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(eng): Computational techniques can be applied to numerically assess key parameters influencing the biotechnological process to better predict the essential features governing macroalgae growth and nutrient removal in aerated tanks, e.g., integrated into multitrophic aquaculture systems. Recent advances in computational hardware and software, such as the discrete element method (DEM) coupled with computational fluid dynamics (CFDs) codes, have enabled flow simulations in biotechnological systems. Here, we perform CFD-DEM simulations of macroalgae motion within aerated tanks to assess the light–dark cycle period as one of the most critical abiotic conditions governing the growth of photosynthetic organisms. This proof-of-concept study, which deals with the challenging problem of the fluid structure interaction in aerated (bubbled) tanks with a highly flexible solid phase, includes a set of detailed 2D CFD simulations for two types of settings differing in the presence or absence of an inner cylinder assembly. Consequently, corresponding regression models for the cycle period are derived, and the initial hypothesis of the assembly’s beneficial role is confirmed. Eventually, the CFD results are verified using an image processing technique on the laboratory scale tank with Ulva sp. and specific 3D CFD-DEM simulations.