Studies of structure and dynamics of biological macro-molecular assemblies by low angle neutron diffraction and inelastic X-ray scattering

Abstract

This thesis is organized into two parts which focus on the studies of the dynamic structure factor and static inter-particle structure factor respectively. In the first part, we have measured and analyzed the dynamic structure factors of aligned 40 wt% calfthymus Na-DNA molecules with the inelastic X-ray scattering (IXS). In the second part, we have developed a new efficient method to calculate the inter-particle structure factor in a simple fluid interacting with a two-Yukawa term potential and apply it to study the kinetic phase diagram and analyze the small angle neutron scattering (SANS) intensity distribution of colloidal systems. By analyzing the dynamic structure factor measured with IXS, the phonon dispersion relations of 40 wt% calf-thymus Na-DNA with different counterion atmosphere are constructed. It is found that the addition of extra counterions will increase phonon damping at small scattering wave vector, Q. At the intermediate Q range (12.5 nm- < Q < 22.5 nm-l), it may even overdamp the phonon so that the phonon feature can not be extracted from the IXS spectra. The measured sound speed is 3100m/s, which is much higher than the sound speed, - 1800m/s, obtained by Brillouin light scattering. This difference shows that the atoms of DNA molecules are closely coupled to the surrounding water molecules.

(cont.) Therefore, the different dynamic response of water molecules in different Q range affects the overall dynamic response of the hydrated DNA molecules. By analyzing the IXS spectra, the intermediate scattering function is extracted and shows a clear two step relaxation with the fast relaxation time ranging from 0.1 to 4 ps and the slow relaxation time ranging from 2 to 800 ps. In order to understand the phase behavior and the interactive potential of a colloidal system, we have developed a new and efficient method to calculate the inter-particle structure factor of a simple fluid interacting with a two-Yukawa term potential. We have applied this method to study the kinetic phase diagram of a system interacting with a short-range attraction and a long-range repulsion. A new glass phase, cluster glass, is determined through the theoretical analysis by the mode coupling theory (MCT). The SANS intensity distribution of cytochrome C protein molecules in solutions is measured and analyzed with our method. A sharp rising intensity at very low Q value has been consistently observed, which is named zero-Q peak. The existence of the zero-Q peak implies that a weak long-range attraction between protein molecules in solutions exists and has a even longer range than the electrostatic repulsion.