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Electronic Transport in DNA – the disorder perspective. Quantum physics on biological nanostructures – a first attempt. Rudolf A Roemer Daphne Klotsa , Matthew Turner Department of Physics and Centre for Scientific Computing. Why nanostructures?. - PowerPoint PPT Presentation
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Electronic Transport in DNA – the disorder perspective
Rudolf A Roemer
Daphne Klotsa, Matthew Turner
Department of Physics and Centre for Scientific Computing
Quantum physics on biological nanostructures – a first attempt
04/21/23Electronic Transport in Disordered Systems and DNA
Why nanostructures?
• New nanotechnologies will fabricate structures substantially smaller, better, and cheaper than current technology permits.
• Innovative nanoscale electronic, optoelectronic, and magnetic devices by combining cutting-edge nanotechnology with frontier knowledge from different disciplines.
[NanoStructures Laboratory, Princeton University]
04/21/23Electronic Transport in Disordered Systems and DNA
Semiconductor nanostructures:Q-dots, -well, SET’s
04/21/23Electronic Transport in Disordered Systems and DNA
“DNA is a wonderful material with which to build. It can act as …”
• Molecular glue• Fuel for molecular engines• Parallel computer• Self-assembled nanostructures
[E. Winfree , Nature 394, 539-544, Aug. 6, 1998]
• scaffold in protein-crystallography• Rigid tiles or girders [J.H. Reif et al., (2003)]
Why DNA? A. Turberfield, PhysicsWorld 16, March 2003, 43-46
and many more …
04/21/23Electronic Transport in Disordered Systems and DNA
Why disorder?
• well-developed theory
• good computational algorithms
• DNA is in solution
there is “disorder”
of electron wave function in 1113 system
04/21/23Electronic Transport in Disordered Systems and DNA
Combining DNA & electronicsConductor:[Fink/Schoenenberger, Nature 398, 407 (1999)]
Semiconductor:
[Porath et al., Nature 403, 635 - 638 (10 Feb 2000)]
Insulator:[Priyadarshy et al., J. Phys. Chem., 100, 17678 (1996)]
5 : 5 : 7
04/21/23Electronic Transport in Disordered Systems and DNA
Do enzymes scan DNA using electric pulses?
"DNA-mediated charge transport for DNA repair" E.M. Boon, A.L. Livingston, N.H. Chmiel, S.S. David, and J.K. Barton, Proc. Nat. Acad. Sci. 100, 12543-12547 (2003).
MutY MutY
MutY MutY
Healthy DNA
Broken DNA
electron
04/21/23Electronic Transport in Disordered Systems and DNA
DNA (Deoxyribonucleicacid)
Linear bio-polymer, backbone of repeated sugar-phosphate units, attached with “bases”
•G uanine
•C ytosine
•A denine
•T hymine
double helix structure
AT, GC, not AC, AG, TC, TGcom
plementary
04/21/23Electronic Transport in Disordered Systems and DNA
• AT, GC pairs via attractive hybridization• diameter 2nm, pitch 3.4 nm, base-pair
separation 0.34 nm, 3bn base-pairs/sequence• 15 base-pairs stable at room T• 3 base-pairs form a codon, unit of information,
so 43=64 “words” for 20 aminoacids and additional operations (stop/start).
• Samples with, say, ‘AGCTAGTA’ code can be ordered with at least 1% accuracy
• Commercial suppliers ship within a few days
DNA basics:…ATCGATCGATGATGTCGA……TAGCTAGCTACTACAGCT…
04/21/23Electronic Transport in Disordered Systems and DNA
Huge amounts of genetic data:
• H. sapiens 30,000 genes 3 109 bp• C. elegans 10,000 genes 108 bp• E. coli 4,380 genes 4,639,221 bp• SARS virus14 genes 29,761 bp
Paradox : ~ 105 proteins in H. sapiens
▬►One gene codes for more than one protein
04/21/23Electronic Transport in Disordered Systems and DNA
Biological function of DNA• Replication:
• Template for RNA coding for proteins: polymerase of DNA RNA proteins (actin, cell rigidity)
• Self-assembly
AGCTGATCAGCTGATC
AG
TCGACTAG
TCGACTAGTCGAC
CTGATC
TAGAGCTGATC
04/21/23Electronic Transport in Disordered Systems and DNA
Is DNA a quantum wire?
• “Absence of dc-Conductivity in -DNA”
De Pablo et al, PRL 86, 4992 (2000):
– Poly-GC strands have one-band of overlapping -orbitals
-DNA overlap drops quickly
• 13 base-pairs, DFT calculation
LUMO/PolyGC
HOMO/PolyGC
LUMO/ -DNA
04/21/23Electronic Transport in Disordered Systems and DNA
The fishbone model Cuniberti et al., PRB 65, 24131(R) (2002)
•tight-binding model with a gap
•Poly-GC: GCGCGCGC…
•explains experiments in Poly-GC
Experiments vs. theory:
04/21/23Electronic Transport in Disordered Systems and DNA
The fishbone model
• Hopping amplitudes are 1 along chain and 2 onto backbone
• Onsite energies are zero, but could be used to model the ionization energies
1 1 ,
.1 .L L
i i qi i
qi
qit i i t iq ii iH h ciq i
04/21/23Electronic Transport in Disordered Systems and DNA
Semiconducting gap in Poly-GC
•Transfer-matrix method:
•Large DNA sequences possible
•Localization lengths give possible extend of electron transfer measurable via fluorescence experiments
111 )( nnnnnn tEt
Ene
rgy
band
Ene
rgy
band
04/21/23Electronic Transport in Disordered Systems and DNA
-DNA:LOCUS NC_001416 48502 bp DNA linear PHG 08-JUL-2002DEFINITION Bacteriophage lambda, complete genome.
•Small differences between -DNA and (R)-DNA
•Computation for complete DNA strand
gap fills
04/21/23Electronic Transport in Disordered Systems and DNA
Influence of backbone disorder
• Backbone (BB) disorder used to model environment/solution into which DNA is immersed
• BB disorder leads to a rescaling of the semi-conducting gap
• This might explain diversity of experimental observations
[Klotsa, RAR, Turner, submitted (2004)]
04/21/23Electronic Transport in Disordered Systems and DNA
Random adhesion of Na-Atoms at backbone
Na
Na Na
New states
DNA is in solution, so there is “disorder”
04/21/23Electronic Transport in Disordered Systems and DNA
The ladder model
• Q-chemical calculations do not find HOMO/LUMO on both bases of a base pair
• Hopping amplitudes between chains is 1/2
, 1,21 2
,1, ,
1 . .,1 ,2L
iii
iq
qi
qH t i i t i iq iq h ci ii q t ii
04/21/23Electronic Transport in Disordered Systems and DNA
Na: binary disorder at the BB
More disorder gives less localization!
Contradiction to folklore!
highly localized
less localized
0E
0E
04/21/23Electronic Transport in Disordered Systems and DNA
Telomeric DNA with Na-BB disorder
Differences in biologically different DNA sequences
highly localized
less localized
TTAGGGTTAGGGTTAGGG…DNA
0E
04/21/23Electronic Transport in Disordered Systems and DNA
The equivalent 1D chain• Exact equivalence to 1D chain with
modified onsite potential:
E
t
E
t
i
i
i
iii
22
~
• Physics of 1D localization is applicable[Klotsa, RAR, Turner, submitted to Proceedings of ICPS27, (2004)
04/21/23Electronic Transport in Disordered Systems and DNA
Centromeric DNA
• chromosome 2 of yeast
• meaningful DNA sequence
• highly repetitive according to biology
813138 base pairs
04/21/23Electronic Transport in Disordered Systems and DNA
Coding vs. non-coding regions
• Biologically there is a huge difference
• What about in transport?
3E
04/21/23Electronic Transport in Disordered Systems and DNA
Outlook:
• Can electronic transport measurement be used to access biological function?– Investigate sub-sequences of DNA with
well-known biological functions– Investigate “trigger” sequences. Is process
transport specific?– Relate to fluorescence experiments
Kelley et al., Science 283, 375 (1999):
“.. Paradigms must now be developed to describe these properties of the DNA p-stack, which can range from insulator- to “wire”-like.”
04/21/23Electronic Transport in Disordered Systems and DNA
Music from DNA
• Music from DNA
The Shamen, S2 Translation - An instrumental piece of music based on the DNA code for the S2
S2: receptor protein for 5-hydroxy tryptamine (Serotonin) and others. One of the most important molecules in the mediation of both ordinary and non-ordinary (or "Shamanic") states of consciousness, which is why the molecule was chosen for this piece.
Serotonin
04/21/23Electronic Transport in Disordered Systems and DNA
Conclusions:• The electronic properties of DNA are an
important challenge for both experiment and theory.
• Applications are manifold if linking of biological with electronic function can be made.
• Present research offers a route into DNA physics via the pathway of disordered systems.
04/21/23Electronic Transport in Disordered Systems and DNA
Disordered Quantum Systems
• DNA: D. Klotsa, M. Turner• Localization: M. Ndawana, J. Stephany, A. Croy, H.
Schulz-Baldes (Berlin)
• Nano-rings: J. He, M. Raikh (Utah)
• Quantum Hall: C. Sohrmann, B. Muzykantskii, P. Cain (Chemnitz)
• Bio-diffusion: D. Skirvin (HRI Warwick)
• Numerical methods: C. Sohrmann, O. Schenk (Basel)
• Funding: EPSRC, Warwick, DFG
04/21/23Electronic Transport in Disordered Systems and DNA
A MIT due to disorder-induced quantum interference:
• Adding disorder to a quantum model of non-interacting electrons gives a transition:
metal insulator
multifractal
disorder
04/21/23Electronic Transport in Disordered Systems and DNA
Challenges at the MIT:
• Is there universality?[Ndawana, RAR, Schreiber, EPJB 27, 399-407 (2002)]
• What about correlations in the disorder? [Ndawana, RAR, Schreiber, accepted in EPL (2004)]
• What about many-body interactions? [Schuster, RAR, Schreiber, Phys. Rev. B 65, 115114-7 (2002)]
• What about other transport quantities such as thermoelectric power?
[RAR, MacKinnon, Villagonzalo, J. Phys. Soc. Jpn. 72 Suppl. A, 167-168 (2003)]
04/21/23Electronic Transport in Disordered Systems and DNA
The Anderson model as a challenge to modern eigenvalue methods:
• Indefinite matrix problematic for iterative solvers, convergence accelerators, preconditioners
• Improving: Colloboration with numerical mathematicians (Basel): PARDISO is faster for large matrices
04/21/23Electronic Transport in Disordered Systems and DNA
The excitonic AB effect for nano-rings
Nano-sized
rings with
radius of
30-50nm exist:
[R. A. Römer and M. E. Raikh, Phys. Rev. B 62, 7045-7049 (2000)]
A. Lorke et al., Microelectronic Engineering 47, 95 (1999).
Excitons are being generated via photoluminescence. What about Aharonov-Bohm effect for this nano-geometry and neutral (quasi-)particle?
04/21/23Electronic Transport in Disordered Systems and DNA
Challenges:
• Trions and other charged excitons[R. A. Römer, M. E. Raikh, phys. stat. sol. (b) 227, 381-385 (2001)]
• Experimental verification:thus far only for trions[Bayer, et al., Phys. Rev. Lett. 90, 186801 (2003)]
• AB effect in an electric field[a current project]
x
V
04/21/23Electronic Transport in Disordered Systems and DNA
(R)-DNA:•Hopping strengths according to DNA content:
•AT-AT 1t
•GC-GC 1t
•DNA-BB 2t
•AT-GC ½ t
•Physics of a random hopping chain
LOCALIZATION!
[10000 base-pairs, random ATCG-DNA sequence]
gap fills
04/21/23Electronic Transport in Disordered Systems and DNA
(R)-DNA: [10000 base-pairs, random ATCG-DNA sequence]
•Hopping strengths according to DNA content:
•AT-AT 1t
•GC-GC 1t
•DNA-BB 2t
•AT-GC 1/10 t
04/21/23Electronic Transport in Disordered Systems and DNA
“DNA is a wonderful material with which to build. It can act as …”
• Molecular glue• Fuel for molecular engines• Parallel computer• Self-assembled nanostructures
[E. Winfree , Nature 394, 539-544, Aug. 6, 1998]
• scaffold in protein-crystallography• Rigid tiles or girders [J.H. Reif et al., (2003)]
Why DNA? A. Turberfield, PhysicsWorld 16, March 2003, 43-46
and many more …
04/21/23Electronic Transport in Disordered Systems and DNA
Telomeric DNA with 6000 base pairs
Buffer sequences at beginning or end of meaningful DNA gene sequences
TTAGGGTTAGGGTTAGGG…DNA
04/21/23Electronic Transport in Disordered Systems and DNA
Telomeric DNA with BB disorder
Large localization lengths even in presence of disorder
04/21/23Electronic Transport in Disordered Systems and DNA
Outlook 2:• What about a two-rung model?
• Results qualitatively similar, but
2rung 1rung
(Quantum chemistry calculations)
2 4 6 8 10BBSiteDis
5
10
15
20
25
30
1gamma 00006000. raw
04/21/23Electronic Transport in Disordered Systems and DNA
Transport in and Physics with DNA
• Molecular glue
• Fuel for molecular engines
• Parallel computer
• Self-assembled nanostructures [E. Winfree , Nature 394, 539-544, Aug. 6, 1998]
• scaffold in protein-crystallography• Rigid tiles or girders [J.H. Reif et al., (2003)]
A. Turberfield, PhysicsWorld 16, March 2003, 43-46
04/21/23Electronic Transport in Disordered Systems and DNA
Energy-Dependence for ladder model