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Extracting bulk properties of self-assembling systems from small simulations

Thomas E Ouldridge1, Ard A Louis1 and Jonathan P K Doye2

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For systems that self-assemble into finite-sized objects, it is sometimes convenient to compute the thermodynamics for a small system where a single assembly can form. However, we show that in the canonical ensemble the use of small systems can lead to significant finite-size effects due to the suppression of concentration fluctuations. We introduce methods for estimating the bulk yields from simulations of small systems and for following the convergence of yields with system size, under the assumptions that the various species behave ideally.


PACS

87.14.G- Nucleic acids

87.14.E- Proteins

87.19.Pp Biothermics and thermal processes in biology

Subjects

Medical physics

Biological physics

Dates

Issue 10 (17 March 2010)

Received 4 October 2009, in final form 13 January 2010

Published 23 February 2010



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