biofilm mechanics
TRANSCRIPT
A Combined Experimental and Numerical Study of Biofilm Detachment
Presented by: Ashkan Safari
Supervisors: Prof. Alojz Ivankovic
Prof. Eoin Casey
1
"Biofilms are responsible for over 80% of
microbial infections in the bodyβ (US National Institutes of Health)
The big picture
2
Undefined Compression
AFM Retraction
Adhesive Joint Failure Test
FV simulation (OpenFOAM)
Mode I Mode II
CZM: Max & GIC
E(t)
Biofilm Mechanics, What We Know?
3
β’ A composite material: cells, EPS, and micro (and macroscale) voids.
β’ Biofilm detachment: increase in external forces or decrease in interface forces.
β’ Heterogeneous structure in time and space,
β’ A combined advanced microscopy methods & various modes of loadings.
β’ Mechanically heterogeneous, throughout thickness and on the surface.
β’ Isotropic or anisotropic?
β’ Strain rate dependency of mechanical properties.
β’ Viscoelastic fluid or viscoelastic solid?
β’ Burger model, Standard linear solid and generalised Maxwell models (No spring).
β’ Ductile Failure behaviour.
Ductile failure
Liquid fraction? Viscoelastic solid
He, Y., et al. (2013), ." PLoS One 8(5): e63750 Aggarwal, S. and R. M. Hozalski
(2010). Biofouling 26(4): 479-486Wilking, J. N., et al., (2011). MRS Bulletin 36(05): 385-391.
This Study: Goals & Methods Used
4
Biofilm maturation, more EPSβ¦.β’ Defining the linear viscoelastic behaviour
β’ Prony series & Hereditary integral form
β’ Comparing different test methods at micro and macroscale levels
β’ Evaluation of elastic modulus at macroscale level:
β’ Mechanical heterogeneity: Indentation & multiple Hertz model fitting
β’ Adhesion effect: Retraction and JKR-based method
β’ Evaluation of failure at biofilm-glass interface under bulk mechanical loads
β’ CZM applicability for mode I and II interfacial separation
β’ AFM retraction analysis for a pure adhesive separation
β’ CZM-base FSI for biofilm detachment under fluid shear stress
Undefined mixed culture mature
biofilm from wastewater system
v
Realistic intact biofilm structureBiofilm sample in this study
πΈ π‘ = πΈ0 + π=1
π
πΈππ β(π‘ ππ
π π‘ =
0
π‘
πΈ π‘ β π πν(π
ππ‘ππ
Stress Relaxation: Compression vs. Rheometry
6
AB
C
A B C
πΈππππ
πΈ=
1 + 3π1 β π1 + π
π2
1 + 3π 1 β 2π π2 πΈππππ =1.8E
π =0.46
*Williams, J. G. and C. Gamonpilas (2008). International Journal of Solids and Structures 45(16): 4448-4459.
S= π β = 1.6
AFM Indentation and Retraction: Hertz vs. JKR
Distance
Contact line X=0-X
+X
Indentation
Retraction
β’ Initial nonlinear part due to EPS,
β’ Variation in EPS, different indentation depths,
β’ Hertz model used, but better to use JKR,
β’ Structural/mechanical homogeneity throughout depth,
β’ Higher indentation, stiffer biofilm due to void closure.
Ξ
Padh
πΈ =β3πππβ
π
3 βπΏ
1 + 4 β2 3
β 3 2
πΉ =πΈ
1 β π2
π2 + π 2
2ππ
π + π
π β πβ ππ ; πΏ =
π
2ππ
π + π
π β π
8
Hertz model Simplified JKR based displacement*
*Grunlan, J. C., X. Xia, D. Rowenhorst and W. W. Gerberich (2001). "Preparation and evaluation of tungsten tips relative to diamond for nanoindentation of soft
materials." Review of Scientific Instruments 72(6): 2804-2810.
Finite Volume Numerical Method - Linear Viscoelastic Model
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Finite Volume Discretization in OpenFOAM
π
ππ‘
π
ππ΅π ππ +
π
ππ΅ππ. π ππ
=
π
ππππππ. π ππ +
π
πππ ππ
Continuum mechanics formulations
π
ππ‘
π
ππ΅π ππ +
π
ππ΅ππ. π ππ =
π
πππππππ. π ππ +
π
πππ ππ
πππ΅π
ππ‘+ π». ππ΅ππ = π». πππ»π + πππ
ππ
ππ‘+ π». ππ = 0
πππ£
ππ‘+ π». πππ = π». π
π π‘ = 0
π‘
2π(π‘ β π πΏπΊ(π
πΏπππ‘ + π°
0
π‘
π π‘ β π π‘π πΏπΊ(π
πΏπππ‘
πΏπ π‘ = 2π π‘ β π πΏπΊ π + π π‘ β π π‘ππΏπΊ π π°
πΏπΊ π =1
2π»πΏπ π + π»πΏπ π π
π΅π=1
π΅π= π
β’ Total work of adhesion vs. pure interfacial separation energy
β’ Dissimilar bimaterial stress distribution
β’ Local stress concentration at the free interface edge
β’ CZM for interfacial crack
Biofilm-Glass Dissimilar Bimaterial Failure: Cohesive Zone Model
10
πππβ = βπΎ(1 + π
πΊπ = 0
πΏπ
π. ππΏ
Interface stress distribution
(/E ratio)
CZM
Homogeneous cohesive crack
Interfacial crack
Experimental Evaluation of Biofilm-glass Interfacial Separation
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A B
A
B
C
D
C D
Mode I interfacial failure
A B C D
A
B
C
D
Mode II interfacial failure
Separation Energy & Maximum Traction β JKR Contact Model
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Padh
π 03 =
3
4
6ππ 2βπΎ
πΈπ ππ = 0.63π 0
π΄ππ = ππ ππ2
ππ ππππππ‘πππ =πππβ
π΄πππππβ = β
3
2βπΎππ
β’ Cohesive or adhesive pull-off force?
β’ Microscale separation energy from AFM retraction 4 orders of magnitude smaller than total failure energy (bulk butt joint test)
average= 66.6 Pa
Numerical Prediction of Mode I and II Separation Initiation
13
B
Material Properties Value
Prony Coefficients
E0, E1 (Pa) 339.6, 100.2
t1, (sec) 8.58
Density, (kg/m3) 1000
Poissonβs Ratio, (-) 0.46
CZM Properties Value
Mode I Maximum Traction (Pa) 205
Mode I Separation Energy (mJ/m2) 0.033
Mode II Maximum Traction (Pa) 150
Mode II Separation Energy (mJ/m2) 0.033
B
average= 59.2 Pa
Biofilm: /E=0.001 Pa-1 (E=1 kPa & =0.46)
Glass: /E=5x10-12 Pa-1 (E=50 GPa & =0.25)
FSI Study of Biofilm Detachment under Fluid Shear Stress
*Walter, M., et al., (2013). "Detachment characteristics of a mixed culture biofilm using particle size analysis." Chemical Engineering Journal 228(0): 1140-1147.
** Abe, Y. (2012). "Cohesiveness and hydrodynamic properties of young drinking water biofilms." water research 46, 1155-1166. 14
β’ Shear Induced Detachment Test in Flow Cell: Particle Size Analysis*:
β’ Frequency of sloughing/average size of particles (>5.0 ΞΌm2) increased significantly at WSS above 0.04Pa (at 18 mm/s)
β’ FSI Simulation: Partitioned FSI approach: one-way coupling.
β’ Mode II CZM/ Dugdale type
β’ WSS of 0.04 Pa assumed as Max,
β’ of less than 0.00001 mJ/m2 by Inverse method (critical= 0.25 m).
β’ Hydrodynamic shear stress is 3 orders of magnitude lower than mechanically
measured value (global versus local properties).**
π = βππ° + 2π πΊ
πΊ =1
2[π»π π + π»π π π]
Solve Fluid
Fixed Solid
Solve Solid
π=π π
ππ₯
π·
FSI Simulation Results
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At the highest flow velocity of 18 mm/s
water flow water flow
Just above the flow velocity of 2 mm/s
Conclusions
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β’ Mature wastewater biofilm generally have a low elastic modulus.
β’ Mechanical properties of this mature biofilm do not depend on the mode of loading applied.
β’ Compressive elastic modulus of biofilm could be an overestimated (a bonded compression)
β’ Strain rate dependency of elastic modulus (at intermediate range).
β’ Viscoelastic solid behaviour described by Generalised Maxwell Model with a free spring.
β’ At microscale level, biofilm is considered mechanically inhomogeneous.
β’ significant influence of adhesion forces on the elastic properties.
β’ Macroscale adhesive joint failure evaluation methods as useful methods in order to investigate the interfacial failure for biofilms.
β’ Cohesive Zone Model can be used as a reliable approach to predict the separation initiation at the crack tip zone at the microscale level.
β’ Interfacial crack initiates due to a local stress concentration at dissimilar biofilm-glass interface edge.
β’ AFM retraction curve analysis as a useful method to obtain CZM parameters.
β’ Biofilm-glass interfacial failure energy is mainly associated with the bulk biofilm deformation than pure separation energy at the interface.
β’ The measured hydrodynamic separation stress (at global scale) and separation energy are found to be 4 orders of magnitude lower than
mechanically measured values by AFM (at local scale), giving a similar crack opening critical distance for both scales of testing.
β’ Uneven biofilm surface on the surface may lead to earlier detachment events due to an increase in shear stress at the localised areas.
β’ Individual biofilm aggregate can detach at earlier stage than a large carpet-like biofilm due to the local stress zone at biofilm-substrate interface.
Publications
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Conference Publications
β’ Safari. A., Casey, E. and Ivankovic, A (2007) A fluid-structure interaction approach to the investigation of detachment from bacterial biofilms. Proceedings of 13th
Annual Conference Bioengineering in Ireland.
β’ Safari, A., IvankoviΔ, A. and TukoviΔ, Z (2008) Numerical Modelling of Viscoelastic Response of Bacterial Biofilm to Mechanical Stress. 14th Annual Conference
Proceedings of Bioengineering in Ireland.
β’ Safari, A., Walter, M., Casey, E., Ivankovic, A (2008) A two-phase flow model of biofilm detachment. Proceedings of the 31st Annual Meeting of the Adhesion Society,
Austin, USA.
β’ Safari, A., IvankoviΔ, A. and TukoviΔ, Z (2008) Numerical Modelling of Fluid-Biofilm. Proceeding of 8th World Congress on Computational Mechanics (WCCM8),
Venice, Italy.
β’ Safari. A., Ivankovic, A., Tukovic, Z (2009) Numerical modelling of viscoelastic response of biofilm to fluid flow stress. Proceedings of 6th International Congress of
Croatian Society of Mechanics (ICCSM), Dubrovnik, Croatia.
β’ Safari. A., Tukovic, Z., Casey, E., Ivankovic, A (2013) Cohesive Zone Modelling of Biofilm-Glass Interfacial Failure, Joint Symposium of Irish Mechanics Society &
Irish Society for Scientific & Engineering Computation, Dublin, Ireland.
Journal Publications
β’ Safari, A, Habimana, O, Allen, A, Casey, E (2014) The significance of calcium ions on Pseudomonas fluorescens biofilms: a structural, and mechanical study.
Biofouling, 30 :859-869.
β’ Walter, M., Safari, A., Ivankovic, A., Casey, E (2013) Detachment characteristics of a mixed culture biofilm using particle size analysis. Chemical Engineering
Journal, 228 :1140-1147.
Submitted Journal Publications
β’ Safari. A., Tukovic, Z., Walter, M., Casey, E., Ivankovic, A (Expected in 2015) Mechanical Properties of a Mature Biofilm from a Wastewater System - From
Microscale to Macroscale Level. For peer review in Biofouling.
β’ Safari. A., Tukovic, Z., Cardiff, Ph., Walter, M., Casey, E., Ivankovic, A (Expected in 2015) Investigation of the Interfacial Separation of a Mixed Culture
Mature Biofilm from a Glass Surface β A Combined Experimental and Cohesive Zone Modelling Study. For peer review in Biotechnology and Bioengineering.