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Charge Transport in DNA - Insights from Simulations
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Introduction acterofDNAunderambient conditions. ThedependenceofDNAconductanceon the distance of the electrodeswas proposed by Tao et al.,[8] however in amacro- scopic fashion. Stepwise decrease of conductancewas reported, as the individual DNAmoleculesbetween theelectrodeswerebreaking. The fundamental features of CT in DNA have been described as well. First, the exponentialdependenceofCTefficiencyon the lengthof theDNAoligomers. Sec- ond, the role of experimental setup that is both crucial and challenging to charac- terize. In conclusion, carefully preparedDNAdevices exhibitedmeasurable con- ductance, and this fact together with the practicable synthesis of even very long DNAmoleculeswere the initial impulses for the contemplations on the potential useofDNA-baseddevices innano-electronics.[14,15] Albeit, thestructureof theDNAspecies in theseexperimentscouldnotberesolved unambiguously. While it was concluded that the structure played a key role in determining the conductance, it could only be guessed on the basis of observed electricpropertieswhat the structural contourswere. Allmentionedexperimental studies share thegeneral featuresof the experimental setup.ADNAoligomerof several tensofbasepairs is linkedtometallic electrodes viaathioalkylgroupattachedusuallytothe3’-endofeachoftheDNAstrands. The distance of electrodes is or can be varied in the experiments, stretching theDNA molecule, and theCTefficiency is affectedby the alteredDNAstructure. This fact directs the focusof the intendedresearchtoaconsiderableextent to themechanical properties of theDNAspeciesunder thegiven conditions. Thepotential ability of DNA to stretch in biological processeswasmentioned already in 1953,[16] in an article thatdirectly followedtheproposalofDNAstructurebyWatson&Crick.[17] The responseofdsDNAstructure to stretching stresshasbeen studiedextensively since the 1990s. First considerations on entropic elasticity of DNA [18] were fol- lowedby studies on theDNA ‘overstretching’,[19, 20] and earlymodeling studies revealed that dsDNAwoulddeformdifferently if the strands are pulled indiffer- ent ways.[21, 22] Also, a structurewas proposed that DNAwould assume upon stretching of the 3’-ends of each strand – so-called S-DNAwithmaintained inter- strand base pairing but unwound, in a sort of a ladder structure. On the other hand, when dsDNA was stretched and supercoiled, another new structure was observed.[23] 6
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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

  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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