Variable Viscosity and Density Biofilm Simulations using an Immersed Boundary Method, Part I: Numerical Scheme and Convergence Results

DOI10.3970/CMES.2014.098.295zbMATH Open1356.76052arXiv1302.3663OpenAlexW32197242MaRDI QIDQ2964941FDOQ2964941

Authors: Jason F. Hammond, Elizabeth J. Stewart, Michael J. Solomon, John G. Younger, David M. Bortz 

Publication date: 27 February 2017

Abstract: In this work we consider how surface-adherent bacterial biofilm communities respond in flowing systems. We simulate the fluid-structure interaction and separation process using the immersed boundary method. In these simulations we model and simulate different density and viscosity values of the biofilm than that of the surrounding fluid. The simulation also includes breakable springs connecting the bacteria in the biofilm. This allows the inclusion of erosion and detachment into the simulation. We use the incompressible Navier-Stokes (N-S) equations to describe the motion of the flowing fluid. We discretize the fluid equations using finite differences and use a geometric multigrid method to solve the resulting equations at each time step. The use of multigrid is necessary because of the dramatically different densities and viscosities between the biofilm and the surrounding fluid. We investigate and simulate the model in both two and three dimensions. Our method differs from previous attempts of using IBM for modeling biofilm/flow interactions in the following ways: the density and viscosity of the biofilm can differ from the surrounding fluid, and the Lagrangian node locations correspond to experimentally measured bacterial cell locations from 3D images taken of Staphylococcus epidermidis in a biofilm.

Full work available at URL: https://arxiv.org/abs/1302.3663

Recommendations

• Variable viscosity and density biofilm simulations using an immersed boundary method, part II: Experimental validation and the heterogeneous rheology-IBM
• Modeling biofilm processes using the immersed boundary method
• Simulating Biofilm Deformation and Detachment with the Immersed Boundary Method
• Immersed boundary approach to biofilm spread on surfaces
• Immersed Boundary Models of Biofilm Spread
• Simulating biofluid-structure interactions with an immersed boundary framework -- a review
• A novel model for biofilm growth and its resolution by using the hybrid immersed interface-level set method
• Phase-field models for biofilms. II: 2-D numerical simulations of biofilm-flow interaction
• Numerical simulation of biofilm processes in closed conduits

zbMATH Keywords

biofilmimmersed boundary methodNavier-Stokes equationmultigridviscoelastic fluidcomputational fluid dynamics

Mathematics Subject Classification ID

Finite difference methods applied to problems in fluid mechanics (76M20) Navier-Stokes equations for incompressible viscous fluids (76D05) Finite difference methods for initial value and initial-boundary value problems involving PDEs (65M06) Physiological flows (76Z05) Physiological flow (92C35)

Cited In (11)

• Variable viscosity and density biofilm simulations using an immersed boundary method, part II: Experimental validation and the heterogeneous rheology-IBM
• Multiscale flux-based modeling of biofilm communities
• A point process model for generating biofilms with realistic microstructure and rheology
• Fragmentation of biofilm-seeded bacterial aggregates in shear flow
• Continuum and discrete approach in modeling biofilm development and structure: a review
• A novel model for biofilm growth and its resolution by using the hybrid immersed interface-level set method
• A posteriori error analysis of fluid-structure interactions: time dependent error
• Immersed Boundary Models of Biofilm Spread
• Simulating Biofilm Deformation and Detachment with the Immersed Boundary Method
• Title not available (Why is that?)
• Modeling biofilm processes using the immersed boundary method

This page was built for publication: Variable Viscosity and Density Biofilm Simulations using an Immersed Boundary Method, Part I: Numerical Scheme and Convergence Results

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2964941)