Archive for May, 2015

Models for photosynthesis, part 2

May 22, 2015

In my previous post on this subject I discussed the question of the status of the variables in the Poolman model of photosynthesis and in the end I was convinced that I had understood which concentrations are to be considered as dynamical unknowns and which as constants. The Poolman model is a modified version of the Pettersson model and the corresponding questions about the nature of the variables have the same answers in both cases. What I am calling the Pettersson model was introduced in a paper of Pettersson and Ryde-Pettersson (Eur. J. Biochem 175, 661) and there the description of the variables and the equations is rather complete and comprehensible. Now I will go on to consider the second question raised in the previous post, namely what the evolution equations are. The evolution equations in the Poolman model are modifications of those in the Pettersson model and are described relative to those in the original paper on the former model. For this reason I will start by describing the equations for the Pettersson model. As a preparation for that I will treat a side issue. In a reaction network a reaction whose rate depends only on the concentrations of the substances consumed in the reaction is sometimes called NAC (for non-autocatalytic). For instance this terminology is used in the paper of Kaltenbach quoted in the previous post. The opposite of NAC is the case where the reaction rate is modulated by the concentrations of other substances, such as activators or inhibitors.

The unknowns in the Pettersson model are concentrations of substances in the stroma of the chloroplast. The substances involved are 15 carbohydrates bearing one or more phosphate groups, inorganic phosphate and ATP, thus 17 variables in total. In addition to ordinary reactions between these substances there are transport processes in which sugar phosphates are moved from the stroma to the cytosol in exchange for inorganic phosphate. For brevity I will also refer to these as reactions. The total amount of phosphate in the stroma is conserved and this leads to a conservation law for the system of equations, a fact explicitly mentioned in the paper. On the basis of experimental data some of the reactions are classified as fast and it is assumed that they are already at equilibrium. They are also assumed to be NAC and to have mass-action kinetics. This defines a set of algebraic equations. These are to be used to reduce the 17 evolution equations which are in principle there to five equations for certain linear combinations of the variables. The details of how this is done are described in the paper. I will now summarize how this works. The time derivatives of the 16 variables other than inorganic phosphate are given in terms of linear combinations of 17 reaction rates. Nine of these reaction rates, which are not NAC, are given explicitly. The others have to be treated using the 11 algebraic equations coming from the fast reactions. The right hand sides $F_i$ of the five evolution equations mentioned already are linear combinations of those reaction rates which are given explicitly. These must be expressed in terms of the quantities whose time derivatives are on the left hand side of these equations, using the algebraic equations coming from the fast reactions and the conservation equation for the total amount of phosphate. In fact all unknowns can be expressed in terms of the concentrations of RuBP, DHAP, F6P, Ru5P and ATP. Call these quantities $s_i$. Thus if the time derivatives of the $s_i$ can be expressed in terms of the $F_i$ we are done. It is shown in the appendix to the paper how a linear combination of the time derivatives of the $s_i$ with coefficients only depending on the $s_i$ is equal to $F_i$. Moreover it is stated that the time derivatives of the $s_i$ can be expressed in terms of these linear combinations.

Consider now the Poolman model. One way in which it differs from the Pettersson model is that starch degradation is included. The other is that while the kinetics for the ‘slow reactions’ (i.e. those which are not classified as fast in the Pettersson model) are left unchanged, the equilibrium assumption for the fast reactions is dropped. Instead the fast reactions are treated as reversible with mass action kinetics. In the thesis of Sergio Grimbs (Towards structure and dynamics of metabolic networks, Potsdam 2009) there is some discussion of the models of Poolman and Pettersson. It is investigated whether information about multistability in these models can be obtained using ideas coming from chemical reaction network theory. Since the results from CRNT considered require mass action kinetics it is implicit in the thesis that the systems are being considered which are obtained by applying mass action to all reactions in the networks for the Poolman and Pettersson models. These systems are therefore strictly speaking different from those of Pettersson and Poolman. In any case it turned out that these tools were not useful in this example since the simplest results did not apply and for the more complicated computer-assisted ones the systems were too large.

In the Pettersson paper the results of computations of steady states are presented and a comparison with published experimental results looks good in a graph presented there. So whay can we not conclude that the problem of modelling the dynamics of the Calvin cycle was pretty well solved in 1988? The paper contains no details on how the simulations were done and so it is problematic to repeat them. Jablonsky et. al. set up simulations of this model on their own and found results very different from those reported in the original paper. In this context the advantage of the Poolman model is that it has been put into the BioModels database so that the basic data is available to anyone with the necessary experience in doing simulations for biochemical models. Forgetting the issue of the reliability of their simulations, what did Petterson and Ryde-Pettersson find? They saw that depending on the external concentration of inorganic phosphate there is either no positive stationary solution (for high values of this parameter) or two (for low values) with a bifurcation in between. When there are two stationary solutions one is stable and one unstable. It looks like there is a fold bifurcation. There is a trivial stationary solution with all sugar concentrations zero for all values of the parameter. When the external phosphate concentration tends to zero the two positive stationary solutions coalesce with the trivial one. The absence of positive stationary solutions for high phosphate concentrations is suggested to be related to the concept of ‘overload breakdown’. This means that sugars are being exported so fast that the production from the Calvin cycle cannot keep up and the whole system breaks down. It would be nice to have an analytical proof of the existence of a fold bifurcation for the Pettersson model but that is probably very difficult to get.

Models for photosynthesis

May 15, 2015

Photosynthesis is a process of central importance in biology. There is a large literature on modelling this process. One step is to identify networks of chemical reactions involved. Another is to derive mathematical models (usually systems of ODE) from these networks. Here when I say ‘model’ I mean ‘mathematical model’ and not the underlying network. In a paper by Jablonsky et. al. (BMC Systems Biology 5: 185) existing models are surveyed and a number or errors and inconsistencies in the literature are pointed out. This reminded me of the fact that a widespread problem in the biological literature is that the huge amount of data being generated these days contains very many errors. Here I want to discuss some issues related to this, concentrating on models for the Calvin cycle of photosynthesis and, in particular, on what I will call the Poolman model.

A point which might seem obvious and trivial to the mathematician is that a description of a mathematical model (I consider here only ODE models) should contain a clear answer to the following two questions. 1) What are the unknowns? 2) What are the evolution equations? One source of ambiguity involved in the first question is the impossibility of modelling everything. It is usually unreasonable to model a whole organism although this has been tried for some simple ones. Even if it were possible, the organism is in interaction with other organisms and its environment and these things cannot also be included. In practise it is necessary to fix a boundary of the system we want to consider and cut there. One way of handling the substances outside the cut in a mathematical model is to set their concentrations to constant values, thus implicitly assuming that to a good approximation these are not affected by the dynamics within the system. Let us call these external species and the substances whose dynamics is included in the model internal species. Thus part of answering question 1) is to decide on which species are to be treated as internal. In this post I will confine myself to discussing question 1), leaving question 2) for a later date.

Suppose we want to answer question 1) for a model in the literature. What are potential difficulties? In biological papers the equations (and even the full list of unknowns) are often banished to the supplementary material. In addition to being less easy to access and often less easy to read (due to typographical inferiority) than the main text I have the feeling that this supplementary material is often subjected to less scrutiny by the referees and by the authors, so that errors or incompleteness can occur more easily. Sometimes this information is only contained in some files intended to be read by a computer rather than a human being and it may be necessary to have, or be able to use, special software in order to read them in any reasonable way. Most of these difficulties are not absolute in nature. It is just that the mathematician embarking on such a process should ideally be aware of some of the challenges awaiting him in advance.

How does this look in the case of the Poolman model? It was first published in a journal in a paper of Poolman, Fell and Thomas (J. Exp. Botany, 51, 319). The reaction network is specified by Fig. 1 of the paper. This makes most of the unknowns clear but leaves the following cases where something more needs to be said. Firstly, it is natural to take the concentration of ADP to be defined implicitly through the concentration of ATP and the conservation of the total amount of adenosine phosphates. Secondly, it is explictly stated that the concentrations of NADP and NADPH are taken to be constant so that these are clearly external species. Presumably the concentration of inorganic phosphate in the stroma is also taken to be constant, so that this is also an external variable, although I did not find an explicit statement to this effect in the paper. The one remaining possible ambiguity involves starch – is it an internal or an external species in this model? I was not able to find anything directly addressing this point in the paper. On the other hand the paper does refer to the thesis of Poolman and some internet resources for further information. In the main body of the thesis I found no explicit resolution of the question of external phosphate but there it does seem that this quantity is treated as an external parameter. The question of starch is particularly important since this is a major change in the Poolman model compared to the earlier Pettersson model on which it is based and since Jablonsky et. al. claim that there is an error in the equation describing this step. It is stated in the thesis that ‘a meaningful concentration cannot be assigned to’ … ‘the starch substrate’ which seems to support my impression that the concentration of starch is an external species. Finally a clear answer confirming my suppositions above can be found in Appendix A of the thesis which describes the computer implementation. There we find a list of variables and constants and the latter are distinguished by being preceded by a dollar sign. So is there an error in the equation for starch degradation used in the Poolman model? My impression is that there is not, in the sense that the desired assumptions have been implemented successfully. The fact that Jablonsky et. al. get the absurd result of negative starch concentrations is because they compute an evolution for starch which is an external variable in the Poolman model. What could be criticised in the Poolman model is that the amount of starch in the chloroplast varies a lot over the course of the day. Thus a model with starch as an external variable could only be expected to give a good approximation to reality on timescales much shorter than one day.

The species-reaction graph

May 14, 2015

In the study of chemical reaction networks important features of the networks are often summarised in certain graphs. Probably that most frequently used is the species graph (or interaction graph), which I discussed in a previous post. The vertices are the species taking part in the network and the edges are related to the non-zero entries of the Jacobian matrix of the vector field defining the dynamics. Since the Jacobian matrix depends in general on the concentrations at which it is evaluated there is a graph (the local graph) for each set of values of the concentrations. Sometimes a global graph is defined as the union of the local graphs. A sign can be attached to each edge of the local graph according to the sign of the corresponding partial derivative. In the case, which does occur quite frequently in practise, that the signs of the partial derivatives are independent of the concentrations the distinction between local and global graphs is not necessary. In the general case a variant of the species graph has been defined by Kaltenbach (arXiv:1210.0320). In that case there is a directed edge from vertex $i$ to vertex $j$ if there is any set of concentrations for which the corresponding partial derivative is non-zero and instead of being labelled with a sign the edge is labelled with a function, namely the partial derivative itself.

Another more complicated graph is the species-reaction graph or directed species-reaction graph (DSR graph). As explained in detail by Kaltenbach the definition (and the name of the object) are not consistent in the literature. The species-reaction graph was introduced in a paper of Craciun and Feinberg (SIAM J. Appl. Math. 66, 1321). In a parallel development which started earlier Mincheva and Roussel (J. Math. Biol. 55, 61) developed results using this type of graph based on ideas of Ivanova which were little known in the West and for which published proofs were not available. In the sense used by Kaltenbach the DSR graph is an object closely related to his version of the interaction graph. It is a bipartite graph (i.e. there are two different types of vertices and each edge connects a vertex of one type with a vertex of the other). In the DSR graph the species define vertices of one type and the reactions the vertices of the other type. There is a directed edge from species $i$ to reaction $j$ if species $i$ is present on the LHS of reaction $j$. There is a directed edge from reaction $i$ to species $j$ if the net production of species $j$ in reaction $i$ is non-zero. The first type of edge is labelled by the partial derivative of flux $j$ with respect to species $i$. The second type is labelled by the corresponding stoichiometric coefficient. The DSR graph determines the interaction graph. The paper of Soliman I mentioned in a recent post uses the DSR graph in the sense of Kaltenbach.

A type of species-reaction graph has been used in quite a different way by Angeli, de Leenheer and Sontag to obtain conditions for the montonicity of the equations for a network written in reaction coordinates.

Proof of the global attractor conjecture

May 14, 2015

In a previous post I discussed the global attractor conjecture which concerns the asymptotic behaviour of solutions of the mass action equations describing weakly reversible chemical reaction networks of deficiency zero (or more generally complex balanced systems). Systems of the latter class are sometimes called toric dynamical systems because of relations to the theory of toric varieties in algebraic geometry. I just saw a paper by Gheorghe Craciun which he put on ArXiv last January (arxiv.org/pdf/1501.0286) where he proves this conjecture, thus solving a problem which has been open for more than 40 years. The result says that for reaction networks of this class the long-time behaviour is very simple. For given values of the conserved quantities there is exactly one positive stationary solution and all other solutions converge to it. What needs to be done beyond the classical results on this problem is to show that a positive solution can have no $\omega$-limit points where some concentration vanishes. This property is sometimes known as persistence.

A central concept used in the proof of the result is that of a toric differential inclusion. This says that the time rate of change of the concentrations is contained in a special type of subset. The paper contains a lot of intricate geometric constructions. These are explained consecutively in dimensions one, two, three and four in the paper. This should hopefully provide a good ladder to understanding.

Arrival in Bretzenheim

May 1, 2015

Since I moved to Mainz two years ago my wife has remained in Berlin and we have been searching for a suitable place to live in Mainz or its surroundings. The original plan was to buy a piece of land on which we could build a house. This turned out to be much more difficult than we expected. The only land within our financial horizons was in small villages with almost no infrastructure or had other major disadvantages from our point of view. Eventually, after wasting a lot of time and effort, we stopped searching in the surroundings and looked for something in Mainz itself. Of course this was not easy but eventually we decided to buy a house (still to be built) within a small housing scheme in the district of Mainz called Bretzenheim. There is very little land available in Mainz and the scheme where we will be living is an example of the way in which the few remaining open spaces are being filled up, driven by the high property prices. The house was finished in March and I moved in on a provisional basis on 1st April, giving up my appartment, exactly two years after starting my job in Mainz. (Goodbye Jackdaws! The first birds I saw in what will be our garden were a Carrion Crow, which I am not taking as a bad omen, and a Black Redstart.) Our belongings left Berlin on 16th April and arrived in Mainz on 17th. Eva came to Mainz definitively on the 16th. So now there can be no doubt that a new era has begun for us.

The new house is conveniently situated. From there I can walk to the mathematics institute in 20 minutes and to the main train station in half an hour. It is near the end of a tram line coming from the station. Very close to where the houses have been built a Merovingian grave was found. When the garden centre a little further up the hill was being built the grave of a Merovingian warrior was found who had been buried with his horse. It is just as well for us that the archeologists did not dig too deep or we might have had to wait a long time before we could move in. Whenever you dig a hole in Mainz you are in danger of encountering a distant past and potential problems with the archeology department of the city. To show what can happen I will give an example. In the district of Gonsenheim there is a small stream, the Gonsbach. At some time when progress was fashionable the winding stream was straightened. Later an EU directive came into force which said that streams like this which had been straightened had to be made winding again, for ecological reasons, within a certain number of years. By now the deadline has been reached, or almost reached for the Gonsbach, and the city has started measures to attempt to comply with the directive. They started to dig and found … a Roman settlement. The work had to be stopped, for archeological reasons. So now, as far as I know, the archeological and ecological regulations and the city officials representing them are in deadlock.

Since I am British it is a curiosity for me that one suggested origin of the name Bretzenheim is that it is named after the Britons. It has been suggested that it could be identified with a certain vicus Brittaniae where the Roman Emperor Severus Alexander was murdered in the year 235. The evidence for this seems limited and an alternative hypothesis says that it was named after a locally important man called Bretzo. I cannot imagine what the Britons would have been doing there. Another theory is that the emperor was murdered in Britain and not in Mainz.