Variable viscosity and density biofilm simulations using an immersed boundary method, part II: Experimental validation and the heterogeneous rheology-IBM

Jay A. Stotsky, Jason F. Hammond, Leonid Pavlovsky, Elizabeth J. Stewart, John G. Younger, Michael J. Solomon, David M. Bortz

Research output: Contribution to journalArticlepeer-review

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Abstract

The goal of this work is to develop a numerical simulation that accurately captures the biomechanical response of bacterial biofilms and their associated extracellular matrix (ECM). In this, the second of a two-part effort, the primary focus is on formally presenting the heterogeneous rheology Immersed Boundary Method (hrIBM) and validating our model by comparison to experimental results. With this extension of the Immersed Boundary Method (IBM), we use the techniques originally developed in Part I ([19]) to treat biofilms as viscoelastic fluids possessing variable rheological properties anchored to a set of moving locations (i.e., the bacteria locations). In particular, we incorporate spatially continuous variable viscosity and density fields into our model. Although in [14,15], variable viscosity is used in an IBM context to model discrete viscosity changes across interfaces, to our knowledge this work and Part I are the first to apply the IBM to model a continuously variable viscosity field.We validate our modeling approach from Part I by comparing dynamic moduli and compliance moduli computed from our model to data from mechanical characterization experiments on Staphylococcus epidermidis biofilms. The experimental setup is described in [26] in which biofilms are grown and tested in a parallel plate rheometer. In order to initialize the positions of bacteria in the biofilm, experimentally obtained three dimensional coordinate data was used. One of the major conclusions of this effort is that treating the spring-like connections between bacteria as Maxwell or Zener elements provides good agreement with the mechanical characterization data. We also found that initializing the simulations with different coordinate data sets only led to small changes in the mechanical characterization results. Matlab code used to produce results in this paper will be available at https://github.com/MathBioCU/BiofilmSim.

Original languageEnglish (US)
Pages (from-to)204-222
Number of pages19
JournalJournal of Computational Physics
Volume317
DOIs
StatePublished - Jul 15 2016

Bibliographical note

Funding Information:
This work was supported in part by the National Science Foundation grants PHY-0940991 and DMS-1225878 to DMB, and PHY-0941227 to JGY and MJS, and by the Department of Energy through the Computational Science Graduate Fellowship program, DE-FG02-97ER25308 , to JAS. This work utilized the Janus supercomputer, which is supported by the National Science Foundation (award number CNS-0821794 ), the University of Colorado Boulder , the University of Colorado Denver, and the National Center for Atmospheric Research . The Janus supercomputer is operated by the University of Colorado Boulder. We would also like to thank the reviewers for several useful suggestions that improved this paper.

Publisher Copyright:
© 2016 Elsevier Inc.

Keywords

  • Biofilm
  • Computational fluid dynamics
  • Immersed boundary method
  • Navier-Stokes equation
  • Viscoelastic fluids

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