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BIBLIOGRAPHY
andM.Orozco. Refinement of theAMBER forcefield for nucleic acids: Im-
proving thedescriptionofα/γ conformers. Biophys. J.,2007. 92,3817–3829.
[114] J.Åqvist. Ion–Water InteractionPotentialsDerived fromFree-EnergyPertur-
bationSimulations. J. Phys.Chem.,1990. 94,21,8021–8024.
[115] AmberTools1.4,2010. Http://ambermd.org.
[116] F. Ryjácˇek. Ambconv, 2002. Http://www.gromacs.org/ Down-
loads/User_contributions/Other_software.
[117] B. Hess, H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije. LINCS: A
linear constraint solver formolecular simulations. J.Comput.Chem.,1997. 18,
12,1463–1472.
[118] D. vander Spoel, E. Lindahl, B.Hess,G.Groenhof,A. E.Mark, andH. J. C.
Berendsen. GROMACS: Fast, flexible, and free. J. Comput. Chem., 2005. 26,
1701–1718.
[119] B.Hess, C.Kutzner,D. vander Spoel, andE. Lindahl. GROMACS 4: Algo-
rithms forhighlyefficient, load-balanced, andscalablemolecular simulation.
J.Chem.TheoryComput.,2008. 4,3,435–447.
[120] P.Hobza,M. Kabelácˇ, J. Šponer, P.Mejzlík, and J. Vondrášek. Performance
of empirical potentialsAMBER,CFF95, CVFF,CHARMM,OPLS, POLTEV),
semiempirical quantumchemicalmethods (AM1,MNDO/M,PM3), and ab
initioHartree–Fockmethod for interactionofDNAbases: Comparisonwith
nonempirical beyond Hartree–Fock results. J. Comput. Chem., 1997. 18, 9,
1136–1150.
[121] M. Zgarbová, M.Otyepka, J. Šponer, P. Hobza, and P. Jurecˇka. Large-scale
compensation of errors in pairwise-additive empirical force fields: compar-
ison ofAMBER intermolecular termswith rigorousDFT-SAPT calculations.
Phys.Chem.Chem.Phys.,2010. 12,35,10476–10493.
[122] M. Rueda, S. G. Kalko, F. J. Luque, andM.Orozco. The Structure andDy-
namicsofDNAin theGasPhase. J.Am.Chem.Soc.,2003. 125,26,8007–8014.
[123] A.Voityuk. Fluctuationof theelectronic coupling inDNA:Multistateversus
two-statemodel. Chem.Phys. Lett.,2006. 439,162–165.
135
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
- 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