We develop methods based on theory of representations of continuous and discrete groups; theory of invariants for the groups not-generated by reflections; and theory of bifurcations of invariants functionals. It is applied to the protein arrangement in Satellite Tobacco Mosaic virus, Cowpea Chlorotic Mottle virus and Sindbis virus (which verify Caspar and Klug selection rules) and in L-A virus, Dengue virus and Murine Polyoma virus (which violate Caspar and Klug rules).

In the present work we develop an approach which associates viral capsid formation with the unconventional crystallization process and propose to describe the capsid self-assembly using a generalization of the Landau theory of crystallization. It is based on the successive application of methods of a) theory of representations of continuous and discrete groups; b) theory of invariants for the groups not-generated by reflections; c) theory of bifurcations of invariant functionals. To compare the predictions of the theory with the available cryoelectronic microscopy and AFM data we use irreducible density distribution functions which generate the protein positions on a spherical capsid.

Viral genome is protected by a solid protein shell (capsid) self-assembled from many copies of identical subunits (one or few proteins). The positions and orientations of subunits display high level of spatial organization well suited to modern structural methods of study. The structural and biochemical data rise a whole number of questions concerning unconventional positional order of subunits in the shell, physical mechanisms of the self-assembly and its thermodynamics. In the present work we develop the theory which explains the formation and classifies the structures of viruses with spherical topology and icosahedral symmetry. We develop an explicit method based on symmetry selection rules, which predicts the positions of centers of mass for the proteins self-assembled in the viral capsid shell. The theory describes in a uniform way both the structures satisfying the well-known Caspar and Klug model for capsid construction and those violating it. The peculiarities of the assembly thermodynamics are discussed. We also show the relation between the protein density distributions obtained and the infectivity properties of several human viruses. To illustrate the notions of the theory and the results obtained we focus on the Dengue virus (DENV) capsid.

We use a custom shear cell coupled to an optical microscope to investigate at the particle level the yielding transition in concentrated emulsions subjected to an oscillatory shear deformation [1]. By performing experiments lasting thousands of cycles on samples at several volume fractions and for a variety of applied strain amplitudes, we obtain a comprehensive, microscopic picture of the yielding transition. We find that irreversible particle motion sharply increases beyond a volume-fraction dependent critical strain, which is found to be in close agreement with the strain beyond which the stress-strain relation probed in rheology experiments significantly departs from linearity. The shear-induced dynamics are very heterogenous: quiescent particles coexist with two distinct populations of mobile and ‘supermobile’ particles. Dynamic activity exhibits spatial and temporal correlations, with rearrangements events organized in bursts of motion affecting localized regions of the sample.

Despite very different structural properties, relaxors exhibit many of the vibrational and thermal properties specific to the glassy state. These include low-lying vibrations (boson peak?), a plateau in the thermal conductivity at low temperature, a strong scattering regime of acoustic waves, a stretched exponential behavior of the relaxational dynamics, and the appearance of two level systems below ~2 K, among others. These features most likely originate from the strong and isotropic disorder at nanometric scale in these two otherwise very different classes of materials. I will discuss these behaviors from the point of view of glass physics.

We report an experimental study on the confinement of oligothiophene derivatives into single-walled carbon nanotubes over a large range of diameter (from 0.68 to 1.93 nm). We evidence by means of Raman spectroscopy and transmission electron microscopy that the supramolecular organizations of the confined oligothiophenes depend on the nanocontainer size. The Raman Radial Breathing Mode frequency is shown to be monitored by both the number of confined molecules into a nanotube section and the competition between oligothiophene/oligothiophene and oligothiophene/tube wall interactions. We finally propose simple Raman criteria to characterize oligothiophene supramolecular organization at the nanoscale.