| In this thesis, polymer and biopolymer structure and dynamics were studied with scanning probe microscopy and computational simulation. In part 1, chapters 1-4, an image charge model was employed to simulate the effect of local dielectric response in electric force microscopy (EFM) of a glass polymer film. Local dielectric spectroscopy of the polymer films was studied with both simulation and EFM experiments. Part 2, chapters 5-12, scanning probe microscopy or atomic force microscopy (AFM) techniques and computational simulations were applied to study DNA flexibility enhancement by HMGB proteins. The study relies on a large amount of statistical works. HMGB protein DNA bending mechanism was under study. The experimental results show that HMGB proteins follow a static kink bending model. Protein aggregation structures: oligomers, cooperative binding modes and rigid filaments were also observed when the concentration of the protein was increased. Such structures made the analysis of the bends more complex. Finally, we conducted a computational simulation to quantify the bends by HMGB proteins. A Monte Carlo simulation was employed to generate bulk amount of simulated DNA molecules. Chi square statistical test was applied to quantify the bends by comparing the simulation with the AFM experiments. Appendix A, B and C are unpublished results or incomplete work on exploratory research. This work is preliminary, but some constructive ideas for future work have been produced. |
