SEMINAIRE MERCREDI 16 JANVIER 2008
14 heures
Salle Séminaire 5
Centre de Physique Théorique
Marseille-Luminy

Francesco Piazza
Ecole Polytechnique Fédérale de Lausanne

Title: Discrete breathers in nonlinear network models of proteins

Abstract: Discrete breathers (DB) are spatially-localized,
time-periodic vibrations that arise under general conditions in
discrete nonlinear systems. While much is known concerning their
existence and stability in spatially periodic media, much less is
known about the interplay of nonlinearity and spatal heterogeneity in
spatially disordered systems, where localization is also fostered as a
result of breaking of translational invariance.

We introduce a coarse-grained topology-based nonlinear network model
of protein dynamics with the aim of investigating the interplay of
spatial disorder and nonlinearity in biological molecules. DB
solutions, characterized both numerically with the surface cooling
technique and analytically, show that localization of energy occurs
generically also in the presence of disorder, but is a site-dependent
and, on a larger scale, fold-dependent process. By studying
approximate analytical solutions, we find that a non-zero energy gap
for exciting a DB at a given site either exists or not, and in the
latter case it vanishes as result of the impossibility of exciting
small-amplitude DBs at all.

Interestingly, our cooling simulations show that localized modes of
nonlinear origin form spontaneously in the stiffest parts of the
structure. Such results provide a straightforward way for
understanding the recently discovered link between local stiffness of
proteins and enzymatic activity. They strongly suggest that nonlinear
phenomena may play an important role in enzyme function, allowing for
a ready energy storage channel during the catalytic process.