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Bacterial Biofilms:
Building Slimy Cities
Gillian Ryan
St. Francis Xavier University
Outline:
 Background
 The Model
 Preliminary Results
 Future plans
Biofilm:
 Community of microorganisms, including
bacteria, fungi, and protozoa, found in aqueous
environments
Division
Quorum
Sensing
Exopolysaccharides
Chemotaxis
Biofilm:
 Picture of a cross
sectional slice of a
biofilm, taken with a
laser scanning
confocal microscope.
Grown in our lab
at StFX
The Model:
Base Forces
r-ij
i
 Preserve Linear
Momentum
Ro  Ri  R j
j
 If rij  Ro :
Ro  r
Fi C   ( Ro  rij )rˆij
1
2
Fi   ( Ro  rij )  ij t rˆij
D
2
Fi   ( Ro  rij ) (rˆij  v~ij )rˆij
R
  2kbT
2
v~ij  v~i  v~j
 ij   ji
Quorum Sensing:
 On/off switch
 Controls EPS production
 Dynamically evaluated
EPS:
 Only produced by biofilm
bacteria
Amount of EPS emitted is a
constant
 EPS spring force binds bacteria
to EPS carrying water and EPScarrying water to EPS-carrying
water
Attractants:
 Amount of positive chemotactic signals emitted
inversely related on number of bacterial neighbors
 Carried by water, which attracts bacteria
 Force is proportional to amount of attractant in water
FA1
FA2
Division & Inhibitors:
 Spring Force holds dividing
bacteria components together
 Inhibitory emissions dependent
on bacterial neighbors
 Probability of division depends
on inhibitor concentration
The Simulation Method:
 Molecular Dynamics, specifically Dissipative Particle
GOOD
Dynamics
(DPD) FOR WATER FLOW !
 Velocity-Verlet Algorithm
1
2
ri (t  t )  ri (t )  tvi (t )  (t ) ai (t )
2
v~i (t  t )  vi (t )  tai (t )
 Fi
ai (t  t ) 
massi
1
vi (t  t )  vi (t )  (t )( ai (t )  ai (t  t ))
2
The Simulation:
 1000 water spheres and 1 free
bacterium
 World is initially a 10x10x10 micron
box with periodic boundary conditions
 System is initialized with zero linear
momentum
Healthy Planktonic Bacteria
Results:
Healthy Biofilm Bacteria
1000 water
Inhibited Bacteria
28 bacteria
Y
Water
Z
X
Z
X
Y
Healthy Planktonic Bacteria
Results:
Healthy Biofilm Bacteria
1000 water
Inhibited Bacteria
99 bacteria
Y
Water
Z
X
Z
X
Y
COMING SOON:
SURFACES!
Acknowledgements:
 David Pink
 Bonnie Quinn
 Laura Filion
 Ryan MacDougall
 NSERC