seminar notice

[pastore at ts.infn.it]

Dipartimento di Fisica Teorica - Universita'  di Trieste and
CNR-INFM Democritos  joint seminar


Prof. Giuseppe Foffi
(Ecole Polytechnique Federale - Lausanne)

Tuesday, September 29, 11.00  Seminar Room (ICTP - Leonardo Building)

Extreme coarse graining: from colloids to biomolecules

Abstract

In this seminar I will review some of the activities of my group. I will
briefly describe the "brute" coarse grained (CG) approach of a colloidal
physicist with its success and its pitfalls. I will then move to describe
three bio-related systems that we are investigating presently:

A)Mixtures of eye-lens proteins. I will introduce these mixtures
explaining their medical relevance with respect to cataract disease and I
will show why they are good candidate to be treated as colloidal systems.
I will introduce the model and its validation with experimental results. I
will discuss how a fine balance of the interactions controls the stability
of the system. Indeed thermodynamic stability is a general phenomena and
the same observation that holds here for the eye-lens proteins could be
extended to other systems that could be of potential interest for food
science as well as material science
B)Diffusion-limited absorption in crowded media: Crowding is a crucial
factor for reactions occurring in vivo. Nevertheless, biological reactions
are usually discussed in the ideal Smoluchowski framework of
non-interacting agents. We generalize the classic Smoluchowski problem to
arbitrary crowding conditions by means of a novel computational scheme
that treats the diffusing particles as hard spheres and allows to
efficiently explore the effects of increasing packing on the encounter
dynamics. In this way, we show and rationalize the emergence of an optimal
packing fraction where the encounter rate hits a maximum. Remarkably,
optimality is
attained far below the dynamical arrest, at concentrations typical of
cellular environments.

C)A CG model for human immunoglobulin (IgG): Immunoglobulins are the
soldiers of the immune system. They bind to what they recognize as
dangerous for the body facilitating the immune response. We have developed
a model for IgG that is based on very simple geometrical assumptions but
that reproduces its main feature, namely the presence of highly flexible
hinge. The model agrees well with the available experiments. With this
model we conducted in-silico binding experiments and we studied the effect
of modifying the interactions on the binding process. We show clearly that
the flexibility of these macromolecules is indeed fundamental to perform
their task.