skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Authors:
; ; ; ; ; ; ORCiD logo
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1347626
Grant/Contract Number:
FG02-97ER25308
Resource Type:
Journal Article: Publisher's Accepted Manuscript
Journal Name:
Journal of Computational Physics
Additional Journal Information:
Journal Volume: 317; Journal Issue: C; Related Information: CHORUS Timestamp: 2017-10-06 09:02:32; 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.
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. doi:10.1016/j.jcp.2016.04.027.
Stotsky, Jay A., Hammond, Jason F., Pavlovsky, Leonid, Stewart, Elizabeth J., Younger, John G., Solomon, Michael J., and Bortz, David M.. 2016. "Variable viscosity and density biofilm simulations using an immersed boundary method, part II: Experimental validation and the heterogeneous rheology-IBM". United States. doi:10.1016/j.jcp.2016.04.027.
@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 = 2016,
month = 7
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1016/j.jcp.2016.04.027

Save / Share:
  • Biofilm processes are of interest to researchers in a variety of fields including bioremediation, oil recovery, waste water treatment, medicine, and dentistry. In this paper we describe how this complex, dynamic, fluid-structure interaction can be modeled successfully using the immersed boundary method. The model presented here includes the coupling of hydrodynamics; substrate reaction, diffusion, and convection; as well as the chemotactic response of swimming microbes. Cell-cell aggregation and cell-substratum adhesion are modeled by generating appropriate binding forces between discrete representations of organisms that may hold them together, or if fluid stresses are large, may yield and release the organisms. Inmore » this paper, we show two-dimensional numerical simulations to demonstrate several different types of scenarios that may be modeled using immersed boundary methods. These simulations indicate the variety of different phenomena one might expect in biofilm processes. 24 refs., 8 figs., 2 tabs.« less
  • An immersed boundary method to achieve the consistency with a desired wall velocity was developed. Existing schemes of immersed boundary methods for incompressible flow violate the wall condition in the discrete equation system during time-advancement. This problem arises from the inconsistency of the pressure with the velocity interpolated to represent the solid wall, which does not coincide with the computational grid. The numerical discrepancy does not become evident in the laminar flow simulation but in the turbulent flow simulation. To eliminate this inconsistency, a modified pressure equation based on the interpolated pressure gradient was derived for the spatial second-order discretemore » equation system. The conservation of the wall condition, mass, momentum and energy in the present method was theoretically demonstrated. To verify the theory, large eddy simulations for a plane channel, circular pipe and nuclear rod bundle were successfully performed. Both these theoretical and numerical validations improve the reliability and the applicability of the immersed boundary method.« less
  • A new Lagrangian particle model based on smoothed particle hydrodynamics (SPH) was developed and used to simulate Darcy scale flow and transport in porous media. The proposed numerical method has excellent conservation properties and treats advection exactly. The method was used in stochastic analysis of miscible density driven fluid flows. It was found that heterogeneity significantly increases dispersion and slows development of Rayleigh-Taylor instability. The presented numerical examples illustrate the advantages of Lagrangian methods for stochastic transport simulations.
  • This study is an experimental investigation of variable density groundwater flow in homogeneous, layered and lenticular porous media. At the scale of the experiments the flow of dissolved mass in water depends upon both forced and free convection. In addition, density differences as low as 0.0008 g/cm{sup 3} (1,000 mg/L NaCl) between a plume of dense water and ambient groundwater in a homogeneous medium produces gravitational instabilities at realistic groundwater velocities. These instabilities are manifest by lobe-shaped protuberances that formed first along the bottom edge of the plume and later within the plume. As the density difference increases to 0.0015more » g/cm{sup 3} (2,000 mg/L NaCl), 0.037 g/cm{sup 3} (5,000 mg/L NaCl), or higher, this unstable mixing due to convective dispersion significantly alters the spreading process. In a layered medium, reductions in hydraulic conductivity of the order of half an order of magnitude or less can influence the flow of the dense plume. Dense water may accumulate along bedding interfaces, which when dipping can result in plume migration velocities larger than ambient groundwater velocities. In a lenticular medium the combination of convective dispersion and nonuniform flow due to heterogeneities result in relatively large dispersion. Scale considerations, further, indicate that convective dispersion may provide an important component of mixing at the field scale.« less