Graduate School in Nonlinear Science
MIDIT OFD CATS
Modelling, Nonlinear Dynamics Optics and Fluid Dynamics Chaos and Turbulence Studies
and Irreversible Thermodynamics Risø National Laboratory Niels Bohr Institute and
Technical University of Denmark Building 128 Department of Chemistry
Building 321 P.O. Box 49 University of Copenhagen
DK-2800 Lyngby DK-4000 Roskilde DK-2100 Copenhagen Ø
Denmark Denmark Denmark
NONLINEARITY-INDUCED CONFORMATIONAL INSTABILITY AND DYNAMICS OF
BIOPOLYMERS
by Sergei Mingaleev
Nonlinear Physics Group
Research School of Physical Sciences and Engineering
The Australian National University
Canberra ACT 0200, Australia
MIDIT-seminar 500
AFTER THE LECTURE MIDIT WILL
CELEBRATE ITS QUINCENTENARY LECTURE
WITH A GLASS OF CHAMPAGNE.
YOU ARE ALL CORDIALLY INVITED!
Tuesday, November 13, 2001, 15.00 h
at IMM, Bldg. 305, Room 018, DTU
Abstract:
We propose a simple phenomenological model for describing the
conformational dynamics of biopolymers via the nonlinearity-induced
buckling and collapse (i.e. coiling up) instabilities. Taking into
account the coupling between the internal and mechanical degrees of
freedom of a semiflexible biopolymer chain, we show that self-trapped
internal excitations (such as amide-I vibrations in proteins, base-pair
vibrations in DNA, or polarons in proteins) may produce the buckling
and collapse instabilities of an initially straight chain. These instabilities
remain latent in a straight infinitely long chain, because the bending
of such a chain would require an infinite energy. However, they manifest
themselves as soon as we consider more realistic cases and take into
account a finite length of the chain. In this case the nonlinear localized
modes may act as drivers giving impetus to the conformational dynamics
of biopolymers. The buckling instability is responsible, in particular,
for the large-amplitude localized bending waves which accompany the
nonlinear modes propagating along the chain. In the case of the collapse
instability, the chain folds into a compact three-dimensional coil.
The viscous damping of the aqueous environment only slows down the folding
of the chain, but does not stop it even for a large damping. We find that
these effects are only weakly affected by the peculiarities of the
interaction potentials, and thus they should be generic for different
models of semiflexible chains carrying nonlinear localized excitations.