Liu Yun, Chen Sow-Hsin, Berti Debora, Baglioni Piero, Alatas Ahmet, Sinn Harald, Alp Ercan, Said Ayman
Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
J Chem Phys. 2005 Dec 1;123(21):214909. doi: 10.1063/1.2128702.
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.
通过非弹性X射线散射（IXS）研究了沿排列的40 wt%小牛胸腺DNA棒状薄膜轴向的声子传播和阻尼。利用广义三有效本征模理论对IXS光谱进行分析，从中提取作为转移能量E =（普朗克常量/2πω）的函数以及转移波矢Q大小的动态结构因子S(Q,E)。DNA样品的S(Q,E)通常由三个峰组成，一个中心瑞利散射峰以及两个对称的斯托克斯和反斯托克斯布里渊边峰。通过分析布里渊峰，可以在约4至30 nm⁻¹的不同Q值下提取声子激发能量和阻尼。从色散关系低于Q = 4 nm⁻¹的线性部分的初始斜率获得高频声速。在该Q范围内获得的高频声速为3100 m/s，这大约是在相似水合水平下Q约为0.01 nm⁻¹时通过布里渊光散射测得的1800 m/s超声速的两倍。我们的观察结果为DNA分子内部动力学与溶剂动力学之间的强耦合提供了进一步证据。研究了二价和三价抗衡离子对沿DNA棒轴向的声子阻尼和传播的影响。发现添加的多价抗衡离子会引入更强的声子阻尼。根据我们的模型分析，添加的抗衡离子使约12.5至约22.5 nm⁻¹范围内的声子过阻尼。提取了中间散射函数，它显示出明显的两步弛豫，快速弛豫时间范围为0.1至4 ps。
