טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
M.Sc Thesis
M.Sc StudentLevine Ariel
SubjectCharge Transport through Ordered DNA Bridges in
Dissipative Molecular Environments
DepartmentDepartment of Chemistry
Supervisor Professor Uri Peskin
Full Thesis textFull thesis text - English Version


Abstract

Understanding charge transport through DNA is important in a wide range of biomedical, material sciences and nano-technological applications. Theoretical modeling of charge transfer through DNA is a difficult task. The size of the system puts the use of exact atomistic level methods out of reach, and different alternative strategies must be used.


An experiment performed by Giese (2004) was a source of great interest as well as dispute regarding the mechanism of charge transport through DNA sequences of type C(A)nCCC (with the complementary sequence). The results of this experiment show two distinct regimes for charge transport. An exponential falloff of the charge transport rate with increasing bridge length for short bridges, which changes into a weak dependence of the rate on the bridge length, for long bridges. In the first part of this work the DNA system used in the experiment is modeled and parameterized using a minimal model approach. Assuming weak coupling to the dissipative molecular environment, charge transport through the system was simulated using reduced density matrix calculations. The model qualitatively reproduced the experimentally observed results, suggesting a unified framework for interpretation of the different transport regimes in terms of bath assisted inelastic transport processes. In particular a new thermally activated ballistic transport mechanism was found to be consistent with the experimental results. Using the minimal model, predictions are made for new experiments in which the temperature, the solvent or the double helix direction would be changed.


In the second part of this work, the effect of strong intra-molecular vibronic coupling on charge transfer through symmetric DNA systems, such as 5’-CATG-3’ (with the complementary sequence), in a dissipative environment is studied. The results demonstrate that in the presence of strong vibronic coupling molecular reorganization can promote CT through the DNA bridge. In particular, vibronic coherences can be observed when the CT dynamics become faster than the de-coherence time induced by the external bath.