Abstract
Based on the semi-classical Holstein Hamiltonian we consider charge transfer along a DNA chain of sites at different thermostat temperatures. Recently, using the computer simulation, it has been shown that the charge distribution in homogeneous chains in thermodynamic equilibrium depends not only on the temperature, but also on the length of the chain. We have studied numerically the case of polyadenine fragments with a defect site in the middle of the chain. The results demonstrate qualitatively similar behavior of thermodynamic equilibrium quantities in the case of the homogeneous chain and of the chain with a defect. Insertion of a trap-site enhances the stability of polaron states.
Highlights
The problem of charge or energy transfer in quasi-one-dimensional biomolecules is very interesting for such fields as biophysics and nanobioelectronics
A qualitative picture of the R(T ) values for such chains in thermodynamic equilibrium is similar to the results for a homogeneous chain without a defect [10]
When the thermal energy of the classical chain Eclass = NkBT is less than the critical value Ecrit, the charge is in the polaron state, R(T ) ∼ 1
Summary
The problem of charge or energy transfer in quasi-one-dimensional biomolecules is very interesting for such fields as biophysics and nanobioelectronics. It is believed that the charge carriers in biopolymers, such as DNA, are polarons or solitons This view has been formed mainly due to the fact that DNA is a quasi-one-dimensional system in which excess charges – electrons or holes – evolve into polaron states in the case of their strong interaction with oscillatory degrees of freedom of a molecule. In this work we consider a homogeneous polyadenine chain with one defect site at the center, which plays the role of a trap for the charge. A sequence, where G plays the role of the 8-oxoguanine which is one of the most common DNA lesions resulting from hole migration along the chain [11]. The resultant damage to DNA bases may be a significant source of mutations that lead to cancer and other human pathologies
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