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Electronic Transport in DNA – the disorder perspective

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?.

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Electronic Transport in DNA – the disorder perspective

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  1. 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

  2. Why nanostructures? [NanoStructures Laboratory, Princeton University] • 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. Electronic Transport in Disordered Systems and DNA

  3. Semiconductor nanostructures:Q-dots, -well, SET’s Electronic Transport in Disordered Systems and DNA

  4. Why DNA? A. Turberfield, PhysicsWorld 16, March 2003, 43-46 “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)] and many more … Electronic Transport in Disordered Systems and DNA

  5. Why disorder? • well-developed theory • good computational algorithms • DNA is in solution -> there is “disorder” |Y|2 of electron wave function in 1113 system Electronic Transport in Disordered Systems and DNA

  6. Combining DNA & electronics Semiconductor: [Porath et al., Nature403, 635 - 638 (10 Feb 2000)] Insulator: [Priyadarshy et al., J. Phys. Chem., 100, 17678 (1996)] Conductor: [Fink/Schoenenberger, Nature398, 407 (1999)] 5 : 5 : 7 Electronic Transport in Disordered Systems and DNA

  7. 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). Healthy DNA electron MutY MutY Broken DNA MutY MutY Electronic Transport in Disordered Systems and DNA

  8. 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, TG complementary Electronic Transport in Disordered Systems and DNA

  9. DNA basics: …ATCGATCGATGATGTCGA… …TAGCTAGCTACTACAGCT… • AT, GC pairs via attractive hybridization • diameter 2nm, pitch 3.4 nm, base-pair separation 0.34 nm, 3bnbase-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 Electronic Transport in Disordered Systems and DNA

  10. 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 virus 14 genes 29,761 bp Paradox : ~ 105 proteins in H. sapiens ▬►One gene codes for more than one protein Electronic Transport in Disordered Systems and DNA

  11. Biological function of DNA • Replication: • Template for RNA coding for proteins: polymerase of DNA -> RNA -> proteins (actin, cell rigidity) • Self-assembly Electronic Transport in Disordered Systems and DNA

  12. Is DNA a quantum wire? • “Absence of dc-Conductivity in l-DNA” De Pablo et al, PRL 86, 4992 (2000): • Poly-GC strands have one-band of overlapping p-orbitals • l-DNA overlap drops quickly • 13 base-pairs, DFT calculation LUMO/PolyGC HOMO/PolyGC LUMO/ l-DNA Electronic Transport in Disordered Systems and DNA

  13. 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: Electronic Transport in Disordered Systems and DNA

  14. 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 Electronic Transport in Disordered Systems and DNA

  15. Semiconducting gap in Poly-GC • Transfer-matrix method: • Large DNA sequences possible • Localization lengths l give possible extend of electron transfer -> measurable via fluorescence experiments Energy band Energy band Electronic Transport in Disordered Systems and DNA

  16. gap fills l-DNA: LOCUS NC_001416 48502 bp DNA linear PHG 08-JUL-2002 DEFINITION Bacteriophage lambda, complete genome. • Small differences betweenl-DNA and l(R)-DNA • Computation for complete DNA strand Electronic Transport in Disordered Systems and DNA

  17. Influence of backbone disorder [Klotsa, RAR, Turner, submitted (2004)] • 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 Electronic Transport in Disordered Systems and DNA

  18. Random adhesion of Na-Atoms at backbone DNA is in solution, so there is “disorder” Na New states Na Na Electronic Transport in Disordered Systems and DNA

  19. 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 Electronic Transport in Disordered Systems and DNA

  20. Na: binary disorder at the BB More disorder gives less localization! Contradiction to folklore! less localized highly localized Electronic Transport in Disordered Systems and DNA

  21. Telomeric DNA with Na-BB disorder TTAGGGTTAGGGTTAGGG…DNA Differences in biologically different DNA sequences less localized highly localized Electronic Transport in Disordered Systems and DNA

  22. The equivalent 1D chain • Exact equivalence to 1D chain with modified onsite potential: • Physics of 1D localization is applicable [Klotsa, RAR, Turner, submitted to Proceedings of ICPS27, (2004) Electronic Transport in Disordered Systems and DNA

  23. Centromeric DNA 813138 base pairs • chromosome 2 of yeast • meaningful DNA sequence • highly repetitive according to biology Electronic Transport in Disordered Systems and DNA

  24. Coding vs. non-coding regions • Biologically there is a huge difference • What about in transport? Electronic Transport in Disordered Systems and DNA

  25. Outlook: 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.” • 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 Electronic Transport in Disordered Systems and DNA

  26. Music from l-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 Electronic Transport in Disordered Systems and DNA

  27. 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. Electronic Transport in Disordered Systems and DNA

  28. 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 Electronic Transport in Disordered Systems and DNA

  29. A MIT due to disorder-induced quantum interference: • Adding disorder to a quantum model of non-interacting electrons gives a transition: disorder metal insulator multifractal Electronic Transport in Disordered Systems and DNA

  30. 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)] Electronic Transport in Disordered Systems and DNA

  31. 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 Electronic Transport in Disordered Systems and DNA

  32. The excitonic AB effect for nano-rings [R. A. Römer and M. E. Raikh, Phys. Rev. B 62, 7045-7049 (2000)] Nano-sized rings with radius of 30-50nm exist: 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? Electronic Transport in Disordered Systems and DNA

  33. 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] V x Electronic Transport in Disordered Systems and DNA

  34. gap fills [10000 base-pairs, random ATCG-DNA sequence] l(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! Electronic Transport in Disordered Systems and DNA

  35. [10000 base-pairs, random ATCG-DNA sequence] l(R)-DNA: • Hopping strengths according to DNA content: • AT-AT -> 1t • GC-GC -> 1t • DNA-BB -> 2t • AT-GC -> 1/10 t Electronic Transport in Disordered Systems and DNA

  36. Why DNA? A. Turberfield, PhysicsWorld 16, March 2003, 43-46 “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)] and many more … Electronic Transport in Disordered Systems and DNA

  37. Telomeric DNA with 6000 base pairs TTAGGGTTAGGGTTAGGG…DNA Buffer sequences at beginning or end of meaningful DNA gene sequences Electronic Transport in Disordered Systems and DNA

  38. Telomeric DNA with BB disorder Large localization lengths even in presence of disorder Electronic Transport in Disordered Systems and DNA

  39. Outlook 2: • What about a two-rung model? (Quantum chemistry calculations) • Results qualitatively similar, but Electronic Transport in Disordered Systems and DNA

  40. Transport in and Physics with DNA A. Turberfield, PhysicsWorld 16, March 2003, 43-46 • 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)] Electronic Transport in Disordered Systems and DNA

  41. Energy-Dependence for ladder model Electronic Transport in Disordered Systems and DNA

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