Ard Louis

Abstract:

The behaviour of two-dimensional patchy particles with 5 and 7 regularly-arranged patches is investigated by computer simulation. For higher pressures and wider patch widths, hexagonal crystals have the lowest enthalpy, whereas at lower pressures and for narrower patches, lower-density crystals with five nearest neighbours and that are based on the (3^2,4,3,4) tiling of squares and triangles become lower in enthalpy. Interestingly, in regions of parameter space near to that where the hexagonal crystals become stable, quasicrystalline structures with dodecagonal symmetry form on cooling from high temperature. These quasicrystals can be considered as tilings of squares and triangles, and are probably stabilized by the large configurational entropy associated with all the different possible such tilings. The potential for experimentally realizing such structures using DNA multi-arm motifs are discussed.

Abstract:

We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the self-assembly process. The relationship between the model's rule set and its resulting self-assembled structure can be viewed as a genotype-phenotype map and incorporated into a genetic algorithm. The rule sets evolve under selection for specified target structures. The corresponding, complex fitness landscape generates rich evolutionary dynamics as a function of parameters such as the population size, search space size, mutation rate, and method of recombination. Furthermore, these systems are simple enough that in some cases the associated model genome space can be completely characterised, shedding light on how the evolutionary dynamics depends on the detailed structure of the fitness landscape. Finally, we apply the model to study the emergence of the preference for dihedral over cyclic symmetry observed for homomeric protein tetramers.