title: Effects of counterion valency on the damping of phonons propagating along the axial direction of liquid-crystalline DNA.
abstract: The phonon propagation and damping along the axial direction of films of aligned 40 wt % calf-thymus DNA rods are studied by inelastic x-ray scattering (IXS). The IXS spectra are analyzed with the generalized three effective eigenmode theory, from which we extract the dynamic structure factor S(Q,E) as a function of transferred energy E=variant Planck's over 2piomega, and the magnitude of the transferred wave vector Q. S(Q,E) of a DNA sample typically consists of three peaks, one central Rayleigh scattering peak, and two symmetric Stokes and anti-Stokes Brillouin side peaks. By analyzing the Brillouin peaks, the phonon excitation energy and damping can be extracted at different Q values from about 4 to 30 nm(-1). A high-frequency sound speed is obtained from the initial slope of the linear portion of the dispersion relation below Q=4 nm(-1). The high-frequency sound speed obtained in this Q range is 3100 ms, which is about twice faster than the ultrasound speed of 1800 ms, measured by Brillouin light scattering at Q approximately 0.01 nm(-1) at the similar hydration level. Our observations provide further evidence of the strong coupling between the internal dynamics of a DNA molecule and the dynamics of the solvent. The effect on damping and propagation of phonons along the axial direction of DNA rods due to divalent and trivalent counterions has been studied. It is found that the added multivalent counterions introduce stronger phonon damping. The phonons at the range between approximately 12.5 and approximately 22.5 nm(-1) are overdamped by the added counterions according to our model analyses. The intermediate scattering function is extracted and it shows a clear two-step relaxation with the fast relaxation time ranging from 0.1 to 4 ps.
authors.affiliation: Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Yun
authors.initials: Y
authors.lastname: Liu
authors.forename: Sow-Hsin
authors.initials: SH
authors.lastname: Chen
authors.forename: Debora
authors.initials: D
authors.lastname: Berti
authors.forename: Piero
authors.initials: P
authors.lastname: Baglioni
authors.forename: Ahmet
authors.initials: A
authors.lastname: Alatas
authors.forename: Harald
authors.initials: H
authors.lastname: Sinn
authors.forename: Ercan
authors.initials: E
authors.lastname: Alp
authors.forename: Ayman
authors.initials: A
authors.lastname: Said
mesh_terms: D004247:DNA / Q000737:chemistry*; D050866:Liquid Crystals; D013016:Sound; D013057:Spectrum Analysis; D014732:Vibration; D014965:X-Rays
chemical_list: D004247:DNA