THE EFFECTS OF VISCOUS WATER ON THE NORMAL MODE VIBRATIONS OF DNA
Abstract
The problem of viscous damping of vibrating DNA polymer is solved in the low-amplitude limit for all acoustic branches of the spectrum. The acoustic spectrum covers the microwave region of frequencies. Analytic solutions are obtained for a model describing the DNA polymer as a smooth circular cylinder. Numerical results are presented for a model describing the DNA polymer as a twisted cylinder of elliptical cross section. The amount of mass loading is determined for both models and the damped spectrum for the mass-loaded oscillator is calculated. The viscous damping is found to be a strong function of frequency. All modes are overdamped in the presence of an infinite amount of water. The calculation is also performed for the DNA polymer in a fiber. Appropriate boundary conditions for determining the viscous forces on the acoustic vibrational modes are discussed. The viscous forces acting on each mode are calculated as functions of both frequency and amount of water in the fiber. The longitudinal acoustic mode is shown to be underdamped in the presence of a finite amount of water. The torsional and transverse acoustic modes remain overdamped. The model of DNA is then used to analyze fluorescence depolarization experiments with DNA. The DNA is modeled as a cylinder with an elliptical cross section and a grooved surface. This model has only one adjustable parameter, the persistence length. The normal mode structures of the torsional and bending motions are treated more rigorously than in previous work. The normal mode dependence of the torsional and bending rigidities as well as the viscous forces are included in the analysis for the first time. The geometry of previous models is shown to lead to values of the torsional and bending rigidities which are too low. The behavior of the fluorescence depolarization in the picosecond and subpicosecond time regions is found, regions for which previous treatments are necessarily unreliable. New features are predicted for the short time regime. Also the short time "wobble", an heretofore unexplained experimental feature is shown to be a consequence of the high frequency normal modes.
Degree
Ph.D.
Subject Area
Condensation
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