Abstract
Modern simulation techniques are beginning to study the dynamic assembly and disassembly of multi-protein systems. In these many- particle simulations it can be very tedious to monitor the formation of specific structures such as fully assembled protein complexes or virus capsids above a background of monomers and partially assembled complexes. How- ever, such analyses can be performed conveniently when the spatial configuration is mapped onto a dynamically updated interaction graph [1]. On the example of Monte Carlo simulations of spherical particles with either isotropic or directed mutual attractions we demonstrate that this combined strategy allows for an efficient and also detailed analysis of complex formation in many-particle systems. Some more examples illustrate how time-dependent many-particle agglomeration can be visualized [2] or classified as either ordered or amorphous.[1] F. Lauck, V. Helms, T. Geyer, J. Chem. Theory Comput. 5 (2009) 641[2] T. Geyer, BMC Biophys. 4 (2011) 7
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