Regensburg 2016 – wissenschaftliches Programm

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CPP: Fachverband Chemische Physik und Polymerphysik

CPP 28: Poster: Computational Physics of Soft Matter

CPP 28.2: Poster

Dienstag, 8. März 2016, 18:15–21:00, Poster B2

SAMC simulation of single peptides in the PRIME20 model — •Arne Böker and Wolfgang Paul — Martin-Luther-Universität Halle-Wittenberg

A number of current problems in medical science can be attributed to misfolding of proteins when these reach non-native free energy minima stabilized by aggregation. Describing these aggregation phenomena for relevant protein sizes requires the use of coarse-grained models. However, strongly coarse-grained computational models tend to simplify the free energy surface in such a way that these local minima are suppressed. To circumvent this problem, the level of coarse graining needs to be chosen appropriately.

PRIME20^[1] is an intermediate-resolution model for proteins. It provides reasonable detail by mapping each amino acid to four beads, but keeps parameter space relatively simple with the set of interactions reduced to 19 parameters. We perform thermodynamic simulations of single PRIME20 chains using the "SAMC"^[2] variation of Wang-Landau Monte Carlo samplng which provides insight in different statistical ensembles at the expense of dynamic information.

^[1] M. Cheon, , I. Chang, C. K. Hall, Proteins 78(2010):2950

^[2] B. Werlich, T. Shakirov, M. P. Taylor, W. Paul, Comp. Phys. Comm. 186(2015):65