Page - (000006) - in Charge Transport in DNA - Insights from Simulations

Table of contents

1. Zusammenfassung 1
2. Summary 3
3. 1 Introduction 5
4. 2 TheoreticalBackground 11
   1. 2.1 MolecularMechanics 11
   2. 2.2 MolecularDynamicsSimulation 13
      1. 2.2.1 Solving theEquationsofMotion 14
      2. 2.2.2 ThermodynamicEnsembles 15
   3. 2.3 QuantumChemistry 18
      1. 2.3.1 DensityFunctionalTheory 18
      2. 2.3.2 ApproximativeDFT–Density-FunctionalTight-Binding 21
   4. 2.4 DynamicsofExcessCharge inDNA 24
      1. 2.4.1 TheMulti-ScaleFramework 25
      2. 2.4.2 TheFragmentOrbitalApproach 26
   5. 2.5 ChargeTransport inDNA 29
      1. 2.5.1 Landauer–BüttikerFramework 29
   6. 2.6 ChargeTransfer inDNA 32
      1. 2.6.1 Basics ofChargeTransfer 32
      2. 2.6.2 Non-adiabaticPropagationSchemes 34
5. 3 SimulationSetup 39
   1. 3.1 TheDNAMolecule 39
      1. 3.1.1 InvestigatedDNASequences 42
   2. 3.2 MDSimulationofDNA 44
   3. 3.3 DNAunderMechanical Stress 45
   4. 3.4 MicrohydratedDNA 46
6. 4 DNAUnderExperimentalConditions 49
   1. 4.1 FreeMDSimulations 50
   2. 4.2 TheStructuralChangesofDNAuponStretching 51
   3. 4.3 IrreversibilityofDNAStretching inSimulations 56
   4. 4.4 Effects ofLowHydration 58
   5. 4.5 Effects ofDecreased IonContent 62
   6. 4.6 Effect ofWater and Ionson theStretchingProfileofDNA 64
   7. 4.7 Conclusion 67
7. 5 ChargeTransport inStretchedDNA 69
   1. 5.1 InvestigatedSequences andStructures 69
   2. 5.2 ChargeTransportCalculations 71
   3. 5.3 SequenceDependentChargeTransport 73
   4. 5.4 DetailedStructuralDifferences 74
   5. 5.5 Conclusion 76
8. 6 ChargeTransport inMicrohydratedDNA 79
   1. 6.1 InvestigatedSequences andStructures 79
   2. 6.2 ChargeTransferParameters 80
   3. 6.3 ChargeTransportCalculations 84
   4. 6.4 DirectDynamicsofChargeTransfer 86
   5. 6.5 Conclusion 87
9. 7 AParametrizedModel toSimulateCT inDNA 89
   1. 7.1 Creating theElectronicCouplings 90
   2. 7.2 Modeling the IonizationPotentials 93
   3. 7.3 TestingwithChargeTransportCalculations 97
   4. 7.4 ChargeTransferExtensions 98
   5. 7.5 TestingwithChargeTransferMethods 102
   6. 7.6 Conclusion 103
10. 8 Conclusion 105
11. Appendix 111
12. A DNAUnderExperimentalConditions 111
    1. A.1 TheStructuralChangesofDNAuponStretching 111
    2. A.2 Effect ofLowHydrationandDecreased IonContent 112
    3. A.3 StretchingofMicrohydratedDNA 116
13. B CTinMicrohydratedDNA 117
    1. B.1 HelicalParameters -CompleteOverview 117
    2. B.2 ElectronicCouplings 118
    3. B.3 IonizationPotentials 119
    4. B.4 ESP InducedbyDifferentGroupsofAtoms 122
    5. B.5 DistanceofChargedAtomGroups fromtheHelicalAxis 123
14. List ofPublications 137