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Charge Transport in DNA - Insights from Simulations
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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
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Charge Transport in DNA Insights from Simulations
Title
Charge Transport in DNA
Subtitle
Insights from Simulations
Author
Mario Wolter
Publisher
KIT Scientific Publishing
Date
2013
Language
English
License
CC BY-SA 3.0
ISBN
978-3-7315-0082-7
Size
17.0 x 24.0 cm
Pages
156
Keywords
Charge Transport, Charge Transfer, DNA, Molecular Dynamics, Quantum Mechanics
Categories
Naturwissenschaften Chemie

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
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Charge Transport in DNA