Web-Books
im Austria-Forum
Austria-Forum
Web-Books
Naturwissenschaften
Chemie
Charge Transport in DNA - Insights from Simulations
Seite - 84 -
  • Benutzer
  • Version
    • Vollversion
    • Textversion
  • Sprache
    • Deutsch
    • English - Englisch

Seite - 84 - in Charge Transport in DNA - Insights from Simulations

Bild der Seite - 84 -

Bild der Seite - 84 - in Charge Transport in DNA - Insights from Simulations

Text der Seite - 84 -

ChargeTransport inMicrohydratedDNA Figure6.3: Maximumof transmission functioncalculatedwith theLandauer–Büttiker method for all of the DNA oligos in the different microhydrated environ- ments. (Medianvalues obtained along15nsMDsimulations.) 6.3 ChargeTransportCalculations The model Hamiltonian containing the obtained CT parameters can be used as a basis for the approximative calculation of the electronic transmission function supportedby the systemwithin theLandauer–Büttiker framework.[127] Here again, the previously developedmulti-scale framework,[45] already success- fully applied to fullyhydratedDNAspecies,[44]wasused. The transmission functionwasevaluated for7,500 snapshots alongeveryMDsim- ulationof15ns. Themaximumvalueof the functionwas recorded for every snap- shot, andthemedianvaluewas takentorepresenteachdistributionsofmax. trans- missionobtained in thatway. Fig.6.3 shows thesemedianvaluesobtained foreach of the DNA sequences, in full aqueous solution as well as in the microhydrated systemsDry1 toDry4. The transmission increases in theDry1 systemincomparison to the fullyhydrated one for five out of sevenDNAoligos. This effect is less obvious for the systems Dry2, possibly due to the slightly distorted helical structure at this level of hy- dration. With further reducedwater content inDry3 andDry4, DNAsuffers from severedistortionsandthetransmissionvanishes infiveof thestudiedDNAspecies. 84
zurück zum  Buch Charge Transport in DNA - Insights from Simulations"
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
Web-Books
Bibliothek
Datenschutz
Impressum
Austria-Forum
Austria-Forum
Web-Books
Charge Transport in DNA