Data‐driven modeling of heterogeneous viscoelastic biofilms

Abstract

Biofilms are typically heterogeneous in morphology, structure, and composition, resulting in nonuniform mechanical properties. The distribution of mechanical properties, in turn, determines the biofilm behavior, such as deformation and detachment. Most biofilm models neglect biofilm heterogeneity, especially at the microscale. In this study, an image‐based modeling approach was developed to transform two‐dimensional optical coherence tomography (OCT) biofilm images to a pixel‐scale non‐Newtonian viscosity map of the biofilm. The map was calibrated using the bulk viscosity data from rheometer tests, based on assumed maximum and minimum viscosities and a relationship between OCT image intensity signals and non‐Newtonian viscosity. While not quantitatively measuring biofilm viscosity for each pixel, it allows a rational spatial allocation of viscosities within the biofilm: areas with lower cell density, for example, voids, are assigned lower viscosities, and areas with high cell densities are assigned higher viscosities. The spatial distribution of non‐Newtonian viscosity was applied in an established Oldroyd‐B constitutive model and implemented using the phase‐field continuum approach for the deformation and stress analysis. The heterogeneous model was able to predict deformations more accurately than a homogenous one. Stress distribution in the heterogeneous biofilm displayed better characteristics than that in the homogeneous one, because it is highly dependent on the viscosity distribution. This study, using a pixel‐scale, image‐based approach to map the mechanical heterogeneity of biofilms for computational deformation and stress analysis, provides a novel modeling approach that allows the consideration of biofilm structural and mechanical heterogeneity. Future research should better characterize the relationship between OCT signal and viscosity, and consider other constitutive models for biofilm mechanical behavior.

Identification and extraction of cementation patterns in sand modified by MICP: New insights at the pore scale

“…Comparison of the results of sand porosity and permeability coefficient tests before and after biocementation revealed [ 72 ] that the overall decrease in porosity and hydraulic conductivity of sands injected with CS only and those injected with BS only and incubated continuously under suitable conditions differed considerably (weakly in the former and significantly in the latter). Considering the nutrients provided by the latter test to sustain microbial growth and the culture environment suitable for microbial community proliferation and construction of biofilm systems [ 84 ], we analyzed that microbial cells and their biofilm systems constructed in conjunction with the EPS acted as positive hydraulic barriers to the permeability of the porous media, and had a certain degree of enhanced potential for microbial mineralization [ 30 ].…”

“…The role of the biofilm as a collector continuously attracts bacteria, further enhancing their deposition [ 23 ]. According to Stoke’s law [ 24 , 27 , 31 ], the settling velocity is proportional to the diameter squared and density of the microbial floc, which shows the importance of biofilm thickness and density in preventing washout [ 24 , 29 , 30 ]. Unfortunately, biofilms degrade over time without a nutrient supply [ 32 ].…”

“…Microbial biofilms have been demonstrated effectiveness in controlling water seepage from hydraulic barriers in soils by reducing fluid flow rate [21][22][23][24][25], pore throat size [25,26], free pore volumes [23,27,28], and flow channels [23,28]. Moreover, microbial biofilms have been shown to enhance the shear strength [25,29,30] and viscosity [23,27,28], thereby positively affecting seepage resistance. The role of the biofilm as a collector continuously attracts bacteria, further enhancing their deposition [23].…”

Effects of biofilm heterogeneity on the apparent mechanical properties obtained by shear rheometry

“…Stress sweep tests were performed to identify the LVR for all three types of agar biofilms, and the rheometer analyses used in this study were all within the LVR. While large deformations may capture the nonlinear region of viscoelasticity (Charlton et al, 2019; Jana et al, 2020; Li et al, 2020, 2021; Xia et al, 2022), we chose to avoid this mechanical behavior to simplify our analyses.…”

“…Rheometry is typically used for homogeneous materials, as it captures bulk rather than spatially varying properties. However, biofilms are known to have high spatial variability of mechanical properties (Boudarel et al, 2018; Li et al, 2022). For example, using microscale techniques, biofilms have been shown to be more compliant near the surface and more rigid near the base (Birjiniuk et al, 2014; Galy et al, 2012; Pavissich et al, 2021; Safari et al, 2015).…”