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SimulationSetup
Figure3.6: Studied microhydrated systems – A13 with varied number of water
molecules.
An additional constant external force was applied to the microhydrated DNA
oligomers, emulating the experimental setupwhere the oligomer is held between
two electrodes. A series of trial simulations with varied magnitude of the ex-
ternal force was performed to estimate the force that would support a double-
strandedstructureofDNA.This forcewasappliedasanharmonic constraintwith
a force constant of 1000 kcal/(mol nm) between the O3’-atoms of the outermost
nucleotides.
Also studiedwere the systemsDry1 andDry2with a smaller numberof counteri-
ons than required for neutralization. The clusterswere stripped randomlyof 1/4,
1/2, 3/4 aswell as off all ions, respectively. MD simulationswere performed for
thesenegatively chargedsystemswith the samesetupasdescribedabove.
ThesimulationsofmicrohydratedDNAwithanexternalpullingforceof increasing
magnitudewereperformedinthesamefashionasthoseof thefullyhydratedDNA.
Asingle loading rateof10pN/nswasappliedhere.
48
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