An imitation model of attached-mobile diatom microalgae

A.M. Lyakh1, P.V. Sapozhnikov2

1A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, RF, Sevastopol, Nakhimov Av., 2

2Shirshov Institute of Oceanology of RAS, RF, Moscow, Nakhimovskiy Av., 36

DOI: 10.33075/2220-5861-2024-2-117-125

UDC 004.94:582.261.1-5                   



The paper describes a computer model for simulating the movement of diatom microalgae on the substrate surface. The model belongs to the class of agent-based models, which implements the behavior of virtual individuals simulating diatom microalgae. The individuals live in discrete time and move on a flat, continuous, bounded surface of a rectangular shape. Individuals are represented by figures with rigid boundaries that cannot be overlapped. At each moment of time, an individual can slide in one of two directions, rotate clockwise or counterclockwise, simultaneously slide and rotate, or remain motionless. The choice of an action is determined randomly. The probability of choosing each action is recorded in a parameter array, the genotype, available to all individuals. An individual can also remember a past action. Given a memory, it recalls and repeats the action with a given probability of repetition. These probabilities are also recorded in the shared genotype. The parameters in the genotype are not fixed, the user can customize them using interface elements. The paper shows how the trajectories of individuals vary at different values of the probabilities. The model is available at

Keywords: organisms locomotion, diatoms, agent-based model, simulation model.

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  1. Round F.E., Crawford R.M., and Mann D.G. The diatoms. Biology and morphology of the genera. Cambridge, Cambridge university press, 1990, 747 p.
  2. Sapozhnikov P.V., Kalinina O.Yu., and Vostokov S.V. Mikroplaston iskusstvennykh polimerov v r. Miass i oz. Turgoyak (Yuzhny Ural, RF) na rannikh stadiyakh kolonizatsii (Microplaston artificial polymers in the Miass River and Lake Turgoyak (Southern Urals, Russia) in the early stages of colonization) // South of Russia: ecology, development, 2023, Vol. 18, No. 3, pp. 133–143.
  3. Wiegand T. and Moloney K.A. Handbook of spatial point-pattern analysis in ecology. New York, Chapman and Hall/CRC, 2013, 512 p.
  4. Cohn S., Manoylov K., and Gordon R. Diatom gliding motility. Scrivener Publishing, 2021. 430 p.
  5. Bondoc-Naumovitz K.G. and Cohn S.A. Motility of biofilm-forming benthic diatoms // Diatom gliding motility. Scrivener Publishing, 2021, pp. 77–109.
  6. Poulsen N., Hennig H., Geyer V.F., Diez S., Wetherbee R., Fitz-Gibbon S., Pellegrini M., and Kroger N. On the role of cell surface associated, mucin-like glycoproteins in the pennate diatom Craspedostauros australis (Bacillariophyceae) // Journal of Phycology, 2022, Vol. 59, No. 1, pp. 54–69.
  7. Sato S. and Medlin L.K. Motility of non-raphid diatoms // Diatom Research, 2006, Vol. 21, No. 2, pp. 473–477.
  8. Pickett-Heaps J., Hill D.R.A., and Blaze K.L. Active gliding motility in an araphid marine diatom, Ardissonea (formerly Synedra) crystallina // Journal of Phycology, 1991, Vol. 27, No. 6, pp. 718–725.
  9. Gutierrez-Medina B., Guerra A.J., Maldonado A.I.P., Rublo Y.C., and Meza J.V.G. Circular random motion in diatom gliding under isotropic conditions // Physical Biology, 2014, Vol. 11, 066006.
  10. Davidovich N.A. Opredeleniya i ponyatiya reproduktivnoy biologii diatomovykh vodorosley (terminologichesky slovar) (Definitions and concepts of reproductive biology of diatom algae (terminology dictionary) // Novosti sistematiki nizshikh rasteny, 2017, Vol. 51, pp. 71–105.
  11. p5.js. URL: (April 07, 2024).
  12. RBush – a high-performance JavaScript R-tree-based 2D spatial index for points and rectangles. URL: (April 11, 2024).
  13. RBush-kNN. k-nearest neighbors search (KNN) for RBush. URL: (April 12, 2024).
  14. Edgar L.A. Diatom locomotion: Coputer assisted analysis of cine film // British Phycological Journal, 1979, Vol. 14, No. 1, pp. 83–101.
  15. Harbich T. Some observation of movements of pinnate diatoms in cultures and their possible interpretation // Diatom gliding motility. Scrivener Publishing, 2021, pp. 1–31.