1. 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

2. 25/08/2014Electronic 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]

3. 25/08/2014Electronic Transport in Disordered Systems and DNA Semiconductor nanostructures: Q-dots, -well, SET’s

4. 25/08/2014Electronic 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 …

5. 25/08/2014Electronic 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 111 3 system

6. 25/08/2014Electronic Transport in Disordered Systems and DNA Combining DNA & electronics Conductor: [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

7. 25/08/2014Electronic 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 Healthy DNA Broken DNA electron

8. 25/08/2014Electronic 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, TG complementary

9. 25/08/2014Electronic 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 4 3 =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…

10. 25/08/2014Electronic Transport in Disordered Systems and DNA Huge amounts of genetic data: H. sapiens30,000 genes3  10 9 bp C. elegans10,000 genes10 8 bp E. coli4,380 genes4,639,221 bp SARS virus14 genes29,761 bp Paradox : ~ 10 5 proteins in H. sapiens ▬►One gene codes for more than one protein

11. 25/08/2014Electronic 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

12. 25/08/2014Electronic 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

13. 25/08/2014Electronic 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:

14. 25/08/2014Electronic 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

15. 25/08/2014Electronic 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 Energy band

16. 25/08/2014Electronic Transport in Disordered Systems and DNA -DNA: LOCUS NC_001416 48502 bp DNA linear PHG 08-JUL-2002 DEFINITION Bacteriophage lambda, complete genome. Small differences between -DNA and (R)-DNA Computation for complete DNA strand gap fills

17. 25/08/2014Electronic 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)]

18. 25/08/2014Electronic Transport in Disordered Systems and DNA Random adhesion of Na-Atoms at backbone Na New states DNA is in solution, so there is “disorder”

19. 25/08/2014Electronic 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

20. 25/08/2014Electronic Transport in Disordered Systems and DNA Na: binary disorder at the BB More disorder gives less localization! Contradiction to folklore! highly localized less localized

21. 25/08/2014Electronic Transport in Disordered Systems and DNA Telomeric DNA with Na-BB disorder Differences in biologically different DNA sequences highly localized less localized TTAGGGTTAGGGTTAGGG…DNA

22. 25/08/2014Electronic Transport in Disordered Systems and DNA 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)

23. 25/08/2014Electronic Transport in Disordered Systems and DNA Centromeric DNA chromosome 2 of yeast meaningful DNA sequence highly repetitive according to biology 813138 base pairs

24. 25/08/2014Electronic Transport in Disordered Systems and DNA Coding vs. non-coding regions Biologically there is a huge difference What about in transport?

25. 25/08/2014Electronic 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.”

26. 25/08/2014Electronic 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

27. 25/08/2014Electronic 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.

28. 25/08/2014Electronic 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

29. 25/08/2014Electronic 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: metalinsulator multifractal disorder

30. 25/08/2014Electronic 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)]

31. 25/08/2014Electronic 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

32. 25/08/2014Electronic 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?

33. 25/08/2014Electronic 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

34. 25/08/2014Electronic 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

35. 25/08/2014Electronic 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

36. 25/08/2014Electronic 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 …

37. 25/08/2014Electronic 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

38. 25/08/2014Electronic Transport in Disordered Systems and DNA Telomeric DNA with BB disorder Large localization lengths even in presence of disorder

39. 25/08/2014Electronic Transport in Disordered Systems and DNA Outlook 2: What about a two-rung model? Results qualitatively similar, but (Quantum chemistry calculations)

40. 25/08/2014Electronic 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

41. 25/08/2014Electronic Transport in Disordered Systems and DNA Energy-Dependence for ladder model