3‐D spatio–temporal structures of biofilms in a water channel

Abstract

We develop a numerical predictive tool for multiphase fluid mixtures consisting of biofilms grown in a viscous fluid matrix by implementing a second-order finite difference discretization of the multiphase biofilm model developed recently on a general purpose graphic processing unit. With this numerical tool, we study a 3-D biomass-flow interaction resulting in biomass growth, structure formation, deformation, and detachment phenomena in biofilms grown in a water channel in quiescent state and subject to a shear flow condition, respectively. The numerical investigation is limited in the viscous regime of the biofilm-solvent mixture. In quiescent flows, the model predicts growth patterns consistent with experimental findings for single or multiple adjacent biofilm colonies, the so-called mushroom shape growth pattern. The simulated biomass growth both in density and thickness matches very well with the experimentally grown biofilm in a water channel. When shear is imposed at a boundary, our numerical studies reproduce wavy patterns, pinching, and streaming phenomena observed in biofilms grown in a water channel.

A mechanistic Individual-based Model of microbial communities

“…However, if the biofilm grows in a moving fluid the structural properties of the biofilm will differ [ 41 ]. Experimental work has shown that high shear forces result in thinner, denser, stronger and filamentous biofilms while low shear forces result in biofilms with mushroom and circular shapes [ 42 ]. It is also reported in the literature that biofilms produce undulating shapes when grown in flow fields [ 23 , 42 ].…”

Effects of water flow on submerged macrophyte-biofilm systems in constructed wetlands

“…Current velocity affected the architecture and dynamics of natural, multiphyla, and cross-trophic level biofilms from a forested piedmont stream 15 . Recently, a 3-D biofilm model was used to illustrate the effects of water flow on biofilms in a water channel and found that excessive shear force could detach or bend the thin-necked biofilm colony (a common structure during biofilm formation), decreasing the biofilm thickness and roughness 36 . The heterogeneity of biofilms was also affected by surface characteristics of plant leaves.…”

Multiscale Flux-Based Modeling of Biofilm Communities

“…In terms of the flux amplitudes β j (see (17)), the exchange flux functions e jk (v(x)) = e k (v(x)), k = 1, 2, 3 (see (12)), are given by the components e k (v) = −v • i k of v corresponding to exchange reactions, where i k is a 6-vector with a 1 in the kth place and 0's elsewhere. In this example,…”

“…where r jk is a consumption/production rate (units of time −1 ) and Y jk is a yield coefficient (units of volume fraction per concentration) [38]. On larger scales, advective transport in a bulk flow may also be of importance and can be included [12,14,22,23,28,51,66] but will not be considered here for simplicity. C is the vector with components of all dissolved concentrations C k exterior to cells.…”

“…Optimization. Equations ( 9) for the metabolic models together with (10) and (12) for the macroscale biofilm model make up the foundations of a kinetics-free system. As already noted, though, system (9) is underdetermined and requires a selection principle for choosing a particular flux vector out of the full solution space.…”