Evolutionary Dynamics in a Simple Model of Self-Assembly

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.

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Cited by in corpus (11)

• From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics
• Genetic correlations greatly increase mutational robustness and can both reduce and enhance evolvability
• On the networked architecture of genotype spaces and its critical effects on molecular evolution
• Designing the self-assembly of arbitrary shapes using minimal complexity building blocks
• Design Strategies for Self-Assembly of Discrete Targets
• Neuroevolutionary learning of particles and protocols for self-assembly
• Edge-effects dominate copying thermodynamics for finite-length molecular oligomers
• The determinism and boundedness of self-assembling structures
• Non-deterministic self-assembly with asymmetric interactions
• Non-deterministic self-assembly of two tile types on a lattice
• A tractable genotype-phenotype map for the self-assembly of protein quaternary structure