Licentiate defense: Polymer physics: Monte Carlo simulation and Renormalization Group theory

  • Date: –12:00
  • Location: Ångströmlaboratoriet, Lägerhyddsvägen 1 Polhemsalen
  • Lecturer: Anna Sinelnikova
  • Organiser: Division of Materials Theory, Department of Physics and Astronomy
  • Contact person: Anna Sinelnikova
  • Licentiatseminarium

External reviewer: Berk Hess, KTH Royal Institute of Technology

Proteins can without any exaggeration be called the "building blocks of life". The proper functioning of all living organisms depends on a proper behaviour of the proteins they consist of. The proper behaviour of proteins depends not only on their chemical structure, but on their three dimensional shape: secondary and tertiary structures. In contrast to using all-to-all atoms interaction we work with coarse-graining model to discover general behaviour of polymer chains. For this reason we utilize an effective Hamiltonian which can describe thermodynamical properties of polymer chains, which should be considered as a first approach to model all polypeptides. This Hamiltonian can reproduce both secondary and tertiary structures of proteins. To investigate the properties of this model we perform classical Monte Carlo simulations, using our own software package. Another problem we address in this thesis is how to distinguish thermodynamical phases of proteins. The conventional definition of phases of polymer systems use scaling laws: different critical exponents correspond to different phases. However, this method needs the length of the chain to be varied, which is not possible to do with heteropolymers where the number of sites is one of the characteristic of the system. We will apply Renormalization Group theory ideas to overcome this difficult. We present a scaling procedure and an observable which RG flow can define the phase of one certain polymer chain. The side effect of this work is a smoothing algorithm which can be applied to any discrete curve and scatter plots.