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TheoreticalBackground
Figure2.5: Schematic representation of the behavior of the wave-function in surface
hopping simulations. The possible course of two simulations is shown.
Reaching the high-coupling region, the two states do not mix like in the
mean-field approach. TheSystemmayhopbetween the states and leave the
region onone of them (Based onFig.5 in [72])
therefore no polarization of theMMenvironment[100–102]. It is not necessary to
choose a representation in advance,without knowing anything about theCTpro-
cess. TheCGHamiltonianneedsnot tobediagonalized(as in the followingsurface
hoppingmethod)with thismethod,which saves computational time. The propa-
gatedwave-function can be transferreddirectly to the classicalMDsimulation by
the mapping to the atomic charges. On the downside, the mean-field approach
suffers fromtheso-calledmean-fielderror. Themain issuehere is thatall adiabatic
states interactwith the samemeanpotential of the environment. This has the ef-
fect, that in homogeneousDNAsequences,where the energetic landscape is very
shallow, thedelocalizationof the charge is overestimatedexcessively.
SurfaceHopping
The othermethodof charge transfer computation in thiswork is the surface hop-
ping (SH) scheme [103]. In this approach, the TDSE is propagated as well, but
the classical system interacts onlywithonepureadiabatic state. Thekeyhere is to
choose thisadiabatic state ineverytimestep. Figure2.5showstwopossiblesurface
hoppingsimulations,wherehoppingoccurs in thehigh-coupling region. Thefinal
states are adiabatic ones, nomixingof adiabatic statesoccurshere.
The propagation of the wave-function then takes place on this adiabatic state
through time. Transitions between the states may occur in every time step an
36
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