Chemical molecules, catalytic reaction network

It is important to study whether such loose reproduction as a set is possible in a mutually catalytic reaction network (also see, e.g., Refs. 10 and 11). If this is possible and if these chemicals also include molecules forming a membrane for compartmentalization, then reproduction of a primitive cell will become possible. In fact, from the chemical nature of lipid molecules, it is not so surprising that a compartment structure is formed. 

Quite recently, Furusawa, Kaneko, and co-workers [26,41] have studied several models of minimal cell consisting of catalytic reaction networks, without assuming the replication process itself. In other words, the molecules are successively synthesized from nutrition chemicals transported from the membrane, where the level 1 model of Section III.B is adopted. They have found a universal statistical law of chemicals for a cell that grows recursively. 

Different from conventional chemical kinetics, the rates in biochemical reactions networks are usually saturable hyperbolic functions. For an increasing substrate concentration, the rate increases only up to a maximal rate Vm, determined by the turnover number fccat = k2 and the total amount of enzyme Ej. The turnover number ca( measures the number of catalytic events per seconds per enzyme, which can be more than 1000 substrate molecules per second for a large number of enzymes. The constant Km is a measure of the affinity of the enzyme for the substrate, and corresponds to the concentration of S at which the reaction rate equals half the maximal rate. For S most active sites are not occupied. For S >> Km, there is an excess of substrate, that is, the active sites of the enzymes are saturated with substrate. The ratio kc.AJ Km is a measure for the efficiency of an enzyme. In the extreme case, almost every collision between substrate and enzyme leads to product formation (low Km, high fccat). In this case the enzyme is limited by diffusion only, with an upper limit of cat /Km 108 — 109M. v 1. The ratio kc.MJKm can be used to test the rapid... 

To unveil general features of a system with mutually catalyzing molecules, we study a system with a variety of chemicals (k molecular species), forming a mutually catalyzing network. The molecules replicate through catalytic reactions, so that their numbers within a cell increase (see Fig. 1 again for schematic representation of the model). 

We start our discussion by emphasizing how flow behavior is related to the transport of molecules and chemical reactions in micrometer- and submicrometer-sized channel networks. We discuss measurement of flow and transport properties and demonstrate how these characteristics translate to a range of diflerent microfluidic applications multiphase flow through porous media [1], human airways [2], miniature cell-biological systems [3, 4], flow in microfluidic catalytic monoUths [5] and the use of interfacial forces as a means for actuation in microdevices [6]. The discussion of multiphase microfluidic systems in this chapter complements several recent reviews on general aspects of transport phenomena in microfluidic systems [37, 174-179]. 

In the Lattice Artificial Chemistry model and also in later extensions of the GARD model, formation of the membrane itself is explicitly included. In GARD every species Aj may, in principle, catalyze every possible reaction in which another species A is formed/decomposed, with a catalytic probability Pij. This / matrix defines the chemical structure of the (auto) catalytic networks. The role and formation of the amphiphilic assembly that becomes the enclosing membrane can be incorporated into the catalytic network by assuming that the same molecules that form the assembly are also responsible for the mutually catalytic functions. This is a model that contains similarities with the sulfide protocell systems discussed earlier. The results of numerical simulations based on extended GARD model versions demonstrated the spontaneous emergence of catalytical assemblies that tend to lie below the Morowitz boundary. 

---