1 / 58

DNA Based Self-Assembly and Nano-Device: Theory and Practice Peng Yin Committee

1. DNA Based Self-Assembly and Nano-Device: Theory and Practice Peng Yin Committee Prof. Reif (Advisor), Prof. Agarwal, Prof. Hartemink Prof. LaBean, Prof. Turberfield, Prof. Yan. Nanofabrication. Nanoelectronics. Nanorobotics. Nanodiagnostics/ therapeutics. Nanocomputation. 2.

kakins
Download Presentation

DNA Based Self-Assembly and Nano-Device: Theory and Practice Peng Yin Committee

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. 1 DNA Based Self-Assembly and Nano-Device: Theory and Practice Peng Yin Committee Prof. Reif (Advisor), Prof. Agarwal, Prof. Hartemink Prof. LaBean, Prof. Turberfield, Prof. Yan

  2. Nanofabrication Nanoelectronics Nanorobotics Nanodiagnostics/ therapeutics Nanocomputation 2 There's Plenty of Room at the Bottom Richard P. Feynman, 1959 • “…a field, in which little has been done, but in which an enormous amount can be done in principle” Nanoworld (1 m = 109nm)

  3. 3 There's Plenty of Room at the Bottom Nanoworld (1 m = 109nm) ?

  4. 4 There's Plenty of Room at the Bottom Nanoworld (1 m = 109nm) How to build things? How to make things move (and do work)? How to compute?

  5. Complementary single strands 3.4 nm Duplex 2 nm 5 DNA 101: DNA – Not merely secret to life • Information encoding: bases: A, T, C, G • Complementarity of bases:A – T; C – G Self-Assembly !

  6. 6 DNA 101: Self-assembly Single strand DNA as Smart glues (Excerpted from Seeman 03)

  7. How to build? How to compute? How to move? DNA Based Self-Assembly Nano-Device Biochem. Lab Fabrication Theoretical Design Mathematical Analysis Computer Modeling 7 DNA Based Self-Assembly & Nano-Device: Theory & Practice Theory & Practice

  8. Complexity - Error Correction – Nanorobotics - Nanocomputing • Complexity of • Self-Assembly • Error Resilient • Self-Assembly • Nanorobotics • Device • Nanocomputing • Device 8 Roadmap: DNA Based Self-Assembly & Nano-Device

  9. Complexity - Error Correction – Nanorobotics - Nanocomputing 9 Roadmap: DNA Based Self-Assembly & Nano-Device • Complexity of • Self-Assembly • Error Resilient • Self-Assembly • Nanorobotics • Device • Nanocomputing • Device

  10. Complexity - Error Correction – Nanorobotics - Nanocomputing 10 Self-Assembly Complexity of Graph Self-Assembly in Accretive Systems and Self-Destructible Systems Joint with Reif, Sahu Reif, Sahu, & Yin (2005) Submitted to FNANO 2005

  11. Seed vertex Temperature Graph Weight function Temperature: τ = 2 Seed vertex Complexity - Error Correction – Nanorobotics - Nanocomputing 11 Accretive Graph Assembly System Sequentially constructible?

  12. Complexity - Error Correction – Nanorobotics - Nanocomputing 12 Problems, Results, & Contributions • Problems • Accretive Graph Assembly Problem • Self-Destructible Graph Assembly Prob. • Results • AGAP is NP-complete • Planar AGAP is NP-complete • #AGAP/Stochastic AGAP is #P-complete • DGAP is PSPACE-complete • Contributions • Cooperative effects of attraction and repulsion • General setting of graphs • Dynamic self-destructible behavior in DGAP model

  13. Complexity - Error Correction – Nanorobotics – Nanocomputing 13 Roadmap: DNA Based Self-Assembly & Nano-Device • Complexity of • Self-Assembly • Error Resilient • Self-Assembly • Nanorobotics • Device • Nanocomputing • Device

  14. Complexity - Error Correction – Nanorobotics – Nanocomputing 14 Self-Assembly Compact Error Resilient Computational DNA Tilings Joint with Reif, Sahu Reif, Sahu, & Yin (2004) DNA 10

  15. Complexity - Error Correction – Nanorobotics – Nanocomputing Tile (Excerpted from Yan et al 03) Computational tiles (Winfree) Pad Output 2 Output 1 Input 2 Input 1 15 Computational Tilings Output 1 = Input 1 XOR Input 2 Output 2 = Input 1 AND Input 2

  16. Complexity - Error Correction – Nanorobotics – Nanocomputing 16 Binary counter Binary counter Computational tiles Seed tile Frame tiles

  17. Complexity - Error Correction – Nanorobotics – Nanocomputing Error! 17 Error in Assembly Binary counter Computational tiles Seed tile Frame tiles

  18. Complexity - Error Correction – Nanorobotics – Nanocomputing 18 Error Resilient Tilings by Winfree Original tiles: Error resilient tiles: (Excerpted from Winfree 03) • Error rate   2 • Assembly size increased by 4

  19. Complexity - Error Correction – Nanorobotics – Nanocomputing 19 Compact Error Resilient Computational Tiles Original tiles: X Y Z XY YZ Error resilient tiles:

  20. Complexity - Error Correction – Nanorobotics – Nanocomputing 20 Compact Error Resilient Computational Tiles Original tiles: X Y Z XY YZ Error resilient tiles:

  21. Complexity - Error Correction – Nanorobotics – Nanocomputing 21 Compact Error Resilient Computational Tiles Original tiles: X Y Z XY YZ Error resilient tiles: Error checking pads • Assembly size not increased • Two way overlay: error rate (5%)  2 (0.25%) • Three way overlay: error rate  (5%)  3 (0.0125%)

  22. Complexity - Error Correction – Nanorobotics – Nanocomputing 22 Computer Simulation (Xgrow, Winfree) Three way overlay Winfree 3x3 construction Winfree 2x2 construction Two way overlay No error correction

  23. Complexity - Error Correction – Nanorobotics - Nanocomputing 23 Roadmap: DNA Based Self-Assembly & Nano-Device • Complexity of • Self-Assembly • Error Resilient • Self-Assembly • Nanorobotics • Device • Nanocomputing • Device

  24. Complexity - Error Correction – Nanorobotics - Nanocomputing (R. Cross Lab) 24 Nano-Device An Autonomous Unidirectional DNA Walker Joint with Yan, Daniell, Turberfield, Reif Yin, Yan, Daniell, Turberfield, & Reif (2004) Angew. Chem. Intl. Ed. Yin, Turberfield, & Reif (2004) DNA 10

  25. Complexity - Error Correction – Nanorobotics - Nanocomputing Restriction enzymes PflM I BstAP I Walker * Ligase 25 Autonomous Unidirectional DNA Walker: Design Anchorage A A B D C Track

  26. Complexity - Error Correction – Nanorobotics - Nanocomputing Sticky ends DNA ligase DNA restriction enzyme 26 DNA 101: Enzyme Ligation, Restriction

  27. Complexity - Error Correction – Nanorobotics - Nanocomputing 27 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* Walker Anchorage * A A B D C Track

  28. Complexity - Error Correction – Nanorobotics - Nanocomputing Ligase 28 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* C D A A*B

  29. Complexity - Error Correction – Nanorobotics - Nanocomputing Ligase 29 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* C D A A*B

  30. Complexity - Error Correction – Nanorobotics - Nanocomputing 30 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*BB* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* PflM I C D A A*B

  31. Complexity - Error Correction – Nanorobotics - Nanocomputing 31 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* B* A D C A

  32. Complexity - Error Correction – Nanorobotics - Nanocomputing Ligase 32 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*BB* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* D A A B*C

  33. Complexity - Error Correction – Nanorobotics - Nanocomputing Ligase 33 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*BB* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* D A A B*C

  34. Complexity - Error Correction – Nanorobotics - Nanocomputing 34 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*BB* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* BstAP I D A A B*C

  35. Complexity - Error Correction – Nanorobotics - Nanocomputing 35 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* C* A D B A

  36. Complexity - Error Correction – Nanorobotics - Nanocomputing 36 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*BB* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* A C*D B A

  37. Complexity - Error Correction – Nanorobotics - Nanocomputing 37 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* D* A C B A

  38. Complexity - Error Correction – Nanorobotics - Nanocomputing 38 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* D*A B C A

  39. Complexity - Error Correction – Nanorobotics - Nanocomputing 39 DNA Walker: Operation • Valid hybridization: • A* + B = A + B* A*B B* + C = B + C* B*C • C* + D = C + D* C*D D* + A = D + A* D*A • Valid cut: • A*B  A + B* B*CB + C* • C*D  C + D* D*AD + A* A* D C B A

  40. Complexity - Error Correction – Nanorobotics - Nanocomputing 40 DNA Walker: Experimental Design

  41. Complexity - Error Correction – Nanorobotics - Nanocomputing 41 Autonomous Motion of the Walker

  42. Complexity - Error Correction – Nanorobotics - Nanocomputing 42 Roadmap: DNA Based Self-Assembly & Nano-Device • Complexity of • Self-Assembly • Error Resilient • Self-Assembly • Nanorobotics • Device • Nanocomputing • Device

  43. Complexity - Error Correction – Nanorobotics - Nanocomputing 43 Nano-Device Designs of DNA Cellular Computing Devices Joint with Sahu, Turberfield, Reif Yin, Turberfield, Sahu, & Reif (2004) DNA 10 Yin, Sahu,Turberfield, & Reif (2005) Submitted to DNA 11

  44. Complexity - Error Correction – Nanorobotics - Nanocomputing 44 DNA Cellular Computing Devices Self-assembly Nanorobotics Nanocomputation (Benenson et al 03) (Yan et al 03) Complex motion Intelligent robotics devices Reusable DNA computers

  45. Complexity - Error Correction – Nanorobotics - Nanocomputing 45 DNA Cellular Computing Devices Finite state automata Turing machine Cellular automata

  46. Complexity - Error Correction – Nanorobotics - Nanocomputing 46 Comp 101: Turing Machine Read/write head Tape Transition rule

  47. Complexity - Error Correction – Nanorobotics - Nanocomputing 47 DNA Turing Machine: Structure Turing machine Transition table: Rule molecules Turing head: Head molecules Data tape: Symbol molecules Autonomous universal DNA Turing machine: 2 states, 5 colors

  48. Complexity - Error Correction – Nanorobotics - Nanocomputing 48 Turing Machine: Operation Turing machine

  49. Complexity - Error Correction – Nanorobotics - Nanocomputing 49 Turing Machine: Operation

  50. Complexity - Error Correction – Nanorobotics - Nanocomputing 50 Turing Machine: Operation

More Related