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2.6ChargeTransfer inDNA
can be called hops or switches. The key issue to be solvedhere is to calculate the
probabilityof suchahop inevery timestepunder thegivencircumstances.
The implementation used in this work is based on the SH algorithm by Persico
et al. [104]. This algorithmuses the local diabatization of the adiabatic states of
the system. The advantage of this is a stable representation of adiabatic states in
regionsof avoidedcrossingor conical intersections.
In the implementedsetup, theeigenproblemof theexcess charge is solved inevery
time step. From this, thewave-function of the excess charge is given as a combi-
nationof the adiabatic states. Then thediabatic states are redefined tobe identical
with the ones at the beginning of the time step. The TDSE is then solved for this
locallydiabaticbasis topropagate thewave-functionof theexcess charge. Thecru-
cial step here is the calculation of the probability to hop from the current state to
one of the calculated new states from the populations. The transition to another
state is thendeterminedbydrawinga randomnumber.
This isanalternativetopropagatingthewave-functionwiththemean-fieldmethod.
The rest of the simulationprotocol is identicalwith that in themean-fieldmethod.
Here again, the propagatedwave-function can be transferred directly to the clas-
sicalMDsimulationby themapping to the atomic charges. The advantage of this
setup is that there is no over-delocalization issue like in themean-field approach.
However, in thismethodtheCGHamiltonianhas tobediagonalized. All represen-
tationsof thequantumsystemconsistof individual states. Therefore it isnecessary
to choosea representation inadvance.
There is no artificial CTwhen the electronic couplings are very lowor even zero.
Andfinally, themicroscopicalreversibility is fulfilled,againincontrast tothemean-
fieldapproach,.
Unfortunately, also the current implementation of the SH method suffers from
some issues, which will be outlined shortly. After a surface hop, the velocities
of the classicalMMatoms are not rescaled. This possiblymeans that there is no
energyconservation. Another issueare the classically forbidden transitions,which
are not treated in our setup. The quantum system is supposed to have enough
energyat any time for thehop tooccur.
37
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