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Reference: Johnston, IG, Ahnert, SE, Doye, JP et al., (2011). Evolutionary dynamics in a simple model of self-assembly. Physical Review E, 83 (6 Pt 2), Article: 066105.Citable link to this page:

 

Evolutionary dynamics in a simple model of self-assembly.

Abstract: We investigate the evolutionary dynamics of an idealized 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 characterized, 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.

Peer Review status:Peer reviewedPublication status:PublishedVersion:Accepted Manuscript Funder: Engineering and Physical Sciences Research Council   Funder: Royal Society   Notes:Iain G. Johnston, Sebastian E. Ahnert, Jonathan P. K. Doye, and Ard A. Louis. Goodwin. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics; v.83:issue.6, 066105 (2011). Copyright 2011 American Physical Society.

Bibliographic Details

Publisher: American Physical Society

Publisher Website: http://www.aps.org/

Journal: Physical Review Esee more from them

Publication Website: http://pre.aps.org/

Issue Date: 2011-6

pages:Article: 066105Identifiers

Urn: uuid:e3b86f2e-5c9c-46cf-a0ca-0138eaab48b8

Source identifier: 120383

Eissn: 1550-2376

Doi: https://doi.org/10.1103/physreve.83.066105

Issn: 1539-3755 Item Description

Type: Journal article;

Language: eng

Version: Accepted ManuscriptKeywords: Adaptation, Physiological Evolution, Molecular Genotype Recombination, Genetic Algorithms Models, Genetic Tiny URL: pubs:120383

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Author: Johnston, IG - institutionUniversity of Oxford fundingEngineering and Physical Sciences Research Council - - - Ahnert, SE - - - D

Source: https://ora.ox.ac.uk/objects/uuid:e3b86f2e-5c9c-46cf-a0ca-0138eaab48b8



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