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7.3TestingwithChargeTransportCalculations
Not onlywill this give a better understanding of the phase shift needed to obtain
the correct correlations, but it is also a crucial parameter for theCTcharacteristics
of the model. Therefore, IP differences between neighboring nucleobases were
calculated fromMDsimulationsof20nsandanalyzed in termsof theirprobability
distributions. Thephaseshiftof the IPwasparametrizedso that thewidthof these
distributionsmatches thedata fromMDsimulations.
Thefinalphaseshiftwasset to1.11perneighborforacosinefunctionwithaperiod
of 2π. Figure7.4 shows thedistributions for thefirst twoneighboringnucleobases
when this phase shift is applied. Note that the modeled standard deviation of
the IP difference becomes inaccurate starting from the second-neighbor correla-
tion. Thiswill have an effect in approaches relyingon the coherent transport, like
the Landauer–Büttikermodel. However, the CTmodel shouldworkwith charge
transfermethods,whichdescribenearest neighborhoppingpredominantly.
7.3 TestingwithChargeTransportCalculations
With the EC and IP constructed, the time-dependent coarse-grainedHamiltonian
can be set up, and the CT model can be tested with charge transport methods
already. The easiest approach is to calculate the transmission function in every
timestepandaverageover the simulation.
As already noted, the CT model does not describe long-range correlations well.
Thus, the calculation of a transmission functionwas done for a sequence of only
three adenine nucleobases. Figure 7.5 shows the averaged transmission function
in comparison to one obtained along an atomistic MD simulation. The overall
formof the transmission function is reproduced accurately for thisDNA species,
apparently. For longer sequences, the transmission functions assumes a triangular
shape as a consequenceof awrongdistributionof IPdifferences starting from the
A1-A4 neighbors. Clearly, this is anartifact of the simple correlationmodel.
97
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