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Strickland WC, Battista NA, Hamlet CL, Miller LA. Planktos: An Agent-Based Modeling Framework for Small Organism Movement and Dispersal in a Fluid Environment with Immersed Structures. Bull Math Biol 2022; 84:72. [PMID: 35689123 DOI: 10.1007/s11538-022-01027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/06/2022] [Indexed: 11/25/2022]
Abstract
Multiscale modeling of marine and aerial plankton has traditionally been difficult to address holistically due to the challenge of resolving individual locomotion dynamics while being carried with larger-scale flows. However, such problems are of paramount importance, e.g., dispersal of marine larval plankton is critical for the health of coral reefs, and aerial plankton (tiny arthropods) can be used as effective agricultural biocontrol agents. Here we introduce the open-source, agent-based modeling software Planktos targeted at 2D and 3D fluid environments in Python. Agents in this modeling framework are relatively tiny organisms in sufficiently low densities that their effect on the surrounding fluid motion can be considered negligible. This library can be used for scientific exploration and quantification of collective and emergent behavior, including interaction with immersed structures. In this paper, we detail the implementation and functionality of the library along with some illustrative examples. Functionality includes arbitrary agent behavior obeying either ordinary differential equations, stochastic differential equations, or coded movement algorithms, all under the influence of time-dependent fluid velocity fields generated by computational fluid dynamics, experiments, or analytical models in domains with static immersed mesh structures with sliding or sticky collisions. In addition, data visualization tools provide images or animations with kernel density estimation and velocity field analysis with respect to deterministic agent behavior via the finite-time Lyapunov exponent.
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Affiliation(s)
- W C Strickland
- Department of Mathematics, University of Tennessee, Knoxville, 227 Ayres Hall, Knoxville, TN, 37996-1320, USA.
| | - N A Battista
- Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, 08628, USA
| | - C L Hamlet
- Department of Mathematics, Bucknell University, Lewisburg, PA, 17837, USA
| | - L A Miller
- Department of Mathematics, University of Arizona, 617 N. Santa Rita Ave., Tuscon, AZ, 85721-0089, USA
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Li S, Roger LM, Kumar L, Lewinski NA, Klein-Seetharaman J, Gagnon A, Putnam HM, Yang J. Digital image processing to detect subtle motion in stony coral. Sci Rep 2021; 11:7722. [PMID: 33833260 PMCID: PMC8032694 DOI: 10.1038/s41598-021-85800-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 02/01/2023] Open
Abstract
Coral reef ecosystems support significant biological activities and harbor huge diversity, but they are facing a severe crisis driven by anthropogenic activities and climate change. An important behavioral trait of the coral holobiont is coral motion, which may play an essential role in feeding, competition, reproduction, and thus survival and fitness. Therefore, characterizing coral behavior through motion analysis will aid our understanding of basic biological and physical coral functions. However, tissue motion in the stony scleractinian corals that contribute most to coral reef construction are subtle and may be imperceptible to both the human eye and commonly used imaging techniques. Here we propose and apply a systematic approach to quantify and visualize subtle coral motion across a series of light and dark cycles in the scleractinian coral Montipora capricornis. We use digital image correlation and optical flow techniques to quantify and characterize minute coral motions under different light conditions. In addition, as a visualization tool, motion magnification algorithm magnifies coral motions in different frequencies, which explicitly displays the distinctive dynamic modes of coral movement. Specifically, our assessment of displacement, strain, optical flow, and mode shape quantify coral motion under different light conditions, and they all show that M. capricornis exhibits more active motions at night compared to day. Our approach provides an unprecedented insight into micro-scale coral movement and behavior through macro-scale digital imaging, thus offering a useful empirical toolset for the coral research community.
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Affiliation(s)
- Shuaifeng Li
- grid.34477.330000000122986657Department of Aeronautics and Astronautics, University of Washington, Seattle, WA 98195-2400 USA
| | - Liza M. Roger
- grid.224260.00000 0004 0458 8737Department of Chemical and Life Science and Engineering, Virginia Commonwealth University, Richmond, VA USA
| | - Lokender Kumar
- grid.254549.b0000 0004 1936 8155Department of Physics, Colorado School of Mines, Golden, CO USA
| | - Nastassja A. Lewinski
- grid.224260.00000 0004 0458 8737Department of Chemical and Life Science and Engineering, Virginia Commonwealth University, Richmond, VA USA
| | - Judith Klein-Seetharaman
- grid.254549.b0000 0004 1936 8155Department of Chemistry, Colorado School of Mines, Golden, CO USA
| | - Alex Gagnon
- grid.34477.330000000122986657School of Oceanography, University of Washington, Seattle, WA USA
| | - Hollie M. Putnam
- grid.20431.340000 0004 0416 2242Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881 USA
| | - Jinkyu Yang
- grid.34477.330000000122986657Department of Aeronautics and Astronautics, University of Washington, Seattle, WA 98195-2400 USA
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Samson JE, Ray DD, Porfiri M, Miller LA, Garnier S. Collective Pulsing in Xeniid Corals: Part I-Using Computer Vision and Information Theory to Search for Coordination. Bull Math Biol 2020; 82:90. [PMID: 32638174 DOI: 10.1007/s11538-020-00759-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 06/04/2020] [Indexed: 11/24/2022]
Abstract
Xeniid corals (Cnidaria: Alcyonacea), a family of soft corals, include species displaying a characteristic pulsing behavior. This behavior has been shown to increase oxygen diffusion away from the coral tissue, resulting in higher photosynthetic rates from mutualistic symbionts. Maintaining such a pulsing behavior comes at a high energetic cost, and it has been proposed that coordinating the pulse of individual polyps within a colony might enhance the efficiency of fluid transport. In this paper, we test whether patterns of collective pulsing emerge in coral colonies and investigate possible interactions between polyps within a colony. We video recorded different colonies of Heteroxenia sp. in a laboratory environment. Our methodology is based on the systematic integration of a computer vision algorithm (ISOMAP) and an information-theoretic approach (transfer entropy), offering a vantage point to assess coordination in collective pulsing. Perhaps surprisingly, we did not detect any form of collective pulsing behavior in the colonies. Using artificial data sets, however, we do demonstrate that our methodology is capable of detecting even weak information transfer. The lack of a coordination is consistent with previous work on many cnidarians where coordination between actively pulsing polyps and medusa has not been observed. In our companion paper, we show that there is no fluid dynamic benefit of coordinated pulsing, supporting this result. The lack of coordination coupled with no obvious fluid dynamic benefit to grouping suggests that there may be non-fluid mechanical advantages to forming colonies, such as predator avoidance and defense.
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Affiliation(s)
- Julia E Samson
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Constance, Germany.,Chair of Biodiversity and Collective Behaviour, Department of Biology, University of Konstanz, Constance, Germany.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Constance, Germany
| | - Dylan D Ray
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maurizio Porfiri
- Department of Mechanical and Aerospace Engineering and Department of Biomedical Engineering, New York University, Tandon School of Engineering, Brooklyn, NY, USA
| | - Laura A Miller
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Simon Garnier
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, USA.
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Collective Pulsing in Xeniid Corals: Part II-Using Computational Fluid Dynamics to Determine if There are Benefits to Coordinated Pulsing. Bull Math Biol 2020; 82:67. [PMID: 32474651 DOI: 10.1007/s11538-020-00741-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/23/2020] [Indexed: 10/24/2022]
Abstract
Coordinated movements have been shown to enhance the speed or efficiency of swimming, flying, and pumping in many organisms. Coordinated pulsing has not been observed in many cnidarians (jellyfish, anemones, corals), as is the case for the xeniid corals considered in our corresponding paper. This observation opens the question as to whether xeniid corals, and cnidarians in general, do not coordinate their pulsing behavior for lack of a hydrodynamic advantage or for other reasons. For example, a diffuse nervous system with lack of substantial sensory input may not be capable of such coordination. Similarly, grouping may serve a defensive role rather than a fluid dynamic role. In this paper, the immersed boundary method is used to quantify the volumetric flux of fluid generated by an individual xeniid coral polyp in comparison with a pair of polyps. Both the distances between the polyps and the phase difference between each polyp are considered. More specifically, the fully coupled fluid-structure interaction problem of a coral polyp driving fluid flow is solved using a hybrid version of the immersed boundary method where the Navier-Stokes equations are solved using a finite differences and the elasticity equations describing the coral are solved using finite elements. We explore three possible hypotheses: (1) pulsing in pairs increases upward flow above the polyps and is thus beneficial, (2) these benefits vary with the polyps' pulsing phase difference, and (3) these benefits vary with the distance between the polyps. We find that there is no substantial hydrodynamic advantage to pulsing in a pair for any phase difference. The volumetric flux of fluid generated by each coral also decreases as the distance between polyps is decreased. This surprising result is consistent with measurements taken from another cnidarian with similar behavior, the upside down jellyfish, in which each medusa drives less flow when in a group.
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Knight K. Corals’ throbbing tentacles keep water flowing to flush away oxygen. J Exp Biol 2019. [DOI: 10.1242/jeb.210591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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