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7.6Conclusion
Toaccess theCTcharacteristics in this sequence, threeparameterswere calculated:
the rate of transfer, thedelocalizationof thehole and theoccupationof thebridge
(A). The rate of transfer is calculated by counting the transfers fromone guanine
to another in a period of 1 ns. Counted are only those transfers, which are not
followed by a back transferwithin 20ps. The delocalization of the hole Srec over
nucleobaseswithoccupations |ai|2 is calculatedby taking the inverseof the sumof
squaredoccupations.
Srec=1/∑(|ai|2)2
Andfinally, thepopulationof thebridge is evaluatedas ameanvalueof theoccu-
pationof theadeninenucleobase.
Table7.6: Comparison of the parametrized CT model with QM/MM simulations of
charge transfer in the sequenceGAGwith themean-field theory
Parameter DNACTmodel QM/MMsimulation
rateof transfer (perns) 2.8±1.1 4.3±2.1
delocalizationof thehole 1.31±0.03 1.40±0.34
populationof thebridge 0.047±0.003 0.062±0.064
Table7.6 shows theobtainedparameters and thevaluesbyT.Kubarˇ ([73], Table4)
are shownasa reference. Comparisonof thesevalues shows that theparametrized
CTmodel is able to reproduce the results ofQM/MMsimulationsof charge trans-
fer with the mean-field method in the sequence GAG accurately. All important
characteristics are reproducedquantitatively.
While fullMD simulations involving theQM/MMscheme need about 2 days to
complete oneof these simulations, theparametrizedCTmodel needs about 5min
for a simulationof the same length (1ns).
7.6 Conclusion
In this chapter, the newlydevelopedparametrizedmodel for theCT inDNAwas
described. Therelevantparameters for theCTwerefitted to results fromQM/MM
103
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