@article{lin_li_2011, title={Nutrient Response Modeling in Falls of the Neuse Reservoir}, volume={47}, ISSN={["1432-1009"]}, DOI={10.1007/s00267-011-9617-4}, abstractNote={In order to study system responses of Falls of the Neuse Reservoir (Falls Lake) to varied nutrient loadings, a coupled three-dimensional hydrodynamic and eutrophication model was applied. The model was calibrated using 2005 and 2006 intensive survey data, and validated using 2007 survey data. Compared with historical hydrological records, 2005 and 2007 were considered as dry years and 2006 was recognized as a normal year. Relatively higher nutrient fluxes from the sediment were specified for dry year model simulations. The differences were probably due to longer residence time and hence higher nutrient retention rate during dry years in Falls Lake. During the normal year of 2006, approximately 70% of total nitrogen (TN) and 80% of total phosphorus (TP) were delivered from the tributaries; about 20% (TN and TP) were from the sediment bottom. During the dry years of 2005 and 2007, the amount of TN released from sediment was equivalent to that introduced from the tributaries, indicating the critical role of nutrient recycling within the system in dry years. The model results also suggest that both nitrogen and phosphorus are limiting phytoplankton growth in Falls Lake. In the upper part of the lake where high turbidity was observed, nitrogen limitation appeared to dominate. Scenario model runs also suggest that great nutrient loading reductions are needed for Falls Lake to meet the water quality standard.}, number={3}, journal={ENVIRONMENTAL MANAGEMENT}, author={Lin, Jing and Li, Jie}, year={2011}, month={Mar}, pages={398–409} }
 @article{wang_xu_lin_hu_2008, title={Anticyclonic Eddies in the Northeastern South China Sea during Winter 2003/2004}, volume={64}, ISSN={["1573-868X"]}, DOI={10.1007/s10872-008-0076-3}, number={6}, journal={JOURNAL OF OCEANOGRAPHY}, author={Wang, Dongxiao and Xu, Hongzhou and Lin, Jing and Hu, Jianyu}, year={2008}, month={Dec}, pages={925–935} }
 @article{lin_xu_cudaback_wang_2008, title={Inter-annual variability of hypoxic conditions in a shallow estuary}, volume={73}, ISSN={["1879-1573"]}, DOI={10.1016/j.jmarsys.2007.10.011}, abstractNote={Water quality data from two monitoring programs in the Pamlico River Estuary (PRE) were analyzed for dissolved oxygen (DO), salinity, temperature, and nutrient concentrations. Data were collected bi-weekly at 8 stations from 1997 to 2003 by East Carolina University and continuously at three stations from 1999 to 2003 by the U.S. Geological Survey. Hypoxic conditions were observed mostly in the upper to middle estuary, but the frequency of hypoxic events varied between years. During June to October in 1997–1999 (referred to as the oxic summers) bottom water hypoxia (DO < 2 mg l− 1) was found in 8.7% of the observations. By contrast, during June to October in 2001–2003 (referred to as the hypoxic summers), 37.9% of the total measurements had DO concentrations less than 2 mg l− 1. The more frequent and/or prolonged hypoxic conditions during the hypoxic summers were closely associated with stronger salinity stratification and greater loadings of nutrient and particulate matter. Salinity stratification appeared to be governed by patterns of freshwater discharge, and frequency of wind mixing events. The "oxic" summers were characterized by continuous low freshwater inflow (except one extremely high flow event due to hurricanes), stronger northeastward wind, and more frequent wind mixing events. In contrast, the hypoxic summers were characterized by frequent moderate freshwater inflow events, and fewer wind mixing events. The greater loadings of nutrient (nitrate, ammonium, and phosphate) and particulate matter during the hypoxic summers were primarily due to higher river discharges. At the head of the PRE, no significant differences were found in concentrations of nutrient and particulate nitrogen between the oxic and the hypoxic summers. In addition, chlorophyll a concentrations were averaged above 30 μg l− 1 (maximum 167 μg l− 1) during the hypoxic summers, significantly higher than those during the oxic summers (averaged around 15 μg l− 1).}, number={1-2}, journal={JOURNAL OF MARINE SYSTEMS}, author={Lin, Jing and Xu, Hongzhou and Cudaback, Cynthia and Wang, Dongxiao}, year={2008}, month={Sep}, pages={169–184} }
 @article{xu_lin_wang_2008, title={Numerical study on salinity stratification in the Pamlico River Estuary}, volume={80}, ISSN={["1096-0015"]}, DOI={10.1016/j.ecss.2008.07.014}, abstractNote={The variations of current circulation, salt intrusion, and vertical stratification under different river flow and wind conditions in the Pamlico River Estuary (PRE) were investigated in this paper using a three-dimensional numerical model. The model was calibrated and verified against water level variation, temperature, and salinity variations during 2003 and 2001, respectively. Eight sensitivity tests were conducted with different river flow and wind conditions specified in the model. Model results show that salinity intruded further upstream under scenarios with low flow, downriver local wind, and remote-wind-caused water level set-up conditions. In contrast, the responses of salinity stratification to different environmental forcing functions were different in different portions of the estuary. Salinity stratification was enhanced under high flow condition at the lower part of the estuary, under upriver wind near the river mouth, under downriver wind at the upstream to middle portion of the estuary, and under remote-wind-caused water level set-up condition at the majority of the estuary except near the river mouth. Model results also show that across-channel wind tended to reduce salt intrusion and salinity stratification in the PRE through increased vertical mixing.}, number={1}, journal={ESTUARINE COASTAL AND SHELF SCIENCE}, author={Xu, Hongzhou and Lin, Jing and Wang, Dongxiao}, year={2008}, month={Oct}, pages={74–84} }
 @article{lin_tournas_burch_monteiro-riviere_zielinski_2008, title={Topical isoflavones provide effective photoprotection to skin}, volume={24}, ISSN={["1600-0781"]}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000254054600002&KeyUID=WOS:000254054600002}, DOI={10.1111/j.1600-0781.2008.00329.x}, abstractNote={Summary}, number={2}, journal={PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE}, author={Lin, Jing-Yi and Tournas, Joshua A. and Burch, James A. and Monteiro-Riviere, Nancy A. and Zielinski, Jan}, year={2008}, month={Apr}, pages={61–66} }
 @article{lin_xie_pietrafesa_xu_woods_mallin_durako_2008, title={Water quality responses to simulated flow and nutrient reductions in the Cape Fear River Estuary and adjacent coastal region, North Carolina}, volume={212}, ISSN={["1872-7026"]}, DOI={10.1016/j.ecolmodel.2007.10.026}, abstractNote={In order to examine system responses to high river discharge events and nutrient loading variations from the drainage basin, a coupled three-dimensional hydrodynamic and water quality model was applied in the Cape Fear River Estuary (CFRE) and its adjacent coastal region. An empirical equation was introduced in the model to represent light limitation for phytoplankton growth due to chromophoric dissolved organic matter (CDOM). Model results show that in the upper to middle estuary, light limitation controls phytoplankton growth while in the lower estuary phytoplankton growth appears to be limited by light intensity during high flow periods, but by nutrient availability during low flow periods. In the coastal ocean, nutrient availability is usually the dominant limiting factor for primary production. Two sensitivity model tests were conducted to predict the system response to reductions in nutrient loading from the drainage basin. By reducing river discharge, the model results show that phytoplankton growth was enhanced within CFRE due to alleviated light limitation and increased residence time. More nutrients were consumed within the CFRE, and less were exported to the coastal region. By reducing nutrient concentrations at the head of the estuary, chlorophyll a concentrations within the CFRE were decreased. Less nutrients were consumed within the CFRE, and only slightly less were exported to the coastal region. The supply of light limiting substances during high flow events acted against the effect of riverine nutrient enhancement on phytoplankton growth, creating a negative feedback mechanism.}, number={3-4}, journal={ECOLOGICAL MODELLING}, author={Lin, Jing and Xie, Lian and Pietrafesa, Leonard J. and Xu, Honqzhou and Woods, Wendy and Mallin, Michael A. and Durako, Michael J.}, year={2008}, month={Apr}, pages={200–217} }
 @article{xu_lin_shen_wang_2008, title={Wind impact on pollutant transport in a shallow estuary}, volume={27}, number={3}, journal={Acta Oceanologica Sinica}, author={Xu, H. Z. and Lin, J. and Shen, J. and Wang, D. X.}, year={2008}, pages={147–160} }
 @article{zhang_lin_2007, title={Dynamics of Jovian atmospheres with applications of nonlinear singular vector method}, volume={55}, ISSN={["0271-2091"]}, DOI={10.1002/fld.1471}, abstractNote={Abstract}, number={8}, journal={INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS}, author={Zhang, Zhiyue and Lin, Jing}, year={2007}, month={Nov}, pages={713–721} }
 @article{lin_xie_pietrafesa_ramus_paerl_2007, title={Water quality gradients across Albemarle-Pamlico estuarine system: Seasonal variations and model applications}, volume={23}, ISSN={["1551-5036"]}, DOI={10.2112/05-0507.1}, abstractNote={Abstract The seasonal variations of water quality parameters as nitrite plus nitrate (NO−;x), total phosphate (PO3−4), chlorophyll a (chl a), and dissolved oxygen (DO) are analyzed across the Croatan-Roanoke-Albemarle-Pamlico-Core Sounds estuarine system (CAPES). Overall, several patterns are observed: The Chowan-Roanoke-Albemarle system is generally phosphorous limiting for phytoplankton growth, whereas both the Tar-Pamlico and the Neuse Rivers are generally nitrogen limiting. The largest PO3−4 gradients exist in the upstream portion of the Albemarle Sound, and the largest NO−x gradients exist in the lower Neuse and the Tar-Pamlico Rivers. Dissolved oxygen appears to have the strongest seasonal signal among the water quality variables, with highest DO values observed during winter (within the CAPES and in the nearshore area) or spring (in the continental shelf and deeper ocean) and lowest during summer. Chlorophyll a concentrations are highest during spring (within the CAPES) or winter (offshore). In contrast, the NOx− and PO3−4 concentrations in both the Tar-Pamlico and Neuse River estuaries are usually higher during the second half of the year. The time differences of the peak nutrient and chl a concentrations suggest that highest algal growth rate (and hence nutrient uptake rate) occurs during spring, and the consumed nutrients are released to the water column through a nutrient recycling method later in the year. A coupled three-dimensional hydrodynamic water quality model is then applied to the entire system. The general model setup and parameter derivation of the model is presented here. The basic observed water quality characteristics such as the nutrient limiting pattern and the spatial gradients across the system are reproduced in the model. The model results also suggest that nutrient fluxes, generated from the diagenesis of deposited organic matter and released from the sediment bed, could be an important mechanism for nutrient recycling in the region.}, number={1}, journal={JOURNAL OF COASTAL RESEARCH}, author={Lin, Jing and Xie, Lian and Pietrafesa, Leonard J. and Ramus, Joseph S. and Paerl, Hans W.}, year={2007}, month={Jan}, pages={213–229} }
 @article{lin_xie_pietrafesa_shen_mallin_durako_2006, title={Dissolved oxygen stratification in two micro-tidal partially-mixed estuaries}, volume={70}, ISSN={["1096-0015"]}, DOI={10.1016/j.ecss.2006.06.032}, abstractNote={The controlling physical factors for vertical oxygen stratification in micro-tidal, partially-mixed estuaries are discussed in this paper. A theoretical deduction shows that vertical stratification of dissolved oxygen (DO) concentration can be explained by the extended Hansen and Rattray's Central Region theory, which suggests that in addition to biological factors such as photosynthesis, biochemical oxygen demand (BOD), sediment oxygen demand (SOD), vertical DO profiles are mainly controlled by physical factors such as surface re-aeration, river flow, and estuarine gravitational circulation. Vertical mixing of DO from surface re-aeration and photosynthesis sets a DO profile of higher concentration near the surface and lower near the bottom. With a positive seaward longitudinal DO gradient, strong river flow and estuarine gravitational circulation can cause lower DO concentrations near the surface and higher near the bottom. The actual vertical oxygen profile is then determined by the relative magnitude of the above-mentioned mechanisms. It is sensitive to two parameters: (1) the strength of the gravitational circulation (uE); and (2) the relative importance between biochemical oxygen demand and vertical diffusivity (α). Vertical DO stratification usually becomes weaker as uE increases. The impact of gravitational circulation on vertical oxygen distribution becomes more important for a larger α. The impact of α on oxygen stratification is profound. As uE (and river flow) increases, DO stratification appears to be less sensitive to the value of α. Surface-to-bottom differences in DO concentrations (ΔDO) is negligible when α is small (α < 0.5). As α increases, ΔDO increases under a weak to moderate gravitational circulation mode (uE ≤ 5 cm s−1). Under a strong gravitational circulation mode, ΔDO becomes negative with a small α (α < 2), and as α continues to increase, ΔDO becomes positive. The newly-deduced governing equation for vertical oxygen stratification is applied to two micro-tidal, partially-mixed estuarine systems: the Cape Fear River Estuary (CFRE) and the Pamlico River Estuary (PRE) of North Carolina. In the CFRE, although strong vertical salinity stratification exists, DO concentrations are usually well mixed. De-coupling between salinity stratification and oxygen stratification is mainly due to a relatively stronger estuarine gravitational circulation and higher freshwater inflow in the system. It appears that river flow and gravitational circulation are the dominant factors in controlling oxygen stratification in the CFRE. In contrast, vertical stratification of DO concentrations is closely correlated with that of salinity in the PRE. In the PRE, the estuarine gravitational mode and river flow are often both very weak, and DO stratification is very sensitive to the value of α. With negligible influence from tidal mixing, the system is more sensitive to vertical mixing regulated by salinity stratification and wind. As a result, vertical DO stratification is closely correlated with salinity stratification in the PRE.}, number={3}, journal={ESTUARINE COASTAL AND SHELF SCIENCE}, author={Lin, Jing and Xie, Lian and Pietrafesa, Len J. and Shen, Jian and Mallin, Michael A. and Durako, Michael J.}, year={2006}, month={Nov}, pages={423–437} }
 @article{shen_lin_2006, title={Modeling study of the influences of tide and stratification on age of water in the tidal James River}, volume={68}, DOI={10.1016/j.eccs.2006.01.014}, number={1-2}, journal={Estuarine, Coastal and Shelf Science}, author={Shen, J. and Lin, J.}, year={2006}, pages={101–112} }
 @article{kuo_park_kim_lin_2005, title={A tidal prism water quality model for small coastal basins}, volume={33}, ISSN={["1521-0421"]}, DOI={10.1080/08920750590883015}, abstractNote={Abstract A tidal prism water quality model (TPWQM) was developed to provide a tool for government agencies for water quality management of small coastal basins. It simulates physical transport using the concept of tidal flushing, includes one of the most sophisticated representations of eutrophication processes in water column and benthic sediment, and employs an innovative solution scheme that is simple, accurate, and computationally efficient. The predictive capability of the water column portion of TPWQM was demonstrated through successful calibration and validation of the model with extensive data sets collected from Lynnhaven Bay, Virginia. The model's general applicability was examined for four other Virginia coastal basins. One value (0.3) of the returning ratio, the only calibration parameter for physical transport, is applicable to all five coastal basins and probably would be adequate for other Virginia coastal basins without further calibration. The values of kinetic parameters determined for Lynnhaven Bay are applicable to at least two of the other four coastal basins. The model underpredicts chlorophyll-a, total carbon, and total phosphorus in two of the tested basins, which is more likely the result of underpredicted nonpoint source loads than the inaccuracy of the kinetic coefficients. Therefore, the set of kinetic coefficients may be applicable to all the Virginia coastal basins with basin-specific refinement in the estimation of nonpoint source loads.}, number={1}, journal={COASTAL MANAGEMENT}, author={Kuo, AY and Park, K and Kim, SC and Lin, JG}, year={2005}, pages={101–117} }