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Functional morphology of the Ediacaran organism Tribrachidium heraldicum

Cite this dataset

Olaru, Andrei et al. (2024). Functional morphology of the Ediacaran organism Tribrachidium heraldicum [Dataset]. Dryad. https://doi.org/10.5061/dryad.dr7sqvb65

Abstract

Tribrachidium heraldicum is among the first large and structurally complex animals, appearing in the fossil record 550 million years ago. By using engineering software to simulate fluid flow around digital models of this organism we recreate details of how it lived, including how it fed and the likely functions of its bizarre anatomy.

README: Functional morphology of the Ediacaran organism Tribrachidium heraldicum

https://doi.org/10.5061/dryad.dr7sqvb65

Tribrachidium morphotype reconstructions for the simulations are in STEP file format that can be imported into CAD or CFD software. Files are labeled by anatomical characters of the morphologies in both the COMSOL and morphology files.

  • bare_hemisphere.stp - hemispherical model with no ornamentation 
  • round_pits.stp - hemispherical null model with rounded apical pits
  • elongate_pits.stp - hemispherical null model with elongated "teardrop" apical pits
  • arms_only.stp - hemispherical model with arms
  • arms_and_bullae.stp - hemispherical null model with arms and bullae 
  • arms_and_round_pits.stp - hemispherical null model with arms and round apical pits
  • arms_and_elongate_pits.stp - hemispherical model with arms and elongated "teardrop" apical pits
  • complete_model_with_round_pits.stp - hemispherical model with arms, bullae, and rounded apical pits
  • complete_model_with_elongate_pits.stp - hemispherical model with arms, bullae, and elongated "teardrop" apical pits

COMSOL Multiphysics setup files for computational fluid dynamics simulations of Tribrachidium morphotypes. All simulations were setup and run in COMSOL Multiphysics 6.2, and then setup files were exported as open .java format. Please contact authors for COMSOL .mph format files if propriety file format is preferred. Filenames correspond to the anatomical characters included in the Tribrachidium morphotype simulated. Java files can be compiled within COMSOL or can be opened in a standard text editor to view encoding contents. 

  • hemisphere.java - simulation file for bare_hemisphere.stp
  • round_pits.java - simulation file for round_pits.stp
  • round_pits_and_arms.java - simulation file for arms_and_round_pits.stp
  • arms_bullae.java - simulation file for arms_bullae.stp 
  • elongate_pits_and_arms.java - simulation file for arms_and_elongate_pits.stp
  • arms.java - simulation file for arms_only.stp
  • complete_model_with_round_pits.java - simulation file for complete_model_with_round_pits.stp
  • complete_model_with_elongate_pits.java - simulation file for complete_model_with_elongate_pits.stp
  • population_complete_model_withelongate_pits.java - simulation file for triangular arrangement of complete_model_with_elongate_pits.stp
  • wide_population_complete_model_with_elongate_pits.java - simulation file for triangular arrangement of complete_model_with_elongate_pits.stp with additional space between individuals

Directories S2.zip, S5.zip, and S20.zip house time slice data from coupled OpenFOAM and LIGGGHTS simulations of flow over the Tribrachidium Mesh.stl model. S2, S5, and S20 correspond to inlet velocities of 2 cm/s, 5 cm/s, and 20 cm/s, respectively. The dataset is the results from Discrete Element Method simulation from CFD-DEM coupling methods. The file are stored in vtk format, and can be visualized by opensource code Paraview.

  • S2 directory - 400 files, number corresponds to timestep. Duration between timestep is 2.5 µs. 
  • S5 directory - 251 files, number corresponds to timestep. Duration between timestep is 2.5 µs.
  • S20 directory - 58 files, number corresponds to timestep. Duration between timestep is 1 µs.

The files in each directory (e.g., S2) are the vtk results of each simulation timestep. Openning with paraview, you can see the following 7 types of data: f (force, vector, in the unit of N); i (0 by default); id (particle id, integer); omega (rotational velocity, vector, in the unit of rad/s); radius (particle radius, scalar, in the unit of m); type (type of particles, 1 by default); v (velocity, vector, in the unit of m/s). You can visualize the results with Glyph tool in Paraview.

All .java, .stp, and .vtk files can also be opened and viewed in a standard text editor. 

## Sharing/Access information

https://zenodo.org/records/11406391

Methods

All .java files are generated from COMSOL Multiphysics 6.2. Once simulations were completed, meshes were cleared, and simulations were exported to .java. Relavent Tribrachidium reconstruction files are saved as STEP shape files.  Remaining data are from coupled OpenFOAM and LIGGGTS simulations using the stl shape file. These datasets can be viewed using ParaView. 

Funding

National Science Foundation, Award: EAR-2007928

Natural Environment Research Council, Award: NE/V010859/2

Alexander von Humboldt Foundation

Vanderbilt University, Searle Undergraduate Research Program (SYBBURE)

Vanderbilt University, Alberstadt, Reeseman, Sterns grant

University of Toronto Mississauga, Postdoctoral Fellowship

Royal Commission for the Exhibition of 1851

Natural Environment Research Council, Award: NE/W00786X/1

K. C. Wong

Royal Society