From Dynamics to Structure and Function of Model Bio-Molecular Systems


Fontaine-Vive, F.

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Delft University Press



The purpose of this thesis was to extend recent works on structure and dynamics of hydrogen bonded crystals to model bio-molecular systems and biological processes. The tools that are used are neutron scattering (NS) and density functional theory (DFT) and force field (FF) based simulation methods. The quantitative and parameter-free link (in the case of DFT methods) between structure and dynamics has been applied to strong hydrogen bonded crystals and bio-polymers such as collagen and DNA.
In several SSHB crystals, DFT normal modes and molecular dynamics calculations revealed the mechanism of proton transfer as being driven by low frequency phonons.
In DNA, the structure-dynamics-function is base-pair opening, which is related to various bio-physical processes like replication and transcription. Force field methods were used and normal mode analysis to identify modes with base-pair opening character. The oriented DNA films for experiments were made using the wet spinning method and the equipment was successfully installed and modernized during the thesis at ILL.