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4.3 IrreversibilityofDNAStretching inSimulations
Figure4.8: Distance/force profile in the stretching/relaxing simulations of A13. Black
– stretching (increasing force), colored – subsequent relaxation from the
pointsA,B,C andD; left – external force removed abruptly, right – force
decreased to zero gradually.
Table4.3: Final structures after the stretching/relaxing simulations.
force removedabruptly forcedecreasedgradually
fromA fromB fromC fromD fromA fromB fromC fromD
A5 helix helix helix ladder A5 ladder ladder ladder ladder
A9 helix helix ladder helix A9 helix ladder ladder separation
A13 helix helix helix helix A13 helix ladder ladder ladder
G5 helix helix ladder ladder G5 ladder ladder ladder separation
G9 helix helix helix ladder G9 ladder ladder ladder separation
G13 helix helix helix helix G13 ladder ladder ladder separation
was not always the casewhen the forcewas removed already in the ladder state
of theDNAoligomer. In some simulations, the ladderwas preserved even in the
free simulation whereas the other simulated DNA species returned to a helical
conformation.
The situation changes dramatically when passing to the simulation with a grad-
ual decrease of the force. Already when the external force was being switched
off from themidpoint of the helix–ladder transition (B), the helical conformation
does not recoverwithin the simulation time. This hysteresis emphasizes the irre-
versible character ofDNAstretching in the performed simulations. Its evenmore
distinctdemonstration is theseparationofDNAstrandsobserved in fourof thesix
simulations after the reversal of external force inpointD.
57
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
- Zusammenfassung 1
- Summary 3
- 1 Introduction 5
- 2 TheoreticalBackground 11
- 3 SimulationSetup 39
- 4 DNAUnderExperimentalConditions 49
- 5 ChargeTransport inStretchedDNA 69
- 6 ChargeTransport inMicrohydratedDNA 79
- 7 AParametrizedModel toSimulateCT inDNA 89
- 8 Conclusion 105
- Appendix 111
- A DNAUnderExperimentalConditions 111
- B CTinMicrohydratedDNA 117
- List ofPublications 137