Jian Shen

Virginia Institute of Marine Science · Department of Physical Sciences

Morphological changes in estuaries are typically discussed on decadal time scales, with reported changes often exceed several decimeters. In our study, we utilized refined in-situ data to investigate bed-level changes and rapid accretion-erosion transitions during tidal cycles off the Changjiang Estuary. A field study employing a high-resolution bo...

The onset of hypoxia is a consequence of the competition between oxygen replenishment, production, and consumption. Dissolved oxygen (DO) levels inside an estuary depend on the balance between physical processes that transport oxygen-rich water into the estuary, including upstream freshwater advection, gravitational circulation, and vertical mixing...

Plain Language Summary Accurately modeling sediment and organic transport necessitates the use of a high‐resolution numerical wave model (NWM). However, the computational expenses of running an NWM within an ecosystem model pose significant challenges. We conducted a study using a machine learning approach based on long short‐term memory to replica...

We used a numerical model to investigate the effects of sea‐level rise (SLR) on the biogeochemical processes in the York River Estuary with extensive tidal marshes. The fully‐coupled hydrodynamic‐water quality‐marsh model accounts for the spatial and temporal variations of physical‐biogeochemical interactions between the tidal marshes and surroundi...

Observations suggest that the existence of tidal marsh can alter the oxygen and nutrient dynamics in adjacent water bodies, but assessing the impacts of large tidal marshes on an estuary is challenging. In this study, we use a modeling approach to investigate the roles of tidal marshes on the estuarine biochemical processes. The marsh model, which...

Climate change and nutrient pollution contribute to the expanding global footprint of harmful algal blooms. To better predict their spatial distributions and disentangle biophysical controls, a novel Lagrangian particle tracking and biological (LPT‐Bio) model was developed with a high‐resolution numerical model and remote sensing. The LPT‐Bio model...

An unusual coastward expansion of the toxic dinoflagellate species Margalefidinium polykrikoides was observed in 2020 summer after a tropical storm passing Chesapeake Bay. Such coastward expansion was only recorded in 2007. A newly developed coupled Lagrangian particle tracking and harmful algal bloom model driven by environmental variables was use...

Municipal intakes of surface water have various uses, and their impacts on the aquatic environment and ecosystem, such as the impingement and entrainment of ichthyoplankton, are a major concern. A robust assessment of the intake impacts on ichthyoplankton in a system generally requires modeling efforts that can simulate the transport and dispersal...

Chlorophyll-a (Chl-a) concentration indicates the abundance of phytoplankton biomass and its spatiotemporal variations fundamentally modulate the ecosystem dynamics in coastal waters. Compared to conventional low-frequency shipboard measurements at a limited number of sampling locations, satellite data provide a better spatial and temporal coverage...

The response of tidal range in tidal marshes under sea-level rise (SLR) is essential to the marsh resilience, but how tidal ranges respond to different marsh evolutions remains unclear. Here, we show the existence of bifurcate responses of tidal range to SLR using both numerical model and theoretical analyses. The tidal range tends to increase if m...

Contamination of oysters with a variety of viruses is one key pathway to trigger outbreaks of massive oyster mortality as well as human illnesses, including gastroenteritis and hepatitis. Much effort has gone into examining the fate of viruses in contaminated oysters, yet the current state of knowledge of nonlinear virus-oyster interactions is not...

Accumulation and remineralization of surface‐produced particulate organic matter (POM) in the water column and seabed link closely to hypoxia and the health of aquatic ecosystems. The POM retention time provides a key timescale to interpret biochemical reaction processes. In this study, we investigated the spatiotemporal variations in the vertical...

Simple mathematical models are derived from mass balances for water and transported substance to provide insight into the relationships between import, export, transport, and internal removal for nonconservative substances in an estuary. Extending previous work, our models explicitly include water and substance inputs from the ocean and are express...

The Changjiang Delta (CD) is one of well-studied large deltas of critical socio-economical and ecological importance regionally and global representativeness. Cumulated field data and numerical modeling has facilitated scientific understanding of its hydro-morphodynamics at multiple spatial and time scales, but the changing boundary forcing conditi...

There was a mistake in the Matlab code we used to generate time series solutions of our model, Eqs. (16)-(18). The corrected text below replaces one paragraph on p. 7, and the figures below replace Fig. 4, Fig. 5 on p. 8. There is no qualitative change to our results. However, there is a quantitative change in the initial dead oyster shell volume B...

The southeastern portion of the Yangtze River Estuary was considered to be the deposition center and the mudbank of the Yangtze River Delta. As the fluvial sediment supply began to decline in the 1980s and the reduction accelerated after the completion of the Three Gorge Dam in 2003, more fluvial sediment was trapped decreasing the suspended sedime...

The Pearl River Estuary (PRE) is a bell-shaped estuary with a narrow deep channel and wide shoals. This unique topographic feature leads to different dynamics of the subtidal estuarine circulation (SEC) in the PRE compared with a narrow and straight estuary. In this study, the nonlinear dynamics of the SEC in the PRE under mean circumstance are ana...

Both abiotic and biotic factors control phytoplankton dynamics. Among the multiple factors regulating the variability of phytoplankton production and biomass, physical transport that distributes both phytoplankton and other substances (e.g., nutrients, salts, and suspended solids) is one of the key factors in coastal aquatic systems. While the effe...

In this study, the influence of sea-level rise (SLR) on seasonal hypoxia and phytoplankton production in Chesapeake Bay is investigated using a 3D unstructured grid model. Three SLR scenarios (0.17 m, 0.5 m, and 1.0 m) were conducted for 1991 to 1995. Results show that the summer hypoxic volume (HV) increases about 2%, 8%, and 16%, respectively for...

Most estuaries are characterized by non‐uniform axial topography with shallow shoals near the mouth. Previous studies have addressed the impacts of the axial topographic variations on mixing and estuarine circulations yet seldom on material transport and retention. This study investigates the longitudinal structure and mechanisms of exchange flow a...

Blooms of Margalefidinium (previously Cochlodinium) polykrikoides occur almost annually in summer in the lower Chesapeake Bay and its tributaries (e.g., the James and York Rivers). The Lafayette River, a sub-tributary of the lower James River, has been recognized as an initiation location for blooms in this region. The timing of bloom initiation va...

Transport rate, as a scale complementary to commonly used transport timescales, is useful for quantifying local transport conditions in estuarine and coastal systems. A specific transport rate computed based on tracer release is highlighted for quantifying the local transport condition for long-standing autochthonous constituents originating from t...

Pathogen, whose abundance is often measured by the concentration of fecal indicator bacterium, is listed as the top cause of waterbody impairments in the US. An accurate estimation of the bacterial loading from watershed is thus fundamentally important for water quality management. Despite advances in watershed modeling, accurate estimation of bact...

Phytoplankton biomass, indicated by chlorophyll-a (Chl-a) concentration, is fundamentally important for aquatic ecosystems. However, accurately simulating Chl-a is always challenging even when using state-of-the-art numerical models. We propose a data-driven modeling framework that combines Empirical Orthogonal Function (EOF) analysis and machine-l...

Water exchange, featured by bottom inflow and surface outflow in a typical estuary, determines the transport and redistribution of salt, nutrients, pollutants, and suspended sediments and organisms. Water exchange in Chesapeake Bay, the largest estuary in the US, has been extensively studied, yet its long-term interannual variability and its relati...

This study investigates the sediment resuspension and the resultant morphological changes over the subaqueous delta front in the Changjiang Estuary (CJE). An in-situ observation platform equipped with multi-sensor instruments was deployed in the CJE to measure the currents, waves, and suspended sediment concentrations (SSC) when a typical remote tr...

The impact of channel deepening and sea-level rise on the environmental integrity of an estuary is investigated using a three-dimensional hydrodynamic-eutrophication model. The model results show that dissolved oxygen (DO) only experienced minor changes, even when the deep channel was deepened by 3 m in the mesohaline and polyhaline regions of the...

A three-dimensional unstructured-grid hydrodynamic and water quality model (SCHISM-ICM) is applied successfully for Chesapeake Bay. The model is validated with observations of salinity, chlorophyll-a, dissolved oxygen, nutrients, and phytoplankton productions from the year 1991 to 1995 for the mainstem and some major tributaries, based on multiple...

Hypoxia is a big concern in coastal waters as it affects ecosystem health, fishery yield, and marine water resources. Accurately modeling coastal hypoxia is still very challenging even with the most advanced numerical models. A data‐driven model for coastal water quality is proposed in this study and is applied to predict the temporal‐spatial varia...

Extensive coastal engineering activities including channel dredging and constructions of large infrastructure have greatly altered hydrodynamics in the Changjiang Estuary. While the changes in longitudinal circulation have been well-documented, limited studies have focused on the alteration in lateral circulation and its impact on estuarine circula...

Stratification in estuaries has received much focus due to its importance in estuarine hydrodynamics and material transport. By utilizing a well‐calibrated numerical model, in this work we investigate the changes in stratification in the deepened and narrowed North Passage of the Changjiang Estuary. Before channel narrowing and deepening, lateral s...

Abundance of fecal coliform (FC) is widely used to indicate the potential presence of pathogens, the No.1 cause of water impairments in the U.S. Despite extensive monitoring efforts, assessing and modeling FC pollution still faces challenges, largely owing to the uncertainties in estimation of overall removal rate (K). This study proposes an altern...

The response of a coastal region to sea-level rise depends on the local physical features, which should therefore be evaluated locally to provide an accurate vulnerability assessment. In this study, we conducted comprehensive analyses of the potential impacts of sea-level rise on the Pearl River Estuary (PRE), China with the aid of a fully calibrat...

A 3-D unstructured-grid hydrodynamic model for the northern Gulf of Mexico was developed, with a hybrid s–z vertical grid and high-resolution horizontal grid for the main estuarine systems along the Texas–Louisiana coast. This model, based on the Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM), is driven by the observed rive...

This study constructs an analytical model to understand the phytoplankton dynamics in a one-dimensional system by integrating the physical and biological processes. We present an analytical solution of phytoplankton distribution along the longitudinal direction of a tidal river. The solution has two components: water age and accumulative growth. Th...

Algal blooms often occur in the tidal freshwater (TF) of the James River estuary, a tributary of the Chesapeake Bay. The timing of algal blooms correlates highly to a summer low-flow period when residence time is long and nutrients are available. Because of complex interactions between physical transport and algal dynamics, it is challenging to pre...

The effects of physical transport processes on the initiation of harmful algal blooms (HABs) in estuaries were investigated through both mathematical model analysis and numerical model experiments. This study highlights the influence of the flushing effect due to physical transport processes on the location of bloom initiation, which is comparable...

We present a 3D unstructured-grid hydrodynamic model for the northwestern Gulf of Mexico that utilizes a high-resolution grid for the main estuarine systems along the Texas-Louisiana coast. This model, based on the Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM) with hybrid horizontal and vertical grids, is driven by the obs...

The pelagic contribution to total gross primary production (GPP) is often used to evaluate the assemblages of primary producers in shallow estuarine and coastal ecosystems that shift between benthic‐dominated and pelagic‐dominated status as a response to nutrient loading change. This study investigated the spatial and temporal variability of the pe...

Flushing of an estuary quantifies the overall water exchange between the estuary and coastal ocean and is crucially important for water quality as well as biological and geochemical processes within the system. While influence of river discharge and tidal exchange are well recognized, the impact of baroclinic processes on the flushing is not yet fu...

Waves, by enhancing surface wind stress and bottom stress, increasing water mixing, and creating water currents, play an important role in modifying the dispersal of river plumes. In this study, we used the COAWST modeling system to study the effects of waves on the dispersal of the Pearl River plume during winter. The waves help retain freshwater...

We extend the 3D unstructured-grid model previously developed for the Upper Chesapeake Bay to cover the entire Bay and its adjacent shelf, and assess its skill in simulating saltwater intrusion and the coastal plume. Recently developed techniques, including a flexible vertical grid system and a 2nd-order, monotone and implicit transport solver are...

There are increasing concerns about the impact of worsened physical condition on hypoxia in a variety of coastal systems, especially considering the influence of changing climate. In this study, an EOF analysis of the DO data for 1985-2012, a long-term numerical simulation of vertical exchange, and statistical analysis were applied to understand th...

The water exchange between the James River and the Elizabeth River, an estuary and sub-estuary system in the lower Chesapeake Bay, was investigated using a 3D numerical model. The conservative passive tracers were used to represent the dissolved substances (DS) discharged from the Elizabeth River. The approach enabled us to diagnose the underlying...

Tidal response to sea-level rise (SLR) varies in different coastal systems. To provide a generic pattern of tidal response to SLR, a systematic investigation was conducted using numerical techniques applied to idealized and realistic estuaries, with model results cross-checked by analytical solutions. Our results reveal that the response of tidal r...

A numerical modeling study of the influence of the lateral flow on the estuarine exchange flow was conducted in the north passage of the Changjiang estuary. The lateral flows show substantial variabilities within a flood-ebb tidal cycle. The strong lateral flow occurring during flood tide is caused primarily by the unique cross-shoal flow that indu...

This study evaluated the impact of human modifications and natural variations (e.g., seasonal riverine fluxes, plant growth, and estuarine environments) on the short-term morphological changes in estuarine tidal flats. Central to the study was an embankment, constructed in 2014, which changed the path of a tidal flat evolution in the Yangtze Estuar...

Driven by estuarine circulation, material released from lower Chesapeake Bay tributaries has the potential to be transported to the upper Bay. How far and what fraction of the material from tributaries can be carried to the upper estuary have not been quantitatively investigated. For an estuary system with multiple tributaries, the relative contrib...

Although both local processes (photosynthesis, respiration, grazing, and settling), and physical transport processes (advection and dispersion) significantly affect local phytoplankton dynamics, it is difficult to separate their contributions and to investigate the relative importance of each process to the local variability of phytoplankton biomas...

Quantification of tidal flat morphological changes at varying timescales is critical from a management point of view. High-resolution tidal flat morphology data, including those for mudflats and salt-marshes, are rare due to monitoring difficulty by traditional methods. Recent advances in Terrestrial Laser Scanner (TLS) technology allow rapid acqui...

Wanquan River is a small river located in Hainan, a tropical island in China. As the third largest river in Hainan, the river plume plays an important role in the regional terrigenous mass transport, coastal circulation, and the coral reef’s ecosystem. Studies have shown that wind forcings significantly influence river plume dynamics. In this study...

Harmful algal blooms (HABs) have frequently occurred in the James River. The State has convened a Scientific Advisory Panel (SAP) to review the James River chlorophyll-a standards. The SAP will conduct a scientific study to review the basis for setting the chlorophyll-a standards. To support the SAP study of chlorophyll-a standards, the State of Vi...

Poquoson River is a tidal coastal embayment located along the Western Shore of the Chesapeake Bay about 4 km south of the York River mouth in the City of Poquoson and in York County, Virginia. Its drainage area has diversified land uses, including high densities of residence, agricultural, salt marsh land uses, as well as a National Wildlife Refuge...

Floodgates or storm surge barriers are increasingly being considered as feasible climate change adaptation strategies to mitigate flooding risk. We developed a numerical modeling approach for a partially mixed estuary to simulate long-term alterations to hydrodynamics and transport processes induced from human modifications; two types of partially...

We develop a new vertically implicit transport solver, based on two total variation diminishing (TVD) limiters in space and time, inside a 3D unstructured-grid model (SCHISM), and apply it to the Upper Chesapeake Bay (UCB), which has complex geometry and sharp pycnocline. We show that the model is able to accurately and efficiently capture the elev...

Concerns have grown over the increase of nutrients and pollutants discharged into the estuaries and coastal seas. The retention and export of these materials inside a system depends on the residence time (RT). A long-term simulation of time-varying RT of the Chesapeake Bay was conducted over the period from 1980 to 2012. The 33-year simulation resu...

Several works have discussed the morphological evolution in the Changjiang Estuary (CJE) in recent years. The erosion of its subaqueous delta in recent decades has been ascribed to a decline in fluvial sediment input. However, the interaction between the reduction of riverine sediment load and human activities in the estuary that could have caused...

As three-dimensional (3-D) aquatic ecosystem models are used more frequently for operational water quality forecasts and ecological management decisions, it is important to understand the relative strengths and limitations of existing 3-D models of varying spatial resolution and biogeochemical complexity. To this end, 2-year simulations of the Ches...

As three-dimensional (3-D) aquatic ecosystem models are becoming used more frequently for operational water quality forecasts and ecological management decisions, it is important to understand the relative strengths and limitations of existing 3-D models of varying spatial resolution and biogeochemical complexity. To this end, two-year simulations...

Restoration strategies for native oyster populations rely on multiple sources of information, which often conflict due to time- and space-varying patterns in abundance and distribution. For instance, strategies based on population connectivity and disease resistance can differ, and extant and historical records of abundance and distribution are oft...

Tide is one of the most important hydrodynamic driving forces and has unique features in the Yangtze Estuary (YE) due to the complex geometry of third-order bifurcations and four outlets. This paper characterizes the tidal oscillations, tidal dampening, tidal asymmetry and tidal wave propagation, which provides insights into the response of the est...

It is instructive and essential to decouple the effects of biological and physical processes on the dissolved oxygen condition, in order to understand their contribution to the interannual variability of hypoxia in Chesapeake Bay since the 1980s. A conceptual bottom DO budget model is applied, using the vertical exchange timescale (VET) to quantify...

Based on the salinity and current data from an intensive field survey carried out in the Modaomen Estuary, Pearl River Delta, China, this study reveals that the behaviors of the two major components of salt transport flux (i.e., the advective salt flux caused by mean advective flow and the tidal salt flux caused by tidal diffusive processes) are qu...

Huangmaohai Estuary is a micro-tidal funnel-shaped estuary, located along the southwestern side of the Pearl River Delta complex. Variations of sediment transport patterns under different conditions of river discharge and tidal mixing are investigated by using field measurements and data analysis during both dry and wet seasons, respectively. The i...

The major patterns of the Changjiang plume have been identified based on the Empirical Orthogonal Function and the freshwater flux analysis of the long-term model simulations driven by the climatological and realistic forcings. Dynamic natures of these patterns with respect to realistic forcings were analyzed. It was found that the Changjiang plume...