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

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.

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Nuclear Engineering

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2005

Author dc:creator

• Liu, Yun

Advisor dc:contributor.advisor

• Sow-Hsin Chen.

• Nuclear Engineering.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/34438

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/34438