partially coherent charge transport in dna
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
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Partially Coherent Charge Transport in DNA
YiJing YanHong Kong University of Science and Technology
ADMOL, 23 – 27 Feb. 2004, Dresden, Germany
Collaborators:
Prof. XinQi LI (Inst. Semiconductor, BeiJing) Dr. Houyu ZHANG (INFM Center S3, Italy) Mr. Ping HAN
Acknowledgment: RGC-HK, NNSF-China
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General IntroductionMotivation: bio-function & molecular device
Characteristics of nano-size: Partially coherent tunneling - Failure of (incoherence) Ohm’s law - Failure of (coherent) superexchange tunneling
0 2 4 6 8 10 12 14 160.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
our theoretical results
Giese et al, Nature (2001) 412:318experimental results
GTT...TGGGCAA...ACCC
log
(rel
ativ
e ra
te)
Numumber of AT-base pairs-4 -2 0 2 4
-1.5
-1.0
-0.5
0.0
0.5
1.0
1.5
Porath et al, Nature (2000) 403:635
theoretical
(GC)30
DNA duplex single molecule
experimental
curr
ent
(nA
)Voltage (V)
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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) DA 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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(J.K.Barton; B.Giese; G.B.Schuster; P.F.Babara)
G•+ATCTTGAGTGGGC TAGAACTCACCC
donoracceptor
Hole chargetrapper
Experimental Observations
Side reactions: deprotonation of G+
w/ surrounding H2O
G G… G Acceptor1 2 n
knk1 kn-1
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G Acceptorkn kjkj-1k1
1 j-
1
j n
IjIj-1 InI1I0
J1 Jj-1 Jj Jn
G G… G Acceptor1 2 n
knk1 kn-1
The Ohm’s Law: Exact ResultsYan/Li/Zhang, JCP (01) 114:8248
ET rate constant Electric conductance
Chemical yield Electric current
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Effect of Finite Incoherence:Partially Coherent Tunneling
via Büttiker’s scattering matrix (Phenomenological model)
T eff(
)/T ef
f(0)
Degree of incoherence
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Key theoretical quantity: Teff(E) (Electron Transmission Function)
Quan. Chem. study of LR-CT in DNA
PCT via Quantum Chemistry Based Green’s Function
DAineffeff ; 2
EEWEdEk T
f(E): Fermi functionW(E,) = f(E) f(E+)
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Transmission Function
Effective DBA Hamiltonian (to be elaborated more)
kjEEEGT kjjkjk for );()(|)(| eff 2
||)()(eff jjEHEH j
N
j
1
0
)()(
eff
eff
EHEEG
1Green’s function:
Local transmission function via Geff(E)
self-energy:-Im j j
D BBNA
reservoirs
Reflection function: Rj 1 – ’ Tjk Tjj
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Formulating the Total Teff(E)
Total transmission coefficient: Teff = |a´A|2/|aD|2 J´A/JD
Current counting
Boundary condition: Jj (in) = Jj (out)
kk JTJTJN
k
1
A,DAD'A kjkjj JTJTJ
N
k
1
DD,'
'JJ
b1 b´1
aD a´A
Zhang et al. JCP (02) 117:4578; D’Amato/Pastawski, PRB (90) 41:7411
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D1
AADeff )1()( KTKTE T
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
},,1 );({ D,D NkETK k },,1 );({ A,A NjETK j
},,1, );({ NkjETT jk
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Quantum Chemistry Determination
G
T
G+
C
A
C
5´ 3´
3´ 5´ HF/6-31G* level
• Individual base energies
• Coupling between different bases in DNA
A semiempirical level
• Base-H2O coupling for complex self-energy S(E)
||)()(eff jjEHEH j
N
j
1
0
D1
AADeff )1()( KKE TTTkeff
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Coupling Between Base Pairs
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Evaluation of Self-Energy
''
')( Re
)(Im
EEE
dEE
VE
EEVE
s
j j
js
sj
jjs
12
2
P
Self-energyin semi-infinite chain
s V
else ; 0
2 ; 42
222
2
EE
VE
s
s
A semiempirical approach to s
(E) for DNA in H2O
spectral density
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Semiempirical Approach to Base-Water Couplings
j(E): same FWHM and area of those in semi-rigid chain model
H2O-H2O coupling eV
22
2
3
3
E
vE j
j unsoleff22
2
3)(
)(jj
jj E
E
EvE
2/1
aq
22aqunsolaq 3
j
jjjjvH2O’s IP
eV
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Transmission Function
D1
AADeff )1()( KKE TTT keffHeff(E)
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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 keff=0.2ps-1
[coincides w/ Barton and Zewail and co-workersPNAS 96 (1999) 6014]
JCP 117 (02) 4578; JTCC 1 (02) 225
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Hopping over G-bases
1eff
nY
1 ; eff nk
effreleff kk / 0.2ps -1
Chemical Yield
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PCT Through AT-bases
Coherent (AT)n-tunneling is valid only for n =1 and 2
0 2 4 6 8 10 12 14 160.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
our theoretical results
Giese et al, Nature (2001) 412:318experimental results
GTT...TGGGCAA...ACCC
log
(rel
ativ
e ra
te)
Numumber of AT-base pairs
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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 Green’s 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
-4 -2 0 2 4
-1.5
-1.0
-0.5
0.0
0.5
1.0
1.5
Porath et al, Nature (2000) 403:635
theoretical
(GC)30
DNA duplex single molecule
experimental
curr
ent
(nA
)
Voltage (V)
Li & Yan, APL (01) 79:2190
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Participation of Interstrand Transfer Pathways