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Activity 8.1 - Enzyme GEL degraddation
T. Abete, A. Coniglio, A. de Candia

We studied a model for gel degradation by the action of enzymes. The gel is schematized as a cubic
lattice, whose sites represent monomers; the enzymes are random walkers that cut bonds over which
they pass. We studied the percolative properties and viscoelatic properties of such system. Our results
are in good agreement with the experimental ones and make also new prediction on the critical
exponents of elastic modulus and viscosity.

Activity 8.2 – Vasculogenesis

We also proposed a simple model for the formation of blood vessels, that reproduces the percolation
transition characterizing the formation of vascular network, and scaling behavior experimentally
observed, with a fractal structure at length scales lower than some characteristical distance, and the
typical structure of the random percolation at longer scales.

Program for 2005

In presence of a weak gradient of certain substances, eucariotic cells undergo a strong polarization,
with a phase separation between two different species of enzymes present inside the cell. This
mechanism is essential for the chemiotaxis. We plan to study a model able to explain this mechanism.

Activity 8.3 – Systems of biological interest
L. Peliti, A. Imparato, F. Tria

We have analyzed the effect that kinetic barriers, such as tertiary structures have on RNA unzipping
experiments, and the way in which by the kinetics of the unzipping one may gather information on the
tertiary structures. We have suggested ways of improving current experimental protocols in order to
optimize their performances.

We have introduced what we consider a minimal model describing the evolution of the Influenza A
virus. The model takes into account the specific immunity acquired by the host, the conjectured
existence of a short-lived generic immunity and the randomness in the infectivity of different viral
strains. We have shown that the absence of any one of these aspects leads to a highly unstable viral
evolutionary behavior, in contrast with observations.

Program for 2005

In micromanipulation experiments, it is possible to obtain information about the equilibrium properties
of a system by monitoring the work exerted on it, and applying the remarkable identity known as the
Jarzynski equality. We have identified ways of evaluating the distribution of the work and shall take
advantage of this information to improve on current experimental and data processing protocols.

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