Video: PAPER_NUFEB_TOOL

This page shows the videos used in the manuscript:

Li B, et al. “NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities.” PLoS Computational Biology 2019, 15 (12).

The input files can be found in \NUFEB\examples\PAPER-NUFEB-TOOL.

(↓ Youtube video)

S1 Video (c1-deform-growth). Growth of a biofilm without flow. The biofilm is initially grown for 9 days without flow. It forms a mushroom-shaped structure in an oxygen-limited condition (1 × 10⁻⁴ kg/m³ ).

(↓ Youtube video)

S2 Video (c1-deform-fixwall-0.2u). Biofilm removal at U_f = 0.2 m/s . Large chunks of microbes detach from the biofilm surface and then remove from the systems. The biofilm morphology changes from a rough to a flat surface.

(↓ Youtube video)

S3 Video (c1-deform-fixwall-0.1u). Biofilm removal at U_f = 0.1 m/s. The top of the biofilm is highly elongated. Small clusters erode from the deforming biofilm and the amount of biomass removed is less than the U_f = 0.2 m/s case.

(↓ Youtube video)

S4 Video (c1-deform-periodicwall-0.2u). Biofilm deformation and detachment with periodic wall at U_f = 0.2 m/s. Microbes crossing the boundary will re-appear on the opposite side of the domain. It can be observed that the detached clusters can re-attached to the biofilm surface or re-agglomerate with other clusters.

(↓ Youtube video)

S5 Video (c2-biofilm-100proc) Growth of a large biofilm system. The multiple species biofilm is grown without flow and reaches 2.3 × 10⁷ particles after 160 hours (CPU time = 30 hours). The biofilm forms a wavy structure because of the high nutrient concentration environment and the non-uniform initial microbial distribution.