2009-09-23
10:15 at HCI J 574

Extreme coarse grainings: from colloids to biomolecules.

Giuseppe Foffi

EPFL

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.