@article{janowitz_kamykowski_liu_2008, title={A three-dimensional wind and behaviorally driven population dynamics model for Karenia brevis}, volume={28}, ISSN={["0278-4343"]}, DOI={10.1016/j.csr.2007.04.016}, abstractNote={The time-dependent three-dimensional distribution of a population of Karenia brevis is explored through the use of an Eulerian model. The model combines a previously developed physiologically based behavioral model of these dinoflagellates with a simple model for a three-dimensional wind driven flow field over a variable-depth continental shelf. The behavioral model is simplified from that used in previous applications and sigma coordinates are utilized in the model. Model results indicate that even for the relatively weak wind driven currents used in our simulation a non-quantized population can develop into two spatially distinct quantized populations in a period as short as 1 day where, for present purposes, a quantized population is one in which all cells are at the same stage of the cell cycle.}, number={1}, journal={CONTINENTAL SHELF RESEARCH}, author={Janowitz, G. S. and Kamykowski, D. and Liu, G.}, year={2008}, month={Jan}, pages={177–188} }
 @article{janowitz_kamykowski_2006, title={Modeled Karenia brevis accumulation in the vicinity of a coastal nutrient front}, volume={314}, ISSN={["0171-8630"]}, DOI={10.3354/meps314049}, abstractNote={The alongshore independent distribution of Karenia brevis, a dominant harmful algal bloom dinoflagellate in the Gulf of Mexico, was investigated in a shelf environment using the Expanded Eulerian physical-biological modeling approach. The physical model included an ocean of variable depth with a frontal region at the 25 m isobath, and moderate upwelling-favorable winds. Nutrients were available from a surface source conceptually associated with outwelling from Florida bays, and from a near bottom offshore source conceptually associated with upwelling or sediment flux. The biological model included physiological rate processes, biochemical quotas, and behavioral responses based on cellular optimization and environmental conditions. The population distribution at the end of a 37 d simulation was examined. It was found that cells accumulated in the vicinity of the nearshore front. This accumulation began as soon as cells arrived near the front from the offshore boundary. Approximately 70 % of the population was concentrated in the vicinity of the front by the end of the simulation. The trapping mechanism was interpreted to be a combination of fluid advection and swimming behavior. Four additional 37 d simulations were performed, where: (1) offshore bottom nutrient source was eliminated, (2) wind stress was doubled, (3) inhibition control on swimming behavior was imposed, and (4) chemotaxis control on swimming behavior was eliminated. Comparison of results from the simulations indicated that chemotaxis can play an important role in frontal accumulation.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Janowitz, Gerald S. and Kamykowski, Daniel}, year={2006}, pages={49–59} }
 @article{burkholder_eggleston_glasgow_brownie_reed_janowitz_posey_melia_kinder_corbett_et al._2004, title={Comparative impacts of two major hurricane seasons on the Neuse River and western Pamlico Sound ecosystems}, volume={101}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0306842101}, abstractNote={Ecosystem-level impacts of two hurricane seasons were compared several years after the storms in the largest lagoonal estuary in the U.S., the Albemarle–Pamlico Estuarine System. A segmented linear regression flow model was developed to compare mass-water transport and nutrient loadings to a major artery, the Neuse River Estuary (NRE), and to estimate mean annual versus storm-related volume delivery to the NRE and Pamlico Sound. Significantly less water volume was delivered by Hurricane Fran (1996), but massive fish kills occurred in association with severe dissolved oxygen deficits and high contaminant loadings (total nitrogen, total phosphorus, suspended solids, and fecal bacteria). The high water volume of the second hurricane season (Hurricanes Dennis, Floyd, and Irene in 1999) delivered generally comparable but more dilute contaminant loads, and no major fish kills were reported. There were no discernable long-term adverse impacts on water quality. Populations of undesirable organisms, such as toxic dinoflagellates, were displaced down-estuary to habitats less conducive for growth. The response of fisheries was species-dependent: there was no apparent impact of the hurricanes on commercial landings of bivalve molluscs or shrimp. In contrast, interacting effects of hurricane floodwaters in 1999 and intensive fishing pressure led to striking reductions in blue crabs. Overall, the data support the premise that, in shallow estuaries frequently disturbed by hurricanes, there can be relatively rapid recovery in water quality and biota, and benefit from the scouring activity of these storms.}, number={25}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Burkholder, J and Eggleston, D and Glasgow, H and Brownie, C and Reed, R and Janowitz, G and Posey, M and Melia, G and Kinder, C and Corbett, R and et al.}, year={2004}, month={Jun}, pages={9291–9296} }
 @article{liu_janowitz_kamykowski_2002, title={Influence of current shear on Gymnodinium breve (Dinophyceae) population dynamics: a numerical study}, volume={231}, ISSN={["0171-8630"]}, DOI={10.3354/meps231047}, abstractNote={A time-dependent, 2-dimensional population dynamics model which incorporates cur- rent shear has been developed based on a time-dependent, 1-dimensional population dynamics model reported in an earlier study. Vertical shear in the horizontal velocity is shown to influence the cross-shelf distribution of a 2-dimensional filament of Gymnodinium breve (Dinophyceae) cells, which alters position in the vertical due to environmentally acclimated diel vertical migration. Three different vertical nitrogen distribution patterns are considered in the simulations: a surface nutrient plume, a bottom nutrient plume, and a uniform concentration in the water column. The simulations demonstrate that G. breve's vertical migratory behavior tends to maintain population coherency despite the tendency of shear in the current to disperse the population, and that the shear can con- tribute to predictable cell cycling within the aggregation. The simulations also show that the vertical distribution pattern of the external nutrient source has significantly influenced the horizontal advec- tion, dispersion and cellular attributes of a G. breve population using the modeled swimming rules.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Liu, G and Janowitz, GS and Kamykowski, D}, year={2002}, pages={47–66} }
 @article{liu_janowitz_kamykowski_2001, title={A biophysical model of population dynamics of the autotrophic dinoflagellate Gymnodinium breve}, volume={210}, ISSN={["0171-8630"]}, DOI={10.3354/meps210101}, abstractNote={A new model of dinoflagellate diel migratory behavior and population dynamics is pre- sented using the Expanded Eulerian Method (Janowitz & Kamykowski 1999, Ecol Model 118:237-247) and adapting the concept of metabolism-influenced swimming orientation (Kamykowski & Yamazaki 1997, Limnol Oceanogr 42:1189-1202; Kamykowski et al. 1998a, in: Anderson et al. (eds) Physiolog- ical ecology of harmful algal blooms, Springer-Verlag, Berlin, p. 581-599; Yamazaki & Kamykowski 2000, Ecol Model 134:59-72). The model is constructed to simulate the observations in a 3 d laboratory mesocosm experiment (Kamykowski et al. 1998b, Mar Ecol Prog Ser 167:105-117; Kamykowski et al. 1998c, J Plankton Res 20:1781-1796) on autotrophic Gymnodinium breve (a red tide dinoflagellate species) under a nutrient-replete condition and in 12 h light:12 h dark cycle. A hypothesis of the accli- mations of the G. breve swimming orientation and speed to the internal biochemical and physiologi- cal state and external environmental conditions is proposed. A hypothesis proposed by Kamykowski et al. (1998b) on G. breve reproduction strategy is tested in the model by considering the 2 daughter cells coming from a parent cell to differ in internal biochemical composition. The model simulations are in good agreement with the observations. Consistent with the observations, the model predicts the surface aggregation of a portion of the population during the light period with decreasing surface aggregation intensity over the 3 d period and approximately uniform vertical distribution of the population through the water column during the dark period as well as the diel convergence and divergence patterns of the mean internal cellular carbon and nitrogen between the surface cells and mid-column cells. As expected, G. breve's internal biochemical and physiological states have a strong influence on its migratory behavior and consequently on its population dynamics. By com- parison to a simulation with a reproduction strategy producing 2 identical daughter cells, it is shown that the reproduction strategy producing 2 daughters different in biochemical composition appears to be the one adopted by all or at least a large portion of the G. breve population in the experiment.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Liu, G and Janowitz, GS and Kamykowski, D}, year={2001}, pages={101–124} }
 @article{liu_janowitz_kamykowski_2001, title={Influence of environmental nutrient conditions on Gymnodinium breve (Dinophyceae) population dynamics: a numerical study}, volume={213}, ISSN={["1616-1599"]}, DOI={10.3354/meps213013}, abstractNote={A model of Gymnodinium breve population dynamics modified from Liu et al. (2001; Mar Ecol Prog Ser 210:101-124) is used to investigate the influence of various nutrient conditions on the population increase of an alongshore population filament of G. breve cells as it moves onshore across a continental shelf. The environmental conditions in the model are derived from measure- ments or theory applicable to bloom development on the west Florida shelf. The simulations indicate that the potential nutrient input patterns here represented by nitrogen sources on the shelf, i.e., off- shore, mid-shelf and coastal upwellings, a Trichodesmium-released surface nitrogen source associ- ated with multi-nutrient ocean fertilization by air-borne dust input, and a coastal surface plume are all eligible to trigger and/or support a G. breve bloom. However, the occurrence, timing, location, duration, and intensity of the bloom are determined by nitrogen concentration, input location, and temporal availability. Some nitrogen support at the offshore initiation stage of population growth may induce earlier bloom development, but without additional nitrogen input in coastal regions, the bloom may not fully develop. As long as the nitrogen is available continuously from offshore through coastal regions, a G. breve population can develop into a fish-killing intensity (1 to 2.5 × 10 5 cells l -1 ) in a month or so from a background concentration of <1000 cells l -1 with a maximum growth rate of ~0.16 doublings d -1 . An explosive growth stage is not present for the total population in the simula- tions in which fish-killing cell concentrations are developed in 30 d. However the illusion of explosive growth may be created by the first appearance of a high G. breve population density at the surface late in bloom development. In some cases, daily averaged surface concentration can increase by a factor of 10 in 2 d and increase from a background level of 500 cells l -1 to bloom levels of 10 4 cells l -1 in 8 d due primarily to surface accumulation resulting from appropriately directed swimming behav- ior. This numerical investigation further demonstrates that the vertical migration of G. breve can play a critical role not only in the efficient utilization of natural resources, but also in the population dis- tribution.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Liu, G and Janowitz, GS and Kamykowski, D}, year={2001}, pages={13–37} }
 @article{janowitz_kamykowski_1999, title={An expanded Eulerian model of phytoplankton environmental response}, volume={118}, ISSN={["0304-3800"]}, DOI={10.1016/S0304-3800(99)00037-X}, abstractNote={An Eulerian approach to modeling plankton physiological responses to environmental factors is developed wherein the time history of cell exposure to two external environmental fields over specified time intervals are utilized as independent variables along with position and time to help characterize the cell population. We seek to find the concentration of cells per unit volume as a function of depth, time, and the time histories of exposure to PAR (photosynthetically active radiation) as it influences internal cellular carbon through phototsynthesis and to nitrate as it influences internal cellular nitrogen through nutrient assimilation. The response under consideration here, vertical swimming, is taken to depend on historical exposure to the external PAR and nitrate fields. The model can be readily extended to other external fields and to more than the one historical time scale here associated with each external field. This type of model joins Lagrangian models as most beneficial when phytoplankton physiology responds to environmental factors in a nonlinear fashion, i.e. when the mean response does not depend on the mean exposure. A simple example is discussed and the impact of wind-driven mixing is explored.}, number={2-3}, journal={ECOLOGICAL MODELLING}, author={Janowitz, GS and Kamykowski, D}, year={1999}, month={Jun}, pages={237–247} }
 @article{driscoll_janowitz_pietrafesa_1998, title={Baroclinically driven estuarine flow: A perturbation approach}, volume={103}, DOI={10.1029/98JC02376}, abstractNote={The residual circulation and density in a shallow estuary of constant depth and width and flowing at high Rayleigh number (Ra) and small internal Froude number (Fr), based on riverine flow (U∞) and the horizontal density variation, are studied. Criteria under which direct tidal effects on the residual flow can be neglected are established. The effects of varying the bottom boundary condition on the velocity field from free slip to no slip are examined using a linear bottom stress boundary condition. The governing equations are nondimensionalized, expanded in a power series in the small parameter, and the zeroth‐ and first‐order equations governing the density field are solved; these solutions yield the zeroth‐ and first‐order results for the velocity field. The equation governing the density field at lowest order is nonlinear and is solved numerically. The results show that for sufficiently large Ra, the mean transport of salt is balanced by baroclinic advection near the mouth and by horizontal turbulent transport farther upstream. For these large Ra the horizontal structure as well as the vertical structure of the flow is strongly affected by the bottom boundary condition with the salinity disturbances determined under the free‐slip condition extending twice as far upstream as the no‐slip results. For smaller Ra, though still large compared to 1, the mean transport is balanced by horizontal mixing throughout the system, and the bottom boundary condition does not affect the horizontal structure. The penetration distance of oceanic waters, with the internal Fr fixed, increases as Ra increases above 24, reaches a maximum upstream penetration distance of Kh/U∞ when Ra reaches 65, and decreases as Ra increases further. The ratio of entrained oceanic waters to riverine inflow is inversely proportional to the internal Fr to the 2/3 power for very large Ra and becomes proportional to Ra as the latter decreases.}, number={C12}, journal={JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS}, author={Driscoll, EA and Janowitz, GS and Pietrafesa, LJ}, year={1998}, month={Nov}, pages={27893–27903} }
 @article{pietrafesa_xie_morrison_janowitz_pelissier_keeter_neuherz_1997, title={Numerical modelling and computer visualization of the storm surge in and around the Croatan-Albemarle-Pamlico Estuary system produced by Hurricane Emily of August 1993}, volume={48}, number={4}, journal={Mausam}, author={Pietrafesa, L. J. and Xie, L. and Morrison, J. and Janowitz, G. S. and Pelissier, J. and Keeter, K. and Neuherz, R. A.}, year={1997}, pages={567–578} }
 @article{stout_janowitz_1997, title={Particle trajectories above sinusoidal terrain}, volume={123}, number={543 pt.A}, journal={Quarterly Journal of the Royal Meteorological Society}, author={Stout, J. E. and Janowitz, G. S.}, year={1997}, pages={1829–1840} }