1

Coplanarity

Hypothesized reaction scheme between species X1 and X2 :

R1

2X1

X2
R2

Mass action rate laws:

Reaction 1: v1 = k1 x21
Reaction 2: v2 = k2 x2
Equations:


x1
x2


=

2v1 + 2v2
v1 v2


=

2k1 x21 + 2k2 x2

k1 x21 k2 x2


=

2x21
x21

2x2
x2

   
k1
0
=
k2
0

Upon collecting data of x1 and x2 , one can plug them into the matrix, and see if there exists k1 and k2 that satisfies
the equation - that is, if the matrix has non-trivial null space. If it doesnt, then the model can be ruled out: either
the reaction scheme or the rate law is considered incorrect. Since mass action kinetics is usually taken as a given in
this context, it is usually the reaction scheme that is considered ruled out.
In this case, the matrix is for sure rank-deficient hence any collected data of x1 and x2 wont rule out the model.
Mass action kinetics is convenient in this case because then the ks enter linearly into the equation.

Model manifold

If we treat steady-state x1 and x2 as data parametrized by k1 and k2 , then the quadratic equation defines a function
mapping from the parameters to data. But after some attempts I cant find any connection between this picture and
the coplanarity picture above.

Follow-up



 

x1
k1
k1
,k=
, and K = diag(k) =
x
k
0
2
2
 2
 2

x1
x
0
1
= diag(
Let x
=
,X
x) =
.
x2
0 x2

Let x =

Coplanarity:
  
 
x1
2v1 + 2v2
2
x =
=
=
x2
v1 v2
1


0
.
k2

 


 2
2
v1
k1 x21
x1
= Nv = N
=N
1
v2
k2 x2
0

0
x2

 
k1
=0
= N Xk
k2

(1)

(N is the stoichiometry matrix.)

Model manifold picture assuming x

as data:


k1 x21
x = N v = N
= N Kx
=0
k2 x2

(2)

x
= ker(N diag(k)).

(3)

Thoughts:
1. The equations above are general: the same can be written for an arbitrary chemical reaction system.
2. The pictures of coplanarity and model manifold are connected through Eqs. 1 and 2 (I do not find the connection
natural or deep, hence the conclusion of no connection before).
3. Yes, treating x
as data model manifold becomes a linear subspace. (Q: Does this offer substantial advantages??)
4. Since diag(k) is always a full-rank square matrix, rank(N diag(k)) = rank(N ), and this gives the number of
constraining equations for the model manifold.
5. x
is usually of higher dimension than x: each x
i is associated with a monomial arising from a reaction with mass
action kinetics hence x
has the same dimension as the number of reactions in the system, while x the same as
the number of species.