Back to Chapter 10: Sections 10.3-10.7
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Back to Chapter 10:Sections 10.3-10.7
Ben Heavner May 10, 2007
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Review: Last Week – Mostly doing Math
From S, we found L such that LS = 0
By definition, dx/dt = Sv, so d/dt Lx = 0 L represents conserved quantities, called pools. Pools are like extreme pathways.
Integrating, we found Lx = a. a is a matrix which gives the size of the pools.
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More Review Different values of x satisfy Lx = a.
We can pick xref such that L(x – xref) = 0• We know such an xref exists because LS = 0.
This transformation changes basis of x (concentration space) to one that is orthogonal to L. transformed concentration space is bounded boundaries are extreme concentration states
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How to Pick xref
xref is orthogonal to si
si . xref = 0
x – xref is orthogonal to li
li . (x – xref) = 0
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Finding the Bounded Concentration SpaceExample 1: “Simple reversible reaction”
PCCP
11
11S =
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Finding L
Matlab:
EDU>> S=[-1 1; 1 -1]S = -1 1 1 -1
EDU>> b = S'b = -1 1 1 -1
EDU>> a=null(b,'r')a = 1 1
EDU>> L=a'L = 1 1
PCCP
L = (1 1)
11
11S =
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Toward Finding xref – start with x
Suppose a1 = 1 Remember Lx = a
PCCP
L = (1 1)
11
11S =
1
1
0
1x
Then one parameterization of x is:
1Lx
10*11*10
111
11*10*11
011
That is, from
or
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Finding xref:Systems of Linear Equations
First criteria for xref:
si . xref = 0
or
PCCP
L = (1 1)
11
11S =
1
1
0
1x
0112
1
ref
ref
x
x
(-1*x1ref) + (1*x2ref) = 0
x1ref = x2ref
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Finding xref:Systems of Linear Equations
Second criteria for xref:
li . (x – xref) = 0
or
PCCP
L = (1 1)
11
11S =
1
1
0
1x
01122
11
ref
ref
xx
xx
[1*(x1-x1ref)] + [1*(x2-x2ref)] = 0x1-x1ref=-x2+x2ref
x1+x2=2xref
Since (x1+x2) = a = 1x1ref = x2ref = 1/2
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Reparamatarizing the Concentration Space: x-xref
Since
1
1
0
1x
x1ref
x 2ref
1212
And
x xref 12
12
11
[0,1] Then
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What we gain by transforming x Move from
unbounded dx/dt = Sv space to bounded L(x-xref)=0 space
Note: x-xref spanned by s1
concentration space through origin
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Further Transformation Examples and Pool Interpretation
“Bilinear association” (“Bimolecular association” in reaction space):
APA + P
2
1a
1
1
1
S
110
101L
1
1
1
1
1
1
refxx
1
1
1
0
2
1
x
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Further Transformation Examples and Pool Interpretation
“Carrier-coupled reaction” (“Cofactor-coupled reaction” in reaction space):
CP + AC + AP
1
1
1
1
43434343
refxx
1
1
1
1
S
1010
0101
1100
0011
L
1
2
2
1
a
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More Pool Interpretation “Rodox carrier coupled reactions”:
R + NADH + H+RH2 + NAD+
01010
10010
00110
01001
10001
001012 NADHHRNADRH
L
11
11
11
11
11
S
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Redox carrier coupled reactions
R + NADH + H+RH2 + NAD+
L =
RH2 NAD R H NADH
1 0 1 0 0
1 0 0 0 1
1 0 0 1 0
0 1 1 0 0
0 1 0 0 1
0 1 0 1 0
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Combining pools
R + NADH + H+RH2 + NAD+
R’R
R’H2 + NAD+R’ + NADH + H+
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Combining pools
0001010
0010010
0100110
1001001
1010001
1100101
'' 22 HRRNADHHRNADRH
L
R + NADH + H+RH2 + NAD+
R’R
R’H2 + NAD+R’ + NADH + H+
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Summary L contains “dynamic invariants” Integrating d/dt (Lx) = 0 gives the pool sizes (a
“bounded affine space”) Three types of convex basis vectors span this
space (like extreme pathways) A reference state can be found to make this
space parallel to L and be orthogonal to the column space
Metabolic pools can be displayed on a compound map