The concept of a siphon is one which I have been more or less aware of for quite a long time. Unfortunately I never had the impression that I had understood it completely. Given the fact that it came up a lot in discussions I was involved in and talks I heard last week I thought that the time had come to make the effort to do so. It is of relevance for demonstrating the property of persistence in reaction networks. This is the property that the -limit points of a positive solution are themselves positive. For a bounded solution this is the same as saying that the infima of all concentrations at late times are positive. The most helpful reference I have found for these topics is a paper of Angeli, de Leenheer and Sontag in a proceedings volume edited by Queinnec et. al.

There are two ways of formulating the definition of a siphon. The first is more algebraic, the second more geometric. In the first the siphon is defined to be a set of species with the property that whenever one of the species in occurs on the right hand side of a reaction one of the species in occurs on the left hand side. Geometrically we replace by the set of points of the non-negative orthant which are common zeroes of the elements of , thought of as linear functions on the species space. The defining property of a siphon is that is invariant under the (forward in time) flow of the dynamical system describing the evolution of the concentrations. Another way of looking at the situation is as follows. Consider a point of . The right hand side of the evolution equations of one of the concentrations belonging to is a sum of positive and negative terms. The negative terms automatically vanish on and the siphon condition is what is needed to ensure that the positive terms also vanish there. Sometimes minimal siphons are considered. It is important to realize that in this case is minimal. Correspondingly is maximal. The convention is that the empty set is excluded as a choice for and correspondingly the whole non-negative orthant as a choice for . What is allowed is to choose to be the whole of the species space which means that is the origin. Of course whether this choice actually defines a siphon depends on the particular dynamical system being considered.

If is an -limit point of a positive solution but is not itself positive then the set of concentrations which are zero at that point is a siphon. In particular stationary solutions on the boundary are contained in siphons. It is remarked by Shiu and Sturmfels (Bull. Math. Biol. 72, 1448) that for a network with only one linkage class if a siphon contains one stationary solution it consists entirely of stationary solutions. To see this let be a stationary solution in the siphon . There must be some complex belonging to the network which contains an element of . If is another complex then there is a directed path from to . We can follow this path backwards from and conclude successively that each complex encountered contains an element of . Thus contains an element of and since was arbitrary all complexes have this property. This means that all complexes vanish at so that is a stationary solution.

Siphons can sometimes be used to prove persistence. Suppose that is a siphon for a certain network so that the points of are potential -limit points of solutions of the ODE system corresponding to this network. Suppose further that is a conserved quantity for the system which is a linear combination of the coordinates with positive coefficents. For a positive solution the quantity has a positive constant value along the solution and hence also has the same value at any of its -limit points. It follows that if vanishes on then no -limit point of that solution belongs to . If it is possible to find a conserved quantity of this type for each siphon of a given system (possibly different conserved quantities for different siphons) then persistence is proved. For example this strategy is used in the paper of Angeli et al. to prove persistence for the dual futile cycle. The concept of persistence is an important one when thinking about the general properties of reaction networks. The persistence conjecture says that any weakly reversible reaction network with mass action kinetics is persistent (possibly with the additional assumption that all solutions are bounded). In his talk last week Craciun mentioned that he is working on proving this conjecture. If true it implies the global attractor conjecture. It also implies a statement claimed in a preprint of Deng et. al. (arXiv:1111.2386) that a weakly reversible network has a positive stationary solution in any stoichiometric compatobility class. This result has never been published and there seems to be some doubt as to whether the proof is correct.