Regensburg 2004 – scientific programme

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SYLS: Life Sciences on the Nanometer Scale - Physics Meets Biology

SYLS 3: Symposium "Life Sciences on the Nanometer Scale - Physics Meets Biology"

SYLS 3.48: Poster

Wednesday, March 10, 2004, 16:00–18:30, B

Exact Enumeration of 3D Lattice Proteins — •Reinhard Schiemann, Michael Bachmann, and Wolfhard Janke — Institut für Theoretische Physik, Universität Leipzig, Augustusplatz 10/11, 04109 Leipzig (Germany)

We investigate the properties of native, i.e. non–degenerate, ground states of lattice proteins in the HP model [1] on the three–dimensional simple cubic lattice. In order to do so, the complete sets of sequences and conformations were enumerated exhaustively for chains of up to 19 monomers. The identification of native ground states was accelerated by generating the set of contact matrices from the set of conformations of a given length.

In a statistical analysis, we compared characteristic properties of HP proteins that have a unique ground state to those of proteins with a degenerate ground state. Such properties are the compactness and designability of conformations, and the content and distribution of hydrophobic monomers. Furthermore, the complete density of states as a function of energy was exactly enumerated for a variety of HP sequences. This information could be used to show that the temperature dependences of the energy and specific heat have a peculiar shape for those HP sequences that have a low ground–state degeneracy and in particular for sequences with non–degenerate ground states.

[1] K.F. Lau and K.A. Dill, Macromolecules 22 (1989) 3986.