Experiments and agent based models of zooplankton movement within complex flow environments

Mustafa Kemal Ozalp, Laura A. Miller, Thomas Dombrowski, Madeleine Braye, Thomas Dix, Liam Pongracz, Reagan Howell, Daphne Klotsa, Virginia Pasour, Christopher Strickland

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


The movement of plankton is often dictated by local flow patterns, particularly during storms and in environments with strong flows. Reefs, macrophyte beds, and other immersed structures can provide shelter against washout and drastically alter the distributions of plankton as these structures redirect and slow the flows through them. Advection-diffusion and agent-based models are often used to describe the movement of plankton within marine and fresh water environments and across multiple scales. Experimental validation of such models of plankton movement within complex flow environments is challenging because of the difference in both time and spatial scales. Organisms on the scale of 1 mm or less swim by beating their appendages on the order of 1 Hz and are advected meters to kilometers over days, weeks, and months. One approach to study this challenging multiscale problem is to insert actively moving agents within a background flow field. Open source tools to implement this sort of approach are, however, limited. In this paper, we combine experiments and computational fluid dynamics with a newly developed agent-based modeling platform to quantify plankton movement at the scale of tens of centimeters. We use Artemia spp., or brine shrimp, as a model organism given their availability and ease of culturing. The distribution of brine shrimp over time was recorded in a flow tank with simplified physical models of macrophytes. These simplified macrophyte models were 3D-printed arrays of cylinders of varying heights and densities. Artemia nauplii were injected within these arrays, and their distributions over time were recorded with video. The detailed three-dimensional flow fields were quantified using computational fluid dynamics and validated experimentally with particle image velocimetry. To better quantify plankton distributions, we developed an agent-based modeling framework, Planktos, to simulate the movement of plankton immersed within such flow fields. The spatially and temporally varying Artemia distributions were compared across models of varying heights and densities for both the experiments and the agent-based models. The results show that increasing the density of the macrophyte bed drastically increases the average time it takes the plankton to be swept downstream. The height of the macrophyte bed had less of an effect. These effects were easily observed in both experimental studies and in the agent-based simulations.

Original languageEnglish (US)
Article number2
Issue number1
StatePublished - Mar 1 2020
Externally publishedYes


  • Agent-based model
  • Computational fluid dynamics
  • Zooplankton

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Biochemistry
  • Biomaterials
  • Molecular Medicine
  • Biomedical Engineering


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