Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble.

Journal article

In this paper, we generalize a methodology [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Phys.: Condens. Matter 22, 104102 (2010)] for dealing with the inference of bulk properties from small simulations of self-assembling systems of characteristic finite size. In particular, schemes for extrapolating the results of simulations of a single self-assembling object to the bulk limit are established in three cases: for assembly involving multiple particle species, for systems with one species localized in space and for simulations in the grand canonical ensemble. Furthermore, methodologies are introduced for evaluating the accuracy of these extrapolations. Example systems demonstrate that differences in cluster concentrations between simulations of a single self-assembling structure and bulk studies of the same model under identical conditions can be large, and that convergence on bulk results as system size is increased can be slow and non-trivial.

Authors: Ouldridge, T

• Journal: Journal of chemical physics
• Volume: 137
• Issue: 14
• Pages: 144105
• Publication date: 2012-10-01
• DOI: 10.1063/1.4757267
• EISSN: 1089-7690
• ISSN: 0021-9606
• Language: English
• Keywords: DNA; Nucleic Acid Conformation; Models, Molecular; Probability Theory; Dimerization