Ard Louis

Abstract:

We investigate how scale-free (SF) and Erdos-Rényi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006) we find that networks with SF(in) topologies, that is SF topology for incoming nodes and ER topology for outgoing nodes, are significantly more evolvable towards specific oscillatory targets than networks with ER topology for both incoming and outgoing nodes. Similar results are found for networks with SF(both) and SF(out) topologies. The functionality of the SF(out) topology, which most closely resembles the structure of biological gene networks (Babu et al., 2004), is compared to the ER topology in further detail through an extension to multiple target outputs, with either an oscillatory or a non-oscillatory nature. For multiple oscillatory targets of the same length, the differences between SF(out) and ER networks are enhanced, but for non-oscillatory targets both types of networks show fairly similar evolvability. We find that SF networks generate oscillations much more easily than ER networks do, and this may explain why SF networks are more evolvable than ER networks are for oscillatory phenotypes. In spite of their greater evolvability, we find that networks with SF(out) topologies are also more robust to mutations (mutational robustness) than ER networks. Furthermore, the SF(out) topologies are more robust to changes in initial conditions (environmental robustness). For both topologies, we find that once a population of networks has reached the target state, further neutral evolution can lead to an increase in both the mutational robustness and the environmental robustness to changes in initial conditions.

Abstract:

In patchy particle systems where there is competition between the self-assembly of finite clusters and liquid-vapour phase separation, reentrant phase behaviour is observed, with the system passing from a monomeric vapour phase to a region of liquid-vapour phase coexistence and then to a vapour phase of clusters as the temperature is decreased at constant density. Here, we present a classical statistical mechanical approach to the determination of the complete phase diagram of such a system. We model the system as a van der Waals fluid, but one where the monomers can assemble into monodisperse clusters that have no attractive interactions with any of the other species. The resulting phase diagrams show a clear region of reentrance. However, for the most physically reasonable parameter values of the model, this behaviour is restricted to a certain range of density, with phase separation still persisting at high densities.