Notes

Winter 2016

Hydrodynamics in Bacteria Collective Intelligence

Part II: d = 3 dimensional

The notes study the coupling dynamics between bacteria intelligent and the water hydrodynamics, with the
assumption that both the bacteria and the water can be treated as incompressible fluids mixed together. Hence,
we use the Navier-Stokes equations for 2 miscible incompressible fluids and let the bacteria growth (combination
of reproduction and death) rate goes to 0.
For simplicity, the equations are written for d = 3 spatial dimension, with b(~x, t) is the number of bacteria per
unit volume of the whole system, c(~x, t) is the number of chemoa per unit volume of the whole system, f (~x, t) is
the number of food per unit volume of the whole system, D is the bacteria-water binary diffusivity, Dc is the
chemoa diffusivity, Df is the food diffusivity, is the chemoa guiding coefficient, is the chemoa production
coefficient, is the food consumption rate, w is the mass density of water, m is the mass of a bacteria, v is the
volume of a bacteria, ~u(~x, t) is the local velocity of the mixture, is the viscosity of water, P (~x, t) is the pressure
and T(~x, t) is the viscous stress tensor. Assume that the volume of chemoa and food is neglectable.
The bacteria mass density:

m
v
Bacteria has a critical density, as they can fill the whole space:
b =

b b =

1
v

(1)

(2)

Define the bacteria volume fraction b and the water volume fraction w :
b = bv , w = 1 b

(3)

The local mass density (x, t) of the mixture is then expressed as:
= b b + w w

(4)

AB = P AB + TAB

(5)

The total stress is defined as:

Phenomenologically, by generalize the Korteweg formula one has the viscous tensor of the form [1]:
1,...,7 = 1,...,7 (b )

(6)

TAB = 1 (A uB + B uA ) + 2 C uC AB + 3 A B + 4 A B b

(7)

+5 A B + 6 A b B b + 7 (A B b + B A b )

(8)

To understand the effective diffusion of the chemoa and the food in a fluid filled with bacteria, if the assumption is
simply that the bacteria is impermeable and the tortuousity is unity  = 1 then [1]:
0
Dc,f
=

w
b
Dc,f = (1 )Dc,f

b

(9)

In this notes, we will use the above model for simplicity. A more accurate model is to consider bacteria to be
spherical objects with no diffusivity inside [2]:
00
Dc,f
=

2w
2b 2b
Dc,f =
Dc,f
2 + b
2+b

(10)

Notes

Winter 2016

The Intel-Hydro Equations

In the limit of small bacteria volume fraction bv  1, the collective intelligence of bacteria can be described by the
Patlak-Keller-Segel equations:
t b D 2 b + A (bA c) = b = 0
(11)
t c Dc 2 c = bf
2

t f Df f = b

(12)
(13)

In the limit where the chemoa guidance is unimportant 0, the mixture between bacteria and water can be
described by the mixing equations [1]:
1
t b + A (b uA ) Dw A ( A b ) = 0

1
t w + A (w uA ) Db A ( x A ) = 0

Also, it is important to remember the mass conservation equation and the Navier-Stokes equation:

(14)
(15)

t + A (uA ) = 0

(16)

t uA + uB B uA x (x u) = B AB

(17)

Combine the 2 descriptions, a possible simple choice for the intel-hydro equations can be written down:
1
t b + A (b uA ) Dw A ( A b ) + A (b A c) = 0



t c + A (cuA ) Dc A (1 b )A c = bf


t f + A (f uA ) Df A (1 b )A f = b

(18)
(19)
(20)

t + A (uA ) = 0

(21)

t uA + uB B uA = B AB

(22)

It should be noted that for bacteria, which is usually floating freely in water as the gravity pulling it down is the
same as bouncy pushing it up:
b = w =
(23)
The intel-hydro equations can now be simplified greatly:
A uA = 0

(24)

t b + uA A b D 2 b + A (bA c) = 0


b
t c + uA A c Dc A (1 )A c = bf
b


b
t f + uA A f Df A (1 )A f = b
b
t uA + uB B uA = B AB

(25)
(26)
(27)
(28)

There are d + 4 equations with d + 4 unknowns b, c, f , P and ~u hence this system is solvable. In d = 1
dimension, the divergence-free condition of the velocity mean must be a constant, therefore the pressure should be
the same everywhere. However such problem doesnt appear in higher dimensional theory. When the bacteria
density is high b 1, the effective diffusion of the chemoa and the food slow down drastically, corresponding to
the natural biological function of strong attraction of bacteria and preventing the resource from leaking out. It
should be noted that bacteria are always swimming, not simply just diffusing, so the model is obviously
inadequate without taking into account the bacteria velocity distribution which should be dependent of many
parameters in the theory.

References

[1] D.Joseph, Y. Renardy; Fundamentals of Two-Fluids Dynamics, Part 2, p359-357

[1] E. Cussler; Diffusion, p174