Dynamic and thermodynamic analysis of a simple model of DNA
Abstract
A new simple model of DNA is presented based on the results of lattice dynamics (LD) calculations in conjunction with the modified self-consistent phonon approximation (MSPA) done on a detailed model of DNA homopolymers. The model emphasizes the intrinsic nonlinearities present in the hydrogen-bonded duplex. The impetus for introducing the simplified model is to analyze the importance of the nonlinearities in the dynamics that lead to denaturation. An initial analysis is done on the possible dynamical excitations that can exist in the system due to the hydrogen bond (HB) nonlinearities. It is found that in a certain regime of base-pair motion, the nonlinearities can prevent dissipation of wave packets and thus suggesting the possibility of energy transfer along the molecule. What is also found, is the ability of the nonlinearities to "pin" excitations on the lattice thus suggesting a possible mechanism for localizing energy along the molecule for biologically significant periods of time. This analysis is done on a "cold" chain, i.e. at T = 0 K. In the latter part of this thesis, this model is shown to be thermodynamically unstable under certain circumstances. This instability is analyzed and general conclusions are drawn concerning the thermodynamics of any interaction similar to the ones used in the present case. As a result of this instability the thermodynamic analysis is done in nonequilibrium situations using stochastic methods to simulate a heat bath. Numerical calculations are performed to study the dissociation of the molecule and the possible effects of the thermal bath on the dynamical excitations mentioned in the previous paragraph. It is found that the dissociation time is very long at room temperature for long molecules.
Degree
Ph.D.
Advisors
Prohofsky, Purdue University.
Subject Area
Molecules|Condensation
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