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

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

doi:10.1016/j.jcp.2016.04.027

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

Authors:

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

Publication Date:: Fri Jul 01 00:00:00 EDT 2016

Sponsoring Org.:: USDOE

OSTI Identifier:: 1347626

Grant/Contract Number:: PHY-0940991; PHY-0941227; DMS-1225878; CNS-0821794; FG02-97ER25308

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: Journal of Computational Physics

Additional Journal Information:: Journal Name: Journal of Computational Physics Journal Volume: 317 Journal Issue: C; Journal ID: ISSN 0021-9991

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Citation Formats


                    Stotsky, Jay A., Hammond, Jason F., Pavlovsky, Leonid, Stewart, Elizabeth J., Younger, John G., Solomon, Michael J., and Bortz, David M. Variable viscosity and density biofilm simulations using an immersed boundary method, part II: Experimental validation and the heterogeneous rheology-IBM.  United States: N. p., 2016. 
Web.  doi:10.1016/j.jcp.2016.04.027.

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                    Stotsky, Jay A., Hammond, Jason F., Pavlovsky, Leonid, Stewart, Elizabeth J., Younger, John G., Solomon, Michael J., & Bortz, David M. Variable viscosity and density biofilm simulations using an immersed boundary method, part II: Experimental validation and the heterogeneous rheology-IBM.  United States.  https://doi.org/10.1016/j.jcp.2016.04.027

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                    Stotsky, Jay A., Hammond, Jason F., Pavlovsky, Leonid, Stewart, Elizabeth J., Younger, John G., Solomon, Michael J., and Bortz, David M. Fri .  
"Variable viscosity and density biofilm simulations using an immersed boundary method, part II: Experimental validation and the heterogeneous rheology-IBM".  United States.  https://doi.org/10.1016/j.jcp.2016.04.027.

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@article{osti_1347626,

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

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

  abstractNote = {},

  doi          = {10.1016/j.jcp.2016.04.027},

  journal      = {Journal of Computational Physics},

  number       = C,

  volume       = 317,

  place        = {United States},

  year         = {Fri Jul 01 00:00:00 EDT 2016},

  month        = {Fri Jul 01 00:00:00 EDT 2016}

}

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https://doi.org/10.1016/j.jcp.2016.04.027

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

Citation Formats

Role of Environmental and Antibiotic Stress on Staphylococcus epidermidis Biofilm Microstructure journal, May 2013

Simulating Biofilm Deformation and Detachment with the Immersed Boundary Method journal, March 2016

Effects of Temperature on the Morphological, Polymeric, and Mechanical Properties of Staphylococcus epidermidis Bacterial Biofilms journal, February 2015

Multicomponent model of deformation and detachment of a biofilm under fluid flow journal, May 2015

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Numerical analysis of blood flow in the heart journal, November 1977

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Immersed Boundary Method for Variable Viscosity and Variable Density Problems Using Fast Constant-Coefficient Linear Solvers I: Numerical Method and Results journal, January 2013

An immersed-boundary method for flow–structure interaction in biological systems with application to phonation journal, November 2008

Immersed Boundary Method for Variable Viscosity and Variable Density Problems Using Fast Constant-Coefficient Linear Solvers II: Theory journal, January 2014

Modeling Viscoelastic Networks and Cell Deformation in the Context of the Immersed Boundary Method journal, November 1998

Boundary conditions for incompressible flows journal, January 1986

$L^p$ Convergence of the Immersed Boundary Method for Stationary Stokes Problems journal, January 2014

Phase Field Models for Biofilms. I. Theory and One-Dimensional Simulations journal, January 2008

Molar Mass, Entanglement, and Associations of the Biofilm Polysaccharide of Staphylococcus epidermidis journal, April 2013

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Artificial biofilms establish the role of matrix interactions in staphylococcal biofilm assembly and disassembly journal, August 2015

3-D Numerical Simulations of Biofilm Flows journal, August 2011

The characterization of functions involved in the establishment and maturation of Klebsiella pneumoniae in vitro biofilm reveals dual roles for surface exopolysaccharides journal, March 2008

Size Distribution of Bacterial Cells journal, January 1972

Properties of Discrete Delta Functions and Local Convergence of the Immersed Boundary Method journal, January 2012

Interaction of two flapping filaments in a flowing soap film journal, July 2003

An Immersed Boundary Method with Formal Second-Order Accuracy and Reduced Numerical Viscosity journal, May 2000

A 3D numerical study of antimicrobial persistence in heterogeneous multi-species biofilms journal, March 2016

An experimentally validated immersed boundary model of fluid–biofilm interaction journal, June 2010

In siturheology of Staphylococcus epidermidis bacterial biofilms journal, January 2013

A Multidimensional Multispecies Continuum Model for Heterogeneous Biofilm Development journal, January 2007

Forces on the surface of small ellipsoidal particles immersed in a linear flow field journal, February 2002

Coupled Electrostatic, Hydrodynamic, and Mechanical Properties of Bacterial Interfaces in Aqueous Media journal, October 2008

Role of Environmental and Antibiotic Stress on Staphylococcus epidermidis Biofilm Microstructure
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Simulating Biofilm Deformation and Detachment with the Immersed Boundary Method
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Effects of Temperature on the Morphological, Polymeric, and Mechanical Properties of Staphylococcus epidermidis Bacterial Biofilms
journal, February 2015

Multicomponent model of deformation and detachment of a biofilm under fluid flow
journal, May 2015

Fluid Dynamic Models of Flagellar and Ciliary Beating
journal, February 2007

Three-dimensional biofilm model with individual cells and continuum EPS matrix
journal, January 2006

Numerical analysis of blood flow in the heart
journal, November 1977

Accurate Projection Methods for the Incompressible Navier–Stokes Equations
journal, April 2001

Contribution of the Klebsiella pneumoniae Capsule to Bacterial Aggregate and Biofilm Microstructures
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Immersed Boundary Method for Variable Viscosity and Variable Density Problems Using Fast Constant-Coefficient Linear Solvers I: Numerical Method and Results
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Immersed Boundary Method for Variable Viscosity and Variable Density Problems Using Fast Constant-Coefficient Linear Solvers II: Theory
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Modeling Viscoelastic Networks and Cell Deformation in the Context of the Immersed Boundary Method
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Boundary conditions for incompressible flows
journal, January 1986

$L^p$ Convergence of the Immersed Boundary Method for Stationary Stokes Problems
journal, January 2014

Phase Field Models for Biofilms. I. Theory and One-Dimensional Simulations
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