In this post I will explore some connections between two themes I have previously written about, dynamical systems empty of information and chemical reaction network theory. In the first of these posts I mentioned a paper of Perelson and Wallwork (PW) and I now want to discuss that paper in more detail, comparing it to CRNT. The formalisms used to describe chemical systems in these two cases are somewhat different. One class of systems considered by PW are the continuous flow stirred tank reactors (CFSTR). As in CRNT these are described by a system of ODE of the form for the vector of concentrations. In the CFSTR the function is written in the form . Here is thought of as describing the dynamics of a closed system while is supposed to describe inflow and outflow and has the form . Here the are fixed non-negative constants. PW assume that has a unique zero and that there is a function such that everywhere with equality only at that zero. This is essentially the only assumption on . They call an object of this kind a chemical vector field. Actually I suspect that there are a couple of other implicit assumptions. These can be found in the paper but are not mentioned in the definition of a chemical vector field. The conclusion is that given any dynamical system and a point of its domain of definition there exists a CFSTR defined by a function , an open neighbourhood of and a diffeomorphism of onto an open subset of the domain of definition of which transforms the restriction of the original vector field to to the restriction of to the image of . The vector field is constructed by starting with an arbitrary CFSTR of the right dimension and deforming while leaving unchanged.

This result can be interpreted as saying that it is possible to embed arbitrary local dynamics into a CFSTR. One possible criticism of this interpretation is to say that it is not clear whether the definition of a ‘chemical vector field’ is really enough to capture the essential properties of vector fields defined by chemical reactions. The construction uses a cut-off function and it is important that in an intermediate step a vector field is constructed which vanishes exactly on an open set but is not zero everywhere. This means that the construction is not capable of ensuring that the function is analytic (). If the function was constructed from a reaction network using mass-action or Michaelis-Menten kinetics then it would be analytic. It is difficult to change this feature of the construction since it is important that the vector field is transported exactly, not only up to a small error. This is necessary to make sure that all local dynamical features are preserved and not only those which are structurally stable.

I think that if is defined by a reaction network as in CRNT then this network can be extended so as to give one which defines , although not uniquely. I have not checked this in detail. Supposing this is the case we can ask the question, which qualitative features of a dynamical system can be reproduced by a function arising in this more restricted way. I would not be surprised if there are results in the literature relevant to this question but I have not done a serious search yet. The wider question is that of the degree and nature of the simplification obtained by specializing from arbitrary dynamical systems to those arising in the framework of CRNT.

July 1, 2011 at 6:10 am |

[...] On Tuesday I went to a session on biochemical reaction networks. This included a talk by Gheorghe Craciun with a large expository component which I found enlightening. He raised the question of when a system of ODE with polynomial coefficients can be interpreted as coming from a system of chemical reactions with mass action kinetics. He mentioned a theorem about this and after asking him for details I was able to find a corresponding paper by Hars and Toth. This is in the Colloquia Mathematica Societatis Janos Bolyai, which is a priori not easily accessible. The paper is, however, available as a PDF file on the web page of Janos Toth. A chemical reaction network gives rise to a system of equations of the form where the and are polynomials with positive coefficients. They represent the contributions from reactions where the species with concentration is on the right and left side respectively. The result of Hars and Toth is that any system of this algebraic form can be obtained from a reaction network. It was pointed out by Craciun in his talk that this means that arbitrarily complicated dynamics can be incorporated into systems coming from reaction networks. If we have a system of the form we can replace it by . This changes the system but does not change the orbits of solutions. If, for instance, we start with the Lorenz system with unknowns , and we can simply translate the coordinates so as to move the interesting dynamics into the region where all coordinates are positive and then multiply the result by . This preserves the strange attractor structure. This result may be compared with the Perelson-Wallwork theorem discussed in a previous post. [...]