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AParametrizedModel toSimulateCT inDNA
Figure7.8: Graphical illustration of the energy landscape in theGAGsequence. Gua-
nines have the lowest IP. Adeninewith higher IP acts as a barrier for the
CT.
Having set up the Hubbard matrix, it now has to be modified in terms of a
self-interaction correction. All-DFT basedmethods suffer from the so-called self-
interactionerror. Tocorrect thisbehavior, the second-order termshave tobescaled
down. Therefore, theelementsof theHubbardmatrixarescaleddownwithafactor
of0.2, the sameas in thepreviouswork [79].
Inner-SphereReorganizationEnergy
So far, the inner-sphere reorganization energy is missing in the CT model. Al-
though this is not connected to theHubbardmatrix at all, it easily can be intro-
ducedby including it into it. Therefore, the inner-sphereRE,whichwasestimated
tobe0.23 eV[79], is subtracted fromthediagonal elementsof theHubbardmatrix.
7.5 TestingwithChargeTransferMethods
At thispoint, themodel is completeandshouldbeable todescribe charge transfer
inDNA.To test this, hole transfer in the shortDNAsequenceGAGwassimulated
100 times for 1ns. This sequencewas chosen because of its special characteristics
for charge transfer. The guanines have lower IP than the adenine in themiddle,
therefore the adenine acts as a bridgewhichhas to be overcomewhenCT should
occur. Figure7.8gives agraphical illustration.
102
Charge Transport in DNA
Insights from Simulations
- Titel
- Charge Transport in DNA
- Untertitel
- Insights from Simulations
- Autor
- Mario Wolter
- Verlag
- KIT Scientific Publishing
- Datum
- 2013
- Sprache
- englisch
- Lizenz
- CC BY-SA 3.0
- ISBN
- 978-3-7315-0082-7
- Abmessungen
- 17.0 x 24.0 cm
- Seiten
- 156
- Schlagwörter
- Charge Transport, Charge Transfer, DNA, Molecular Dynamics, Quantum Mechanics
- Kategorien
- Naturwissenschaften Chemie
Inhaltsverzeichnis
- Zusammenfassung 1
- Summary 3
- 1 Introduction 5
- 2 TheoreticalBackground 11
- 3 SimulationSetup 39
- 4 DNAUnderExperimentalConditions 49
- 5 ChargeTransport inStretchedDNA 69
- 6 ChargeTransport inMicrohydratedDNA 79
- 7 AParametrizedModel toSimulateCT inDNA 89
- 8 Conclusion 105
- Appendix 111
- A DNAUnderExperimentalConditions 111
- B CTinMicrohydratedDNA 117
- List ofPublications 137