & Sciences Articles

We report on a new experimental method based on initial-state radiation (ISR) in e-p scattering, which exploits the radiative tail of the elastic peak to study the properties of electromagnetic processes and to extract the proton charge form factor (G(E)(P)) at extremely small Q(2). The ISR technique was implemented in an experiment at the three-spectrometer facility of the Mainz Microtron (MAMI). This led to a precise validation of radiative corrections far away from elastic line and provided first measurements of G(E)(P) for 0.001 <= Q(2) <= 0.004 (GeV/c)(2). (C) 2017 The Authors. Published by Elsevier B.V.

A Test Bed For Coastal And Ocean Modeling, R. A. Luettich Jr., L. D. Wright, C. R. Nichols, R. Baltes, M. A.M. Friedrichs, Et Al

VIMS Articles

No abstract provided.

A Noncanonical Binding Site In The Evh1 Domain Of Vasodilator-Stimulated Phosphoprotein Regulates Its Interactions With The Proline Rich Region Of Zyxin, Lucila Andrea Acevedo, Alexander I. Greenwood, Linda K. Nicholson

Arts & Sciences Articles

Vasodilator-stimulated phosphoprotein (VASP) is a processive actin polymerase with roles in the control of cell shape and cell migration. Through interaction with the cytoskeletal adaptor protein Zyxin, VASP can localize to damaged stress fibers where it serves to repair and reinforce these structures. VASP localization is mediated by its N-terminal Ena/VASP homology (EVH1) domain, which binds to the (W/F)Px phi P motif (most commonly occurring as FPPPP) found in cytoskeletal proteins such as vinculin, lamellipodin, and Zyxin. Sequentially close clusters of four or five of these motifs frequently occur, as in the proline rich region of Zyxin with four such …

Drifts, Currents, And Power Scrape-Off Width In Solps-Iter Modeling Of Diii-D, E. T. Meier, R. J. Goldston, E. G. Kaveeva, M. A. Makowski, S. Mordijck

Arts & Sciences Articles

The effects of drifts and associated flows and currents on the width of the parallel heat flux channel (lambda(q)) in the tokamak scrape-offlayer (SOL) are analyzed using the SOLPS-ITER 2D fluid transport code. Motivation is supplied by Goldston's heuristic drift (HD) model for lambda(q), which yields the same approximately inverse poloidal magnetic field dependence seen in multi-machine regression. The analysis, focusing on a DIII-D H-mode discharge, reveals HD-like features, including comparable density and temperature fall-off lengths in the SOL, and up-down ion pressure asymmetry that allows net cross-separatrix ion magnetic drift flux to exceed net anomalous ion flux. In experimentally …

Transcriptome Of Neonatal Prebotzinger Complex Neurones In Dbx1 Reporter Mice, John A. Hayes, (…), Ronald D. Smith, Gregory D. Smith, Margaret S. Saha, Christopher A. Del Negro

Arts & Sciences Articles

We sequenced the transcriptome of brainstem interneurons in the specialized respiratory rhythmogenic site dubbed preBotzinger Complex (preBotC) from newborn mice. To distinguish molecular characteristics of the core oscillator we compared preBotC neurons derived from Dbx1-expressing progenitors that are respiratory rhythmogenic to neighbouring non-Dbx1-derived neurons, which support other respiratory and non-respiratory functions. Results in three categories are particularly salient. First, Dbx1 preBotC neurons express kappa-opioid receptors in addition to mu-opioid receptors that heretofore have been associated with opiate respiratory depression, which may have clinical applications. Second, Dbx1 preBotC neurons express the hypoxia-inducible transcription factor Hif1a at levels three-times higher than non-Dbx1 …

Broadband Near-Field Infrared Spectroscopy With A High Temperature Plasma Light Source, D. J. Lahneman, T. J. Huffman, Peng Xu, M. M. Qazilbash

Arts & Sciences Articles

Scattering-type scanning near-field optical microscopy (S-SNOM) has enormous potential as a spectroscopy tool in the infrared spectral range where it can probe phonon resonances and carrier dynamics at the nanometer lengths scales. However, its applicability is limited by the lack of practical and affordable table-top light sources emitting intense broadband infrared radiation in the 100 cm(-1) to 2,500 cm(-1) spectral range. This paper introduces a high temperature plasma light source that is both ultra-broadband and has much more radiant power in the infrared spectral range than conventional, table-top thermal light sources such as the globar. We implement this plasma lamp …

Chesapeake Bay Hypoxia Coastal Ocean Modeling Testbed, M.A.M. Friedrichs, Carl T. Friedrichs, I.D. Irby, A.J. Bever

Presentations

No abstract provided.

Adapt Virginia: A New Web Portal About Climate Change Adaptations (Www.Adaptva.Org), Center For Coastal Resources Management, Virginia Institute Of Marine Science

Reports

Rivers & Coast is a periodic publication of the Center for Coastal Resources Management, Virginia Institute of Marine Science. The goal of Rivers & Coast is to keep readers well informed of current scientific understanding behind key environmental issues related to watershed rivers and coastal ecosystems of the Chesapeake Bay.