Use of SHYFEM open source hydrodynamic model for time scales analysis in a semi-enclosed basin

Lagrangian simulations contribute to the study and comprehension of particulate-matter transport, its dissolution and dispersion in the oceans. Parcels is an open-source, Python-based module for Lagrangian ocean simulations. It is a known tool in the oceanographic community that has been applied to a variety of case studies, such as the tracing of microplastics, the backtracking of ocean floor plankton, and the migration of fish. In this module, particles are advected over time according to a selected flow field, where those particles can represent particulate-matter, biota or other objects with physical, hydrodynamic or biogeochemical properties. In this contribution, we present the substantial extensions of Parcels with respect to usability, physics modelling aspects of particle advection, and computational aspects of versatile, scalable and efficient simulations.Specifically, a suite of simple, concise notebook tutorials are tailored to novice user, covering step-by-step simulation setup instructions, whereas self-contained special-issue tutorials address advanced- and proficient user requirements. The considerable expansion of supported OGCM flow field input formats (e.g. MITgcm, POP and MOM5, among others) is a major interest in Parcels v2.2 for our steadily-growing user base.The new version further integrates previously-published physics methods into practical lagrangian particle simulations. As such, we implement an analytical advection scheme in addition to existing Runge-Kutta advection schemes. Furthermore, two-dimensional advection-diffusion is upgraded with the Milstein stochastic integration scheme and improved documentation. Those capabilities enable a more consistent modelling of diffusion- and uncertainty-dominated fluid transport processes.The case studies performed with previous versions indicate increased computational demands. Simulations are run over long decadal time scales as well as over day-periods with sub-second temporal increments, involving multiple basins and global scenarios, while also modelling increasingly complex particle processes. Overall, our developments respond to the big-data requirements of modern oceanographic studies, which include the aspects of (i) high record volume (i.e. large number of particles), (ii) high dimensionality in multi-variate records, (iii) high spatial resolution, (iv) high temporal resolution, (v) high scenario (i.e. case study) variability and (vi) the prevention of numerical error accumulation over long simulation time scales.The novel features of Parcels v2.2 are illustrated on distinct case studies within our contribution, in order to connect the technical features to their impact on particulate-matter ocean transport studies.

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Assessing the potential impact of glacial lake outburst floods on individual objects using a high-performance hydrodynamic model and open-source data

The Science of The Total Environment ◽

10.1016/j.scitotenv.2021.151289 ◽

2021 ◽

pp. 151289

Author(s):

Huili Chen ◽

Jiaheng Zhao ◽

Qiuhua Liang ◽

Sudan Bikash Maharjan ◽

Sharad Prasad Joshi

Keyword(s):

Open Source ◽

Hydrodynamic Model ◽

High Performance ◽

Glacial Lake ◽

Outburst Floods ◽

Glacial Lake Outburst Floods ◽

Open Source Data ◽

Source Data ◽

Potential Impact ◽

Individual Objects

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Inhomogeneous dominance patterns of competing phytoplankton groups in the wake of an island

Nonlinear Processes in Geophysics ◽

10.5194/npg-17-715-2010 ◽

2010 ◽

Vol 17 (6) ◽

pp. 715-731 ◽

Cited By ~ 14

Author(s):

D. Bastine ◽

U. Feudel

Keyword(s):

Functional Groups ◽

Time Scales ◽

Hydrodynamic Model ◽

Phytoplankton Community ◽

Coastal Upwelling ◽

Nutrient Transport ◽

Trophic Levels ◽

Biological Time ◽

Temporal Abundance ◽

Spatio Temporal

Abstract. We investigate the competition between two different functional groups of phytoplankton in the wake of an island close to a coastal upwelling region. We couple a simple biological model with three trophic levels and a hydrodynamic model of a von Kármán vortex street. The spatio-temporal abundance shows that the different phytoplankton groups dominate in different regions of the flow. The composition of the phytoplankton community varies e.g. for the different vortices. We study the mechanism leading to these inhomogeneous dominance patterns by investigating the nutrient transport in the flow and the interplay of hydrodynamic and biological time scales.

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LVSEM: Past Present and Future

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100180574 ◽

1990 ◽

Vol 48 (1) ◽

pp. 364-365

Author(s):

James B. Pawley

Keyword(s):

Field Emission ◽

Line Width ◽

Time Scales ◽

Silicon Oxide ◽

Beam Current ◽

High Brightness ◽

High Beam ◽

Fixed Charges ◽

Beam Voltage ◽

Deposited Metal

Past: In 1960 Thornley published the first description of SEM studies carried out at low beam voltage (LVSEM, 1-5 kV). The aim was to reduce charging on insulators but increased contrast and difficulties with low beam current and frozen biological specimens were also noted. These disadvantages prevented widespread use of LVSEM except by a few enthusiasts such as Boyde. An exception was its use in connection with studies in which biological specimens were dissected in the SEM as this process destroyed the conducting films and produced charging unless LVSEM was used.In the 1980’s field emission (FE) SEM’s came into more common use. The high brightness and smaller energy spread characteristic of the FE-SEM’s greatly reduced the practical resolution penalty associated with LVSEM and the number of investigators taking advantage of the technique rapidly expanded; led by those studying semiconductors. In semiconductor research, the SEM is used to measure the line-width of the deposited metal conductors and of the features of the photo-resist used to form them. In addition, the SEM is used to measure the surface potentials of operating circuits with sub-micrometer resolution and on pico-second time scales. Because high beam voltages destroy semiconductors by injecting fixed charges into silicon oxide insulators, these studies must be performed using LVSEM where the beam does not penetrate so far.

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