Observing & Modeling: VIMS Journal Articles

The following list is based on a search of VIMS-authored research articles from Thomson Reuters' Web of Science© using the title search term model* and the keyword search terms AUV, glider, ROV, or simulation. The list is updated at least biannually.

  1. Zhang, Y.J., et al., 2015. A new vertical coordinate system for a 3D unstructured-grid model. Ocean Modelling, 85: p. 16-31. http://doi.org/10.1016/j.ocemod.2014.10.003
  2. Zhang, X.Z., et al., 2015. Modeling larval connectivity of the Atlantic surfclams within the Middle Atlantic Bight: Model development, larval dispersal and metapopulation connectivity. Estuarine Coastal and Shelf Science, 153: p. 38-53. http://doi.org/10.1016/j.ecss.2014.11.033
  3. Shen, X.T. and J.P.Y. Maa, 2015. Modeling floc size distribution of suspended cohesive sediments using quadrature method of moments. Marine Geology, 359: p. 106-119. http://doi.org/10.1016/j.margeo.2014.11.014
  4. Xiao, Y.J. and M.A.M. Friedrichs, 2014. The assimilation of satellite-derived data into a one-dimensional lower trophic level marine ecosystem model. Journal of Geophysical Research-Oceans, 119(4): p. 2691-2712. http://doi.org/10.1002/2013jc009433
  5. Xiao, Y. and M.A.M. Friedrichs, 2014. Using biogeochemical data assimilation to assess the relative skill of multiple ecosystem models in the Mid-Atlantic Bight: effects of increasing the complexity of the planktonic food web. Biogeosciences, 11(11): p. 3015-3030. http://doi.org/10.5194/bg-11-3015-2014
  6. Walters, D., et al., 2014. Interactions between barrier islands and backbarrier marshes affect island system response to sea level rise: Insights from a coupled model. Journal of Geophysical Research-Earth Surface, 119(9): p. 2013-2031. http://doi.org/10.1002/2014jf003091
  7. Thanassekos, S., M.J. Cox, and K. Reid, 2014. Investigating the Effect of Recruitment Variability on Length-Based Recruitment Indices for Antarctic Krill Using an Individual-Based Population Dynamics Model. Plos One, 9(12). http://doi.org/10.1371/journal.pone.0114378
  8. Sagarese, S.R., et al., 2014. Application of generalized additive models to examine ontogenetic and seasonal distributions of spiny dogfish (Squalus acanthias) in the Northeast (US) shelf large marine ecosystem. Canadian Journal of Fisheries and Aquatic Sciences, 71(6): p. 847-877. http://doi.org/10.1139/cjfas-2013-0342
  9. Priest, G.R., et al., 2014. Tsunami impact to Washington and northern Oregon from segment ruptures on the southern Cascadia subduction zone. Natural Hazards, 72(2): p. 849-870. http://doi.org/10.1007/s11069-014-1041-7
  10. Kaufman, D.E., et al., 2014. Biogeochemical variability in the southern Ross Sea as observed by a glider deployment. Deep-Sea Research Part I-Oceanographic Research Papers, 92: p. 93-106. http://doi.org/10.1016/j.dsr.2014.06.011
  11. Jarvis, J.C., M.J. Brush, and K.A. Moore, 2014. Modeling loss and recovery of Zostera marina beds in the Chesapeake Bay: The role of seedlings and seed-bank viability. Aquatic Botany, 113: p. 32-45. http://doi.org/10.1016/j.aquabot.2013.10.010
  12. Hine, P.M., et al., 2014. Ultrastructural comparison of Bonamia spp. (Haplosporidia) infecting ostreid oysters. Diseases of Aquatic Organisms, 110(1-2): p. 55-63. http://doi.org/10.3354/dao02747
  13. Heywood, K.J., et al., 2014. Ocean processes at the Antarctic continental slope. Philosophical Transactions of the Royal Society a-Mathematical Physical and Engineering Sciences, 372(2019). http://doi.org/10.1098/rsta.2013.0047
  14. Glaser, S.M., H. Ye, and G. Sugihara, 2014. A nonlinear, low data requirement model for producing spatially explicit fishery forecasts. Fisheries Oceanography, 23(1): p. 45-53. http://doi.org/10.1111/fog.12042
  15. Dean, R.G., et al., 2014. Sediment Diversions on the Lower Mississippi River: Insight from Simple Analytical Models. Journal of Coastal Research, 30(1): p. 13-29. http://doi.org/10.2112/Jcoastres-D-12-00252.1
  16. Corbett, D.R., et al., 2014. Formation and preservation of sedimentary strata from coastal events: Insights from measurements and modeling. Continental Shelf Research, 86: p. 1-5. http://doi.org/10.1016/j.csr.2014.06.011
  17. Bever, A.J. and C.K. Harris, 2014. Storm and fair-weather driven sediment-transport within Poverty Bay, New Zealand, evaluated using coupled numerical models. Continental Shelf Research, 86: p. 34-51. http://doi.org/10.1016/j.csr.2013.07.012
  18. Bertin, X., et al., 2014. A modeling-based analysis of the flooding associated with Xynthia, central Bay of Biscay. Coastal Engineering, 94: p. 80-89. http://doi.org/10.1016/j.coastaleng.2014.08.013
  19. Azevedo, A., et al., 2014. A cross-scale numerical modeling system for management support of oil spill accidents. Marine Pollution Bulletin, 80(1-2): p. 132-147. http://doi.org/10.1016/j.marpolbul.2014.01.028
  20. Xu, X., et al., 2013. Diagnostics to assess toxicokinetic-toxicodynamic models with interval-censored data. Environmetrics, 24(5): p. 332-341. http://doi.org/10.1002/Env.2216
  21. Wang, J.C. and M.C. Newman, 2013. Projected Hg dietary exposure of 3 bird species nesting on a contaminated floodplain (South River, Virginia, USA). Integrated Environmental Assessment and Management, 9(2): p. 285-293. http://doi.org/10.1002/ieam.1366
  22. van Maanen, B., G. Coco, et al. 2013. Modeling the morphodynamic response of tidal embayments to sea-level rise. Ocean Dynamics 63(11-12): 1249-1262. doi 10.1007/S10236-013-0649-6
  23. Sturdivant, S. K., M. J. Brush, et al. 2013. Modeling the Effect of Hypoxia on Macrobenthos Production in the Lower Rappahannock River, Chesapeake Bay, USA. PLOS One 8(12). ARTN e84140 doi 10.1371/journal.pone.0084140
  24. Klein, N. J., A. J. Beck, et al. 2013. Regression modeling of the North East Atlantic Spring Bloom suggests previously unrecognized biological roles for V and Mo. Frontiers in Microbiology 4. Artn 45 doi 10.3389/Fmicb.2013.00045
  25. Zhang, X. Z., D. Haidvogel, et al. 2012. Coupled Physical and Biological Modeling of Atlantic Surfclam Larval Transport and Sub-Population Connectivity in the Middle Atlantic Bight and Georges Bank. Journal of Shellfish Research 31(1): 363-363.
  26. Wan, Y. S., Z. G. Ji, et al. 2012. Three dimensional water quality modeling of a shallow subtropical estuary. Marine Environmental Research 82: 76-86. doi 10.1016/J.Marenvres.2012.09.007
  27. Shen, J., B. Hong, et al. 2012. Modeling of polychlorinated biphenyls (PCBs) in the Baltimore Harbor. Ecological Modelling 242: 54-68. doi 10.1016/J.Ecolmodel.2012.05.025
  28. Rice, K. C., B. Hong, et al. 2012. Assessment of salinity intrusion in the James and Chickahominy Rivers as a result of simulated sea-level rise in Chesapeake Bay, East Coast, USA. Journal of Environmental Management 111: 61-69. doi 10.1016/J.Jenvman.2012.06.036
  29. Pinto, L., A. B. Fortunato, et al. 2012. Development and validation of a three-dimensional morphodynamic modelling system for non-cohesive sediments. Ocean Modelling 57-58: 1-14. doi 10.1016/J.Ocemod.2012.08.005
  30. Li, C. G., J. P. Y. Maa, et al. 2012. Solving generalized lattice Boltzmann model for 3-D cavity flows using CUDA-GPU. Science China-Physics Mechanics & Astronomy 55(10): 1894-1904. doi 10.1007/S11433-012-4856-9
  31. Kirillin, G., H. P. Grossart, et al. 2012. Modeling sinking rate of zooplankton carcasses: Effects of stratification and mixing. Limnology and Oceanography 57(3): 881-894. doi 10.4319/Lo.2012.57.3.0881
  32. Cho, K. H., H. V. Wang, et al. 2012. A modeling study on the response of Chesapeake Bay to hurricane events of Floyd and Isabel. Ocean Modelling 49-50: 22-46. Doi 10.1016/J.Ocemod.2012.02.005
  33. Saba, V. S., M. A. M. Friedrichs, et al. 2011. An evaluation of ocean color model estimates of marine primary productivity in coastal and pelagic regions across the globe. Biogeosciences 8(2): 489-503. 10.5194/bg-8-489-2011
  34. Hofmann, E. E., B. Cahill, et al. 2011. Modeling the Dynamics of Continental Shelf Carbon. Annual Review of Marine Science, Vol 3 3: 93-122. 10.1146/annurev-marine-120709-142740
  35. Tom, K. R., M. C. Newman, et al. 2010. Modeling Mercury Biomagnification (South River, Virginia, USA) to Inform River Management Decision Making. Environmental Toxicology and Chemistry 29(4): 1013-1020. Doi 10.1002/Etc.117
  36. Saba, V. S., M. A. M. Friedrichs, et al. 2010. Challenges of modeling depth-integrated marine primary productivity over multiple decades: A case study at BATS and HOT. Global Biogeochemical Cycles 24: -. Artn Gb3020
  37. Doi 10.1029/2009gb003655
  38. Luo, Y. W., M. A. M. Friedrichs, et al. 2010. Oceanic heterotrophic bacterial nutrition by semilabile DOM as revealed by data assimilative modeling. Aquatic Microbial Ecology 60(3): 273-U143. Doi 10.3354/Ame01427
  39. Hong, B., N. Panday, et al. 2010. Modeling water exchange between Baltimore Harbor and Chesapeake Bay using artificial tracers: Seasonal variations. Marine Environmental Research 70(1): 102-119. Doi 10.1016/J.Marenvres.2010.03.010
  40. Druon, J. N., A. Mannino, et al. 2010. Modeling the dynamics and export of dissolved organic matter in the Northeastern US continental shelf. Estuarine Coastal and Shelf Science 88(4): 488-507. Doi 10.1016/J.Ecss.2010.05.010
  41. Brush, M. J. and S. W. Nixon 2010. Modeling the role of macroalgae in a shallow sub-estuary of Narragansett Bay, RI (USA). Ecological Modelling 221(7): 1065-1079. Doi 10.1016/J.Ecolmodel.2009.11.002
  42. Brush, M. J. and L. A. Harris 2010. Introduction to the special issue of Ecological Modelling: "Advances in Modeling Estuarine and Coastal Ecosystems: Approaches, Validation, and Applications" Preface. Ecological Modelling 221(7): 965-968. Doi 10.1016/J.Ecolmodel.2010.01.001
  43. Shen, J. and W. P. Gong 2009. Influence of model domain size, wind directions and Ekman transport on storm surge development inside the Chesapeake Bay: A case study of extratropical cyclone Ernesto, 2006. Journal of Marine Systems 75(1-2): 198-215. Doi 10.1016/J.Jmarsys.2008.09.001
  44. Bever, A. J., C. K. Harris, et al. 2009. Deposition and flux of sediment from the Po River, Italy: An idealized and wintertime numerical modeling study. Marine Geology 260(1-4): 69-80. Doi 10.1016/J.Margeo.2009.01.007
  45. Warner, J. C., C. R. Sherwood, et al. 2008. Development of a three-dimensional, regional, coupled wave, current, and sediment-transport model. Computers & Geosciences 34(10): 1284-1306. Doi 10.1016/J.Cageo.2008.02.012
  46. Ihde, T. F., J. M. Hoenig, et al. 2008. An Index-Removal Abundance Estimator That Allows for Seasonal Change in Catchability, with Application to Southern Rock Lobster Jasus edwardsii. Transactions of the American Fisheries Society 137(3): 720-735.
  47. Park, J.-Y. and J. T. Wells 2007. Spit Growth and Downdrift Erosion: Results of Longshore Transport Modeling and Morphologic Analysis at the Cape Lookout Cuspate Foreland. Journal of Coastal Research 23(3): 553-568.
  48. McAnally, W. H., A. Teeter, et al. 2007. Management of fluid mud in estuaries, bays, and lakes. II: Measurement, modeling, and management. Journal of Hydraulic Engineering-ASCE 133(1): 23-38.
  49. Ji, Z. G., G. D. Hu, et al. 2007. Three-dimensional modeling of hydrodynamic processes in the St. Lucie Estuary. Estuarine Coastal and Shelf Science 73(1-2): 188-200.
  50. Friedrichs, C. T. and M. E. Scully 2007. Modeling deposition by wave-supported gravity flows on the Po River prodelta: From seasonal floods to prograding clinoforms. Continental Shelf Research 27(3-4): 322-337.
  51. Shen, J. and J. Lin 2006. Modeling study of the influences of tide and stratification on age of water in the tidal James River. Estuarine Coastal and Shelf Science 68(1-2): 101-112.
  52. Shen, J., J. J. Jia, et al. 2006. Inverse estimation of nonpoint sources of fecal coliform for establishing allowable load for Wye River, Maryland. Water Research 40(18): 3333-3342.
  53. Shen, J., W. Gong, et al. 2006. Water level response to 1999 Hurricane Floyd in the Chesapeake Bay. Continental Shelf Research 26(19): 2484-2502.
  54. Doney, S. C. and H. W. Ducklow 2006. A decade of synthesis and modeling in the US Joint Global Ocean Flux Study. Deep-Sea Research Part Ii-Topical Studies in Oceanography 53(5-7): 451-458.
  55. Harris, C. K., P. A. Traykovski, et al. 2005. Flood dispersal and deposition by near-bed gravitational sediment flows and oceanographic transport: A numerical modeling study of the Eel River shelf, northern California. Journal of Geophysical Research-Oceans 110(C9): -.
  56. Maa, J. P. Y., C. H. Hobbs, et al. 2004. Potential impacts of sand mining offshore of Maryland and Delaware: Part I - Impacts on physical oceanographic processes. Journal of Coastal Research 20(1): 44-60.
  57. Scully, M. E., C. T. Friedrichs, et al. 2003. Numerical modeling of gravity-driven sediment transport and deposition on an energetic continental shelf: Eel River, northern California. Journal of Geophysical Research-Oceans 108(C4): -.
  58. Latour, R. J., M. J. Brush, et al. 2003. Toward ecosystem-based fisheries management: Strategies for multispecies modeling and associated data requirements. Fisheries 28(9): 10-22.
  59. Brylawski, B. J. and T. J. Miller 2003. Bioenergetic modeling of the blue crab (Callinectes sapidus) using the fish bioenergetics (3.0) computer program. Bulletin of Marine Science 72(2): 491-504.
  60. Sin, Y. and R. L. Wetzel 2002. Ecosystem modeling analysis of size-structured phytoplankton dynamics in the York River estuary, Virginia (USA). II. Use of a plankton ecosystem model for investigating controlling factors on phytoplankton and nutrient dynamics. Marine Ecology-Progress Series 228: 91-101.
  61. Sin, Y. and R. L. Wetzel 2002. Ecosystem modeling analysis of size-structured phytoplankton dynamics in the York River estuary, Virginia (USA). I. Development of a plankton ecosystem model with explicit feedback controls and hydrodynamics. Marine Ecology-Progress Series 228: 75-90.
  62. Oguz, T., H. W. Ducklow, et al. 2001. Modeling the response of top-down control exerted by gelatinous carnivores on the Black Sea pelagic food web. Journal of Geophysical Research-Oceans 106(C3): 4543-4564.
  63. Maa, J. P. Y. 2001. Discussion on the article "Numerical modeling of flow characteristics in a rotating annular flume" by  Yang, Z.,  Baptista, A.,  Darland, J. [Dyn. Atmos. Oceans 31 (2000) 271-294]. Dynamics of Atmospheres and Oceans 33(4): 321-323.
  64. Liu, W. C., M. H. Hsu, et al. 2001. A modeling study of water quality in main channel and estuarine wetland. Journal of Environmental Science and Health Part a-Toxic/Hazardous Substances & Environmental Engineering 36(5): 641-660.
  65. Koeve, W. and H. W. Ducklow 2001. JGOFS synthesis and modeling: The North Atlantic Ocean. Deep-Sea Research Part Ii-Topical Studies in Oceanography 48(10): 2141-2154.
  66. Buonaccorsi, V. P., J. R. McDowell, et al. 2001. Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans). Molecular Ecology 10(5): 1179-1196.
  67. Best, E. P. H., C. P. Buzzelli, et al. 2001. Modeling submersed macrophyte growth in relation to underwater light climate: modeling approaches and application potential. Hydrobiologia 444(1-3): 43-70.
  68. Oguz, T., H. W. Ducklow, et al. 2000. Modeling distinct vertical biogeochemical structure of the Black Sea: Dynamical coupling of the oxic, suboxic, and anoxic layers. Global Biogeochemical Cycles 14(4): 1331-1352.
  69. Shen, J., J. D. Boon, et al. 1999. A modeling study of a tidal intrusion front and its impact on larval dispersion in the James River estuary, Virginia. Estuaries 22(3A): 681-692.
  70. Mitra, S. and R. M. Dickhut 1999. Three-phase modeling of polycyclic aromatic hydrocarbon association with pore-water-dissolved organic carbon. Environmental Toxicology and Chemistry 18(6): 1144-1148.
  71. Hsu, M. H., A. Y. Kuo, et al. 1999. Water quality modeling of the Tanshui estuarine system in northern Taiwan. Journal of Environmental Science and Health Part a-Toxic/Hazardous Substances & Environmental Engineering 34(7): 1415-1453.
  72. Ip, J. T. C., D. R. Lynch, et al. 1998. Simulation of estuarine flooding and dewatering with application to Great Bay, New Hampshire. Estuarine Coastal and Shelf Science 47(2): 119-141.
  73. Hsu, M. H., A. Y. Kuo, et al. 1998. Modeling estuarine hydrodynamics and salinity for wetland restoration. Journal of Environmental Science and Health Part a-Toxic/Hazardous Substances & Environmental Engineering 33(5): 891-921.
  74. Kuo, A. Y. and K. Park 1995. A Framework for Coupling Shoals and Shallow Embayments with Main Channels in Numerical Modeling of Coastal-Plain Estuaries. Estuaries 18(2): 341-350.
  75. Wetzel, R. L. 1994. Modeling the Microbial Loop - an Estuarine Modelers Perspective. Microbial Ecology 28(2): 331-334.
  76. Sharples, J., J. H. Simpson, et al. 1994. Observations and Modeling of Periodic Stratification in the Upper York River Estuary, Virginia. Estuarine Coastal and Shelf Science 38(3): 301-312.
  77. Kjerfve, B., H. E. Seim, et al. 1992. Modeling of the Residual Circulation in Broken Bay and the Lower-Hawkesbury River, Nsw. Australian Journal of Marine and Freshwater Research 43(6): 1339-1357.
  78. Evans, D. A. and R. J. Huggett 1991. Statistical Modeling of Intensive Tbt Monitoring Data in 2 Tidal Creeks of the Chesapeake Bay. Marine Environmental Research 32(1-4): 169-186.
  79. Kator, H. I., P. V. Hyer, et al. 1983. A Combined Field-Numerical Modeling Approach for Prediction of Fecal Coliform Densities with Respect to a Representative Marine Buffer Zone. Estuaries 6(3): 269-270.