Speaker 1: Achille Giacometti
Title: Pattern of Symmetry Breaking and Emergence of New Phases in Biopolymers
Abstract: We discuss the relation between the emergence of new phases and pattern symmetry breaking within the framework of simple models of biopolymers. We start with a simple model for synthetic polymers where consecutive beads are held together, with the steric constraint that overlap of non-consecutive are forbidden, and a pairwise attractive square well potential accounting for hydrophobic effect. We then discuss successive reduction of the spherical symmetry as induced by the local tangent to the polymer chain. In the first case, we will replace spherical beads with disks thus providing the correct local cylindrical symmetry induced by the tangent to the polymer chain. This can be equivalently implemented by still using spherical beads but including a three body potential to the interactions. The resulting thick polymer or tube model presents, in addition to the high temperature coil phase and the low temperature collapsed phase, the emergence of an intermediate “marginally stable phase “ consisting of ground state configurations reminiscent of the alpha helices and beta sheets, the building blocks of globular proteins native states. An alternative way of breaking the spherical symmetry consists of allowing partial overlap of consecutive spherical beads. We will discuss similarities and differences between the phase diagram of this overlapping beads model and the tube model, using numerical simulations supported by analytical arguments. Finally, we will discuss the effect of a further symmetry breaking of the cylindrical symmetry obtained by the addition to each backbone bead of additional beads along the negative normal of the chain, to mimic the presence of side chain in real proteins. This will originate the emergence of new phases within the previously obtained marginally compact phase.
Speaker 2: Tatjana Skrbic
Title: The elixir phase of chain molecules
Abstract: We identify a hitherto unstudied phase of matter, the elixir phase, in a simple model of a short chain molecule, whose backbone does not have any spurious symmetries. This phase has multiple ground states made up of building blocks of helices and almost planar sheets akin to protein native folds. Our results provide an explanation for the finite number of protein folds and the ubiquitous lock-key geometric mechanism of protein-protein and protein-ligand interactions; they offer a blueprint for creating nifty nanomachines by housing them in this phase of matter; and they allow for the wondrous possibility of life elsewhere in the cosmos relying on this phase of matter but being quite different in detail from life on eart
Prof. Achille Giacometti and Dr. Tatjana Skrbic, Dipartimento di Scienze Molecolari e Nanosistemi, Universita' Ca' Foscari di Venezia, Italy, are visiting Prof. Michele Cascella in Oslo.
The Hylleraas seminars alternate between Oslo (room V205) and Tromsø (room C302), and are broadcasted by video conference to the other place. It is possible to follow the seminars externally upon request.