Partially Coherent Charge Transport in DNA

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Partially Coherent Charge Transport in DNA

• YiJing Yan
• Hong Kong University of Science and Technology

Collaborators Prof. XinQi LI (Inst.
Semiconductor, BeiJing) Dr. Houyu ZHANG (INFM
Center S3, Italy) Mr. Ping HAN Acknowledgment
RGC-HK, NNSF-China
ADMOL, 23 27 Feb. 2004, Dresden, Germany
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General Introduction

• Motivation bio-function molecular device
• Characteristics of nano-size Partially coherent
  tunneling
• - Failure of (incoherence) Ohms law
• - Failure of (coherent) superexchange tunneling

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Electron Transfer Rate vs. Conduction
Established correspondence (in formulation)
ET rate constant ? Electric
conductance Chemical yield ? Electric
current Donor/Acceptor ?
Electrodes (chem. potential) DmDA ?
eV (applied voltage) See reviews, Nitzan,
Ann. Rev. Phys. Chem. 52 (2001) 681
Yan Zhang, J. Theo. Comput. Chem. 1 (2002) 225
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Experimental Observations

• (J.K.Barton B.Giese G.B.Schuster
  P.F.Babara)
•  
• GATCTTGAGTGGG
• C TAGAACTCACCC
•  

acceptor
donor
Side reactions deprotonation of G w/
surrounding H2O
Hole charge trapper
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The Ohms Law Exact Results
Yan/Li/Zhang, JCP [phone]
ET rate constant ? Electric
conductance Chemical yield ? Electric current
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Effect of Finite IncoherencePartially Coherent
Tunneling via Büttikers scattering matrix
(Phenomenological model)
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PCT via Quantum Chemistry Based Greens Function
f(E) Fermi function
W(E,m) f(E) - f(Em)

• Key theoretical quantity Teff(E)
• (Electron Transmission Function)
• Quan. Chem. study of LR-CT in DNA

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Transmission Function

• Effective DBA Hamiltonian (to be elaborated more)

reservoirs
self-energy -Im Sj ? Dj

• Greens function

• Local transmission function via Geff(E)

• Reflection function Rj ? 1 S Tjk ? Tjj

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Formulating the Total Teff(E)
l      Total transmission coefficient Teff
aA2/aD2 ? JA/JD l Current counting l
Boundary condition Jj (in) Jj (out)
Zhang et al. JCP [phone]
DAmato/Pastawski, PRB (90) 417411
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Total Transmission Function

• Total LR-ET transmission coefficient, via simple
  current counting with the boundary condition of
  Jj (in) Jj (out) , where j ? D or A, is

coherent
incoherent
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Quantum Chemistry Determination
keff
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Coupling Between Base Pairs
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Evaluation of Self-Energy
spectral density
Self-energy in semi-infinite chain
A semiempirical approach to Ss(E) for DNA in H2O
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Semiempirical Approach to Base-Water Couplings
Dj(E) same FWHM and area of those in semi-rigid
chain model
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Transmission Function
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About the Time Scale of 5 ps
The calculated transfer rate for the 5-GTGGG-3
DNA duplex in water is found to be
keff0.2ps-1 coincides w/ Barton and Zewail and
co-workers PNAS 96 (1999) 6014
JCP 117 (02) 4578 JTCC 1 (02) 225
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Hopping over G-bases
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PCT Through AT-bases
Coherent (AT)n-tunneling is valid only for n 1
and 2
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Summary

• Systematically established theories/models of
  long-range electron transfer/transport (LR-ET)
• -- ET rate ? electric conduction
• -- PCT via scattering matrix
• -- PCT via Greens function
• Small fraction of incoherence can dramatically
  alter/enhance LR-ET behaviors
• Quantum chemistry determination of mechanism
• for LR-ET in DNA in H2O

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Thanks !
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PCT Through AT-bases
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Electric Conductivity Theory vs. Experiment on
Single DNA Molecule
Li Yan, APL [phone]
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Participation of Interstrand Transfer Pathways