Collaboration tools and techniques for large model datasets

Author Posting. © The Author(s), 2007. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Journal of Marine Systems 69 (2008): 154-161, doi:10.1016/j.jmarsys.2007.02.013.In MREA and many other marine applications, it is common to have multiple models running with different grids, run by different institutions. Techniques and tools are described for low-bandwidth delivery of data from large multidimensional data sets, such as those from meteorological and oceanographic models, directly into generic analysis and visualization tools. Output is stored using the NetCDF CF Metadata Conventions, and then delivered to collaborators over the web via OPeNDAP. OPeNDAP datasets served by different institutions are then organized via THREDDS catalogs. Tools and procedures are then used which enable scientists to explore data on the original model grids using tools they are familiar with. It is also low-bandwidth, enabling users to extract just the data they require, an important feature for access from ship or remote areas. The entire implementation is simple enough to be handled by modelers working with their webmasters – no advanced programming support is necessary.S. Carniel was partially supported by the Office of Naval Research (ONR grant number N00014-05-1-0730). I. Janekovic was supported by the Croatian Ministry of Science, Education and Sport (grant number 0098113)

Accurate Charge-Dependent Nucleon-Nucleon Potential at Fourth Order of Chiral Perturbation Theory

We present the first nucleon-nucleon potential at next-to-next-to-next-to-leading order (fourth order) of chiral perturbation theory. Charge-dependence is included up to next-to-leading order of the isospin-violation scheme. The accuracy for the reproduction of the NN data below 290 MeV lab. energy is comparable to the one of phenomenological high-precision potentials. Since NN potentials of order three and less are known to be deficient in quantitative terms, the present work shows that the fourth order is necessary and sufficient for a reliable NN potential derived from chiral effective Lagrangians. The new potential provides a promising starting point for exact few-body calculations and microscopic nuclear structure theory (including chiral many-body forces derived on the same footing).Comment: 4 pages Revtex including one figur

Near-bottom circulation and dispersion of sediment containing Alexandrium fundyense cysts in the Gulf of Maine during 2010–2011

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 96–111, doi:10.1016/j.dsr2.2013.11.003.The life cycle of Alexandrium fundyense in the Gulf of Maine includes a dormant cyst stage that spends the winter predominantly in the bottom sediment. Wave-current bottom stress caused by storms and tides induces resuspension of cyst-containing sediment during winter and spring. Resuspended sediment could be transported by water flow to different locations in the Gulf and the redistribution of sediment containing A. fundyense cysts could alter the spatial and temporal manifestation of its spring bloom. The present study evaluates model near-bottom flow during storms, when sediment resuspension and redistribution are most likely to occur, between October and May when A. fundyense cells are predominantly in cyst form. Simulated water column sediment (mud) concentrations from representative locations of the Gulf are used to initialize particle tracking simulations for the period October 2010–May 2011. Particles are tracked in full three-dimensional model solutions including a sinking velocity characteristic of cyst and aggregated mud settling (0.1 mm s−1). Although most of the material was redeposited near the source areas, small percentages of total resuspended sediment from some locations in the western (~4%) and eastern (2%) Maine shelf and the Bay of Fundy (1%) traveled distances longer than 100 km before resettling. The redistribution changed seasonally and was sensitive to the prescribed sinking rate. Estimates of the amount of cysts redistributed with the sediment were small compared to the inventory of cysts in the upper few centimeters of sediment but could potentially have more relevance immediately after deposition.Research support to all authors, except DJM and VAS, was provided by U.S. Geological Survey. DJM gratefully acknowledges financial support of the National Oceanic and Atmospheric Administration (Grant NA06NOS4780245 for the Gulf of Maine Toxicity (GOMTOX) program) and the Woods Hole Center for Oceans and Human Health through National Science Foundation Grant OCE-1314642 and National Institute of Environmental Health Sciences Grant 1P01ES021923-01. VAS was supported by the North East Consortium Grant NA05NMF4721057

Investigating the importance of sediment resuspension in Alexandrium fundyense cyst population dynamics in the Gulf of Maine

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 79–95, doi:10.1016/j.dsr2.2013.10.011.Cysts of Alexandrium fundyense, a dinoflagellate that causes toxic algal blooms in the Gulf of Maine, spend the winter as dormant cells in the upper layer of bottom sediment or the bottom nepheloid layer and germinate in spring to initiate new blooms. Erosion measurements were made on sediment cores collected at seven stations in the Gulf of Maine in the autumn of 2011 to explore if resuspension (by waves and currents) could change the distribution of over-wintering cysts from patterns observed in the previous autumn; or if resuspension could contribute cysts to the water column during spring when cysts are viable. The mass of sediment eroded from the core surface at 0.4 Pa ranged from 0.05 kg m−2 near Grand Manan Island, to 0.35 kg m−2 in northern Wilkinson Basin. The depth of sediment eroded ranged from about 0.05 mm at a station with sandy sediment at 70 m water depth on the western Maine shelf, to about 1.2 mm in clayey–silt sediment at 250 m water depth in northern Wilkinson Basin. The sediment erodibility measurements were used in a sediment-transport model forced with modeled waves and currents for the period October 1, 2010 to May 31, 2011 to predict resuspension and bed erosion. The simulated spatial distribution and variation of bottom shear stress was controlled by the strength of the semi-diurnal tidal currents, which decrease from east to west along the Maine coast, and oscillatory wave-induced currents, which are strongest in shallow water. Simulations showed occasional sediment resuspension along the central and western Maine coast associated with storms, steady resuspension on the eastern Maine shelf and in the Bay of Fundy associated with tidal currents, no resuspension in northern Wilkinson Basin, and very small resuspension in western Jordan Basin. The sediment response in the model depended primarily on the profile of sediment erodibility, strength and time history of bottom stress, consolidation time scale, and the current in the water column. Based on analysis of wave data from offshore buoys from 1996 to 2012, the number of wave events inducing a bottom shear stress large enough to resuspend sediment at 80 m ranged from 0 to 2 in spring (April and May) and 0 to 10 in winter (October through March). Wave-induced resuspension is unlikely in water greater than about 100 m deep. The observations and model results suggest that a millimeter or so of sediment and associated cysts may be mobilized in both winter and spring, and that the frequency of resuspension will vary interannually. Depending on cyst concentration in the sediment and the vertical distribution in the water column, these events could result in a concentration in the water column of at least 104 cysts m−3. In some years, resuspension events could episodically introduce cysts into the water column in spring, where germination is likely to be facilitated at the time of bloom formation. An assessment of the quantitative effects of cyst resuspension on bloom dynamics in any particular year requires more detailed investigation.Research support to Donald M. Anderson and Bruce A. Keafer provided through the Woods Hole Center for Oceans and Human Health; National Science Foundation Grants OCE-0430724 and OCE-0911031; and National Institute of Environmental Health Sciences Grant 1-P50-ES012742-01; the ECOHAB Grant program through NOAA Grants NA06NOS4780245 and A09NOS4780193; the MERHAB Grant program through NOAA Grant NA11NOS4780025; and the PCMHAB Grant program through NOAA Grant NA11NOS4780023. Research support to all other authors was provided by U.S. Geological Survey

Modelling nucleon-nucleon scattering above 1 GeV

Motivated by the recent measurement of proton-proton spin-correlation parameters up to 2.5 GeV laboratory energy, we investigate models for nucleon-nucleon (NN) scattering above 1 GeV. Signatures for a gradual failure of the traditional meson model with increasing energy can be clearly identified. Since spin effects are large up to tens of GeV, perturbative QCD cannot be invoked to fix the problems. We discuss various theoretical scenarios and come to the conclusion that we do not have a clear phenomenological understanding of the spin-dependence of the NN interaction above 1 GeV.Comment: 36 pages, 8 figure

Chiral two-pion exchange and proton-proton partial-wave analysis

The chiral two-pion exchange component of the long-range pp interaction is studied in an energy-dependent partial-wave analysis. We demonstrate its presence and importance, and determine the chiral parameters c_i (i=1,3,4). The values agree well with those obtained from pion-nucleon amplitudes.Comment: 13 pages, no figure

Introduction to special section on the U.S. IOOS coastal and ocean modeling testbed

Strong and strategic collaborations among experts from academia, federal operational centers, and industry have been forged to create a U.S. IOOS Coastal and Ocean Modeling Testbed (COMT). The COMT mission is to accelerate the transition of scientific and technical advances from the coastal and ocean modeling research community to improved operational ocean products and services. This is achieved via the evaluation of existing technology or the development of new technology depending on the status of technology within the research community. The initial phase of the COMT has addressed three coastal and ocean prediction challenges of great societal importance: estuarine hypoxia, shelf hypoxia, and coastal inundation. A fourth effort concentrated on providing and refining the cyberinfrastructure and cyber tools to support the modeling work and to advance interoperability and community access to the COMT archive. This paper presents an overview of the initiation of the COMT, the findings of each team and a discussion of the role of the COMT in research to operations and its interface with the coastal and ocean modeling community in general. Detailed technical results are presented in the accompanying series of 16 technical papers in this special issue

Sediment dispersal in the northwestern Adriatic Sea

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C11S03, doi:10.1029/2006JC003868.Sediment dispersal in the Adriatic Sea was evaluated using coupled three-dimensional circulation and sediment transport models, representing conditions from autumn 2002 through spring 2003. The calculations accounted for fluvial sources, resuspension by waves and currents, and suspended transport. Sediment fluxes peaked during southwestward Bora wind conditions that produced energetic waves and strengthened the Western Adriatic Coastal Current. Transport along the western Adriatic continental shelf was nearly always to the south, except during brief periods when northward Sirocco winds reduced the coastal current. Much of the modeled fluvial sediment deposition was near river mouths, such as the Po subaqueous delta. Nearly all Po sediment remained in the northern Adriatic. Material from rivers that drain the Apennine Mountains traveled farther before deposition than Po sediment, because it was modeled with a lower settling velocity. Fluvial sediment delivered to areas with high average bed shear stress was more highly dispersed than material delivered to more quiescent areas. Modeled depositional patterns were similar to observed patterns that have developed over longer timescales. Specifically, modeled Po sediment accumulation was thickest near the river mouth with a very thin deposit extending to the northeast, consistent with patterns of modern sediment texture in the northern Adriatic. Sediment resuspended from the bed and delivered by Apennine Rivers was preferentially deposited on the northern side of the Gargano Peninsula, in the location of thick Holocene accumulation. Deposition here was highest during Bora winds when convergences in current velocities and off-shelf flux enhanced delivery of material to the midshelf.The authors are grateful for funding and support from the Office of Naval Research’s Coastal Geosciences and Marine Modeling programs, the U.S. Geological Survey, and NATO’s SACLANT-CEN

Nucleon-Nucleon Interaction: A Typical/Concise Review

Nearly a recent century of work is divided to Nucleon-Nucleon (NN) interaction issue. We review some overall perspectives of NN interaction with a brief discussion about deuteron, general structure and symmetries of NN Lagrangian as well as equations of motion and solutions. Meanwhile, the main NN interaction models, as frameworks to build NN potentials, are reviewed concisely. We try to include and study almost all well-known potentials in a similar way, discuss more on various commonly used plain forms for two-nucleon interaction with an emphasis on the phenomenological and meson-exchange potentials as well as the constituent-quark potentials and new ones based on chiral effective field theory and working in coordinate-space mostly. The potentials are constructed in a way that fit NN scattering data, phase shifts, and are also compared in this way usually. An extra goal of this study is to start comparing various potentials forms in a unified manner. So, we also comment on the advantages and disadvantages of the models and potentials partly with reference to some relevant works and probable future studies.Comment: 85 pages, 5 figures, than the previous v3 edition, minor changes, and typos fixe

Variational analysis of drifter positions and model outputs for the reconstruction of surface currents in the central Adriatic during fall 2002

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C04004, doi:10.1029/2007JC004148.In this paper we present an application of a variational method for the reconstruction of the velocity field in a coastal flow in the central Adriatic Sea, using in situ data from surface drifters and outputs from the ROMS circulation model. The variational approach, previously developed and tested for mesoscale open ocean flows, has been improved and adapted to account for inhomogeneities on boundary current dynamics over complex bathymetry and coastline and for weak Lagrangian persistence in coastal flows. The velocity reconstruction is performed using nine drifter trajectories over 45 d, and a hierarchy of indirect tests is introduced to evaluate the results as the real ocean state is not known. For internal consistency and impact of the analysis, three diagnostics characterizing the particle prediction and transport, in terms of residence times in various zones and export rates from the boundary current toward the interior, show that the reconstruction is quite effective. A qualitative comparison with sea color data from the MODIS satellite images shows that the reconstruction significantly improves the description of the boundary current with respect to the ROMS model first guess, capturing its main features and its exchanges with the interior when sampled by the drifters.Four of the authors are supported by the Office of Naval Research, V.T. and A.G. under grants N00014-05-1-0094 and N00014-05-1-0095, P.M.P. under grant N00014-03-1-0291, and S.C. under grant N00014-05-1-0730. CNR-ISMAR activity was partially supported by P.O.R. ‘‘CAINO’’ (Regione Puglia), VECTOR (Italian MIUR) project, and ECOOP (EU project)