Homework 4, Problem 3

The Allee Effect

Homework 4, Problem 4a
The Ricker Model
Homework 4, Problem 4a
The Beverton-Holt Model
 The Chemostat

Group Model Building Exercise

 The Chemostat
• An apparatus for the continuous culture of
bacterial populations in a steady state.
• Nutrients are supplied continuously to the
culture vessel.
• The cells in the vessel grow continuously on
these nutrients.
• Residual nutrients and cells are removed from
the vessel at the same rate by an overflow,
thus maintaining the culture at a constant
volume.
 The Chemostat

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are needed to see this picture.
 Your Task
• Derive a mathematical model of
bacteria growth in a chemostat
• Use the model to design the system so
that
– The flow rate will not be so great as to
wash out the entire culture
– The nutrient replenishment is sufficiently
rapid so the culture is able to grow
normally
 Building The Model
• Variables

Nutrient Concentration C(t) mass/vol

in growth chamber

Bacteria Density N(t) #/vol

in growth chamber
 Building The Model
• Parameters

Stock Nutrient C0mass/vol

Concentration

Volume of growth V vol.

Chamber

Inflow/Outflow Rate F vol/time

Bacteria growth rate k 1/time

Yield constant 1/ #/mass

 Assumptions
• Growth chamber is well mixed
– No spatial variations
• There is a single, growth limiting
nutrient
• Bacteria growth rate depend on nutrient
availability, that is k = k(C)
• Nutrient depletion occurs continuously
as result of reproduction
 The Model
dN F
 k(C)N  N
dt V
reproduction outflow

 dC F F
 k(C)N  C  C0
dt V V
consumption outflow inflow


 What Should k(C) Be?
• Last time, when deriving logistic growth,
we assumed k(C) = C
– Bacteria growth increases linearly with
nutrient concentration
• Jacques Monod found that following
function provided the best fit to data for
bacteria feeding on a single nutrient:
rC
k(C)  Monod Function
aC
 The Monod Function
• This growth
function is rC
k(C) 
aC
monotonically
increasing with
limit r as C → r

infinity.
• The parameter r is r/2
the maximum
growth rate
• The parameter a is C
a
called that half-
saturation constant
 Sample Parameter Values
• For E.coli grown on glucose at 30
degrees Celsius
r = 1.35 per hour
a = 0.004 g/liter
1/ = 0.23
If glucose is plentiful so that the
specific growth rate is maintained at r
= 1.35, the model predicts a doubling
time of approximately half and hour.
 Bacteria Growth Without
Maintenance
dN rC
 N
dt a  C

dC rC
  N
dt aC

• The steady state for the bacteria

depends on the initial conditions.
 Back to the Chemostat
dN rC
 N  dN
dt a  C
dC rC
  N  dC  dC0
dt aC

• d = F/V is the dilution rate (1/time)
• If 
the chemostat were filled it would take 1/d
hours to empty it. For this reason, 1/d is the mean
residence time of bacteria cells in the chemostat
 Nondimensionalize
Choose Arbitrary Scales:
N C
n c   Tt
A B
Substitute in Model:
dn rBc
 AT  An  dAn
dt a Bc
dc rBc
BT   An  dBc  dC0
dt a  Bc



 Nondimensionalize
N C
n c   Tt
A B

dn r c d
Simplify
 n n
dt T a  c T
 
B
dc Ar c d dC0
 n c
dt a
BT  c T BT
B
Choices

Tr Ba BT
A
 r
Td dC0
B
T
 Nondimensionalize
N C
n c   dt
ad a
r

dn r  c
 dt  d 1 c n  n

dc c C0
 nc 
dt 1 c a
Rename 
Only 2 parameter
r C0 groupings govern
 a1  a2 
d a the dynamics
 Analysis of The Model
dn c
 a1 nn
dt 1 c
dc c
 n  c  a2
dt 1 c

Steady States

c n1  0 c1  a2
0  a1 nn
1 c
c  1  c  1
0 n  c  a2 n 2  a1a2   2 a 1
1 c
 1 1
a 1

 Analysis of The Model
dn c
 a1 nn
dt 1 c
dc c
 n  c  a2
dt 1 c

Steady States
 c1  a2
Exists iff n1  0 Exists iff
1 a1  1
a2   1  1
a1 1 n 2  a1a2  c2 
 a1 1
  1 1
a

 Stability
c c
Let f (n,c)  a1 nn g(n,c)   n  c  a2
1 c 1 c

Compute f f
 a11  (n e ,c e
) a12  (n e ,c e )
x y

g g
a21  (n e ,c e ) a22  (n e ,c e )
x y
 
Let   a11  a22   a11a22  a12 a21
 
   2  4
1,2 
2
Stability of Continuous Models
• In a continuous model, a steady state
will be stable provided that eigenvalues
are both negative (if real) or have
negative real part (if complex).
• As with discrete models complex
eigenvalues are associated with
oscillatory solutions.
 Necessary and Sufficient
Conditions
• For a system of two equations, a
steady state will be stable if:

  a11  a22  0
  a11a22  a12 a21  0



 Stability of Chemostat
• For n1 = 0, c1 = a2

f aa f
a11  (0,a2 )  1 2 1 a12  (0,a2 )  0
x 1 a2 y

g a2 g
a21  (0,a2 )   0 a22  (0,a1 )  1
x 1 a2 y
 

a1a2  a1a2 

 2     1
1 a2 1 a2 
 Stability of Chemostat
• For n1 = 0, c1 = a2

 a1a2 ? a1a2 ?

   1 0  20
1 a2  1 a2

 > 0 if: 1  < 0 if  > 0

a2  ,a1  1 
 1 a1

So the elimination state is stable whenever the nontrivial

steady state does not exist.
 Stability of the Chemostat
• For n2, c2
f f a1n 2
a11  (n 2 ,c 2 )  0 a12  (n 2 ,c 2 )  0
x y (1 c 2 ) 2

g 1 g n2
a21  (0,a2 )    0 a22  (0,a1 )   1  0
 x a
1 y (1 c 2 ) 2

 n 2  n2
   2
 1 0  2
0
 (1 c 2 )   (1 c 2 )

Therefore the nontrivial steady state is stable whenever it exists.

 Stability of the Chemostat
• Check for oscillations:    2  4
1,2 
2
Is   4  0?
2

 n 2  n2
    1
0  2
0
(1 c 2 )
2
 (1 c 2 )
  2
    2

n2 n2 n2
  4  
2
2
 1  4 
2   2
1  0
(1 c 2 ) 
 (1 c 2 )  (1 c 2 ) 


Therefore no oscillations are possible.

 Conclusions
• It is always possible to design the
chemostat so that at steady state there
will be bacteria populating the growth
chamber.
• For the nontrivial steady state to exist
we must have:
1
a2  ,a1  1
a1 1
 Interpretation
What do these results mean in term of the original parameters?

That is what should the flow rate, the volume, and the stock
nutrient concentration be in order to ensure continuous
culture?

This is part of HW 5
 Phase Portraits
• A graphical picture that summaries the
behavior of a system of two ODEs.
• Example
dx
 xy  y
dt
dy
 xy  x
dt
 Nullclines
• Nullclines are curves of zero slope
– That is curves for which
dx dy
0 and 0
dt dt
– Therefore steady states are located at the
intersection nullclines
 
 x-Nullclines
dx
 xy  y  0 y(x 1)  0
dt
y 0 x 1

• On these lines, the slope (velocity) in the x-
direction is zero
  can be in the y-direction
• The only movement
(ie up or down)
 y-Nullclines
dy
 xy  x  0 x(y 1)  0
dt
x 0 y 1

• On these curves, the slope (velocity) in the y-

direction is zero
  can be in the x-direction
• The only movement
(ie left or right)
 Graph the Nullclines
x-nullclines y 1
y
y-nullclines

x 0
1

 x 1

1
 x y 0
• Label the Steady States
• Mark the Direction of Motion 
 Direction of Motion On y = 0
dx
y  xy  y
dt
dy
 xy  x
1 dt



x
1

dx dy
On y = 0: 0  x  0
dt dt
So movement is in the negative y-direction (down)
Direction of Motion On x = 1
dx
y  xy  y
dt
dy
 xy  x
1 dt



x
1

dx dy
On x = 1: 0  y 1
dt dt
So movement is down for y < 1 and up for y > 1
Direction of Motion On x = 0
dx
y  xy  y
dt
dy
 xy  x
1 dt



x
1

dx dy
On x = 0:  y 0
dt dt
So movement is in the negative x-direction (left)
 Direction of Motion On y = 1
dx
y  xy  y
dt
dy
 xy  x
1 dt



x
1

dx dy
On y = 1:  x 1 0
dt dt
So movement is left for x < 1 and right for x > 1
 Fill in the Direction Field
dx
y  xy  y
dt
dy
 xy  x
1 dt



x
1
All trajectories move away from the non-trivial steady state, therefore
x = 1, y = 1 is unstable.
Some trajectories move towards the origin, but some move away;
therefore x = 0, y=0 is unstable.
Note that arrows change direction across a steady state.
Actual Phase Portrait
 Another Example
dx dy
 x2  y xy
dt dt

• Determine nullclines

– x-nullclines:
• On this curve, slope (velocity) in the x-direction is zero

 
• Trajectories can only move off of this curve in the y-direction (up or down)

– y-nullclines:
• On this curve, slope (velocity) in the x-direction is zero
• Trajectories can only move off of this curve in the y-direction (up or down)

y  x2


yx
 Graph the Nullclines
dx dy
 x2  y xy
dt dt
y

x-nullclines
  y  x2
y-nullclines
1 yx



 x
1

• Plot nullclines, label steady states, mark direction of motion

Direction of Motion On y = x
y  x2
y
yx dx
 x2  y
dt
 dy
1 xy
 dt


1  x

On y = x: dy dx
0  x 2  x  x(x 1)
So movement is left dt
if x < 1 and right if dt
x>1
Direction of Motion On y = x2
y  x2
y
yx dx
 x2  y
dt
 dy
1 xy
 dt


1  x

On y = x2: dx dy
0  x  x 2  x(1 x)
So movement is up ifdt
x < 1 and down ifdt
x>1
 Fill in the Direction Field
y  x2
y
yx dx
 x2  y
dt
 dy
1 xy
 dt


1  x

Some trajectories move towards the nontrivial steady state, but others
move away; therefore x = 1, y = 1 is unstable.
Trajectories seem to move toward the origin, therefore the origin could be
stable.
Note that arrows change direction across a steady state.
Actual Phase Portrait
 Classifying Steady States
• Unstable Node (Source)
– Both eigenvalues are real
and positive
 0  0  2  4
• Saddle Point (unstable)
– Eigenvalues have opposite
  
sign
 0
 Classifying Steady States
• Unstable Spiral (Source)
– Complex eigenvalues with
positive real part
 0  2  4
• Neutral Center
– Complex eigenvalues with zero

realpart
 0  2  4
 Classifying Steady States
• Stable Spiral (Sink)
– Complex eigenvalues with
negative real part
 0  2  4
• Stable Node (Sink)
– Eigenvalues are real and
 
negative

 0  0
 Summary
  2  4

 

    2  4
1,2 
2

• The local stability properties of steady states of a nonlinear

system of two equations can be ascertained by

determining b and g and noting the region of parameter
space in which they lie.
 Global Behavior From Local
Information
• For systems of 2 equations, local
stability properties of steady states can
be used to determine global behavior.
• There are a limited number of ways that
trajectories can flow in the phase plane
(due to continuity)
 Properties of Trajectories in
the Phase Plane

• Solution curves can only intersect at

steady states
• If a solution curve is a closed loop, it
must enclose at least one steady state.
– That steady state cannot be a saddle point
 Asymptotic Behavior of
Trajectories
• Trajectories in the phase plane can
– Approach a steady steady
– Approach infinity
– Approach a closed loop (a limit cycle)
• A trajectory itself may be a closed loop or else it may
approach or recede from one
– Be a heteroclinic trajectory
• Connects two different steady states
– Be a homoclinic trajectory
• Returns to the the same steady state