München 2004 – scientific programme

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MO: Molekülphysik

MO 12: Poster I

MO 12.27: Poster

Tuesday, March 23, 2004, 14:00–16:00, Schellingstr. 3

Influence of the Bead–Bead Interaction on the Rotational Dynamics of Nonrigid Macromolecules in Solution. — •Alexander Uvarov and Stephan Fritzsche — Universität Kassel, D–34132 Kassel, Germany

To understand the relaxation mechanisms of macromolecules, i.e. their relaxation from a nonequilibrium into their equilibrium state, remains one of the central problems in studying proteins and DNA in solution. During the last years, therefore, a large number of experiments and molecular dynamic simulations [1] have been carried out in order to analyze the statical and relaxational properties of macromolecules. An alternative description of biomolecules is offered by statistical methods if they are treated in terms of their molecular subsystems, the so–called beads of the macromolecule.

In this contribution, we present and discuss the Internal Diffusion equation which describes the time evolution of the conformational phase–space distribution function of a nonrigid macromolecule. To investigate the effects of the bead–bead interaction potential on the orientation and relaxation of the macromolecules, the end–to–end autocorrelation function of the macromolecule, immobilized on a surface, has been calculated for a hookean, fene and dna bead–bead potentials. Moreover, the rotational diffusion coefficient of the macromolecule has been computed and compare with theories which start from a rigid–rod model [2].

[1] B. Liu and B. Dünweg, J. Chem. Phys. 118, (2003), 8061

[2] M. Doi, S. F. Edwards, The Theor. of Polym. Dynam. (Oxf. Univ. Press, 1986); R. Pecora, J. M. Deutch, J. Chem. Phys. 83, (1985), 4823