Web-Books
in the Austria-Forum
Austria-Forum
Web-Books
Naturwissenschaften
Chemie
Charge Transport in DNA - Insights from Simulations
Page - 5 -
  • User
  • Version
    • full version
    • text only version
  • Language
    • Deutsch - German
    • English

Page - 5 - in Charge Transport in DNA - Insights from Simulations

Image of the Page - 5 -

Image of the Page - 5 - in Charge Transport in DNA - Insights from Simulations

Text of the Page - 5 -

CHAPTER1 Introduction The investigation of charge transfer processes constitutes an interface between physics, chemistry and biology. Chemical reactions are often accompanied by chargetransferprocessesnotonly inthe laboratory,butalso inbiologicalprocesses. Here,DNAoccupiesanoutstandingposition intheresearcherscommunity. Itsnat- ural feature to support charge transfer is seen in processes like radiative damage andrepairofDNAstrands in livingorganisms. In the lastyears, theevolvingfield ofmolecular electronicshasbroughtDNAinto the focusasapotential element for electronic circuits at the molecular scale. Special features like self-assembly and self-recognitionare aunique characteristic ofDNAoligomers. The conductivity of DNA has been studied intensively in the recent years.[1, 2] Yet, there are still features of charge transport (CT) that have not been resolved unambiguously yet. The research of CT in nucleic acids started with measure- mentsperformedon longDNAstrandsof several thousandbasepairs, in the form of ‘ropes’[3] or on supercoiledDNA.[4] In these early times, diametrically differ- ent conductivity of DNA under different conditions was reported, ranging from superconductivity[5] to insulation.[6] ThepioneeringstudyofCTin individualDNAoligomersappeared in2000,[7] and several further single-molecule experiments have been reported since then.[8–13] All of these studies are in aqualitative agreementupon the semi-conducting char- 5
back to the  book Charge Transport in DNA - Insights from Simulations"
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 theStretchingProleofDNA 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
Web-Books
Library
Privacy
Imprint
Austria-Forum
Austria-Forum
Web-Books
Charge Transport in DNA