Tombolato, Fabio (2008) Theoretical and computational methods for soft matter problems. [Ph.D. thesis]
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The present thesis deals with the development and implementation of models for problems in soft condensed matter, at the interface between biology and material science. In particular, two projects have been carried out. The first focuses on the molecular origin of chirality in liquid crystalline solutions of semiflexible polyelectrolytes like DNA, columnar aggregates of deoxyguanosine tetramers (G-wires) and filamentous becteriophages. The second project deals with the integration between theoretical and experimental methods for the study of membrane-proteins systems, starting from the analysis of ESR spectra of spin labelled proteins. Both projects have been carried out in collaboration with experimental groups.
This thesis is organised in two parts. In the first part, from chapter 1 to chapter 4, the work on chiral amplification in liquid crystalline solutions of polyelectrolytes is presented. In chapter 1, the phenomenon of chiral amplification is introduced and the main properties of liquid crystals are summarised. In chapters 2 and 3 the theoretical model which has been developed to connect the molecular and phase chirality of rigid polyelectrolytes is presented, together with its application to solutions of B-DNA and colloidal suspensions of M13 virus. In chapter 4, this model is extended to semiflexible polymers.
The second part, from chapter 5 to chapter 9, deals with the theoretical and computational methods used to analyse ESR experiments on spin labeled proteins. Chapter 5 is a short introduction to peripheral proteins, the Site-Directed Spin Labelling (SDSL) technique and ESR lineshape simulations. In chapters 6 and 7, a method for the analysis of the ESR spectra of spin labeled proteins is proposed, based on the structural and motional characteristics of typical spin labels in their environment. In chapter 9, the model is applied to the investigation of controversial aspects of ?-Synuclein binding to lipid bilayers. Chapter 8 reports on Molecular Dynamics simulations of a fragment ?-Synuclein, in the presence of a POPC bilayer.
Finally, chapter 10 presents a summary of the two projects, with some highlights on the relevant results obtained in this thesis.
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