Scribd Logo
Upload

Welcome to Scribd!

  • 13 views

    Compact Error Resilient Computational DNA Tiling Assemblies: John Reif, Sudheer Sahu, Peng Yin

    Uploaded by

    shoshank655
    This document discusses techniques for making DNA tile self-assembly more error resilient by modifying the tile design. It presents the original approach of using error checking pads on the tiles, which reduces the error rate from ε to ε^2. A new compact approach is introduced using a "two-way overlay" scheme where one mismatch causes at least one more mismatch, again reducing the error rate from ε to ε^2 without increasing the assembly size. A "three-way overlay" scheme is proposed to reduce the error rate further from ε to ε^3 by ensuring one mismatch causes at least two more mismatches. Simulation results validate the approaches.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPT, PDF, TXT or read online from Scribd
    Flag for inappropriate content

    You might also like

    Compact Error Resilient Computational DNA Tiling Assemblies: John Reif, Sudheer Sahu, Peng Yin

    Uploaded by

    shoshank655
    13 views22 pages
    This document discusses techniques for making DNA tile self-assembly more error resilient by modifying the tile design. It presents the original approach of using error checking pads on the tiles, which reduces the error rate from ε to ε^2. A new compact approach is introduced using a "two-way overlay" scheme where one mismatch causes at least one more mismatch, again reducing the error rate from ε to ε^2 without increasing the assembly size. A "three-way overlay" scheme is proposed to reduce the error rate further from ε to ε^3 by ensuring one mismatch causes at least two more mismatches. Simulation results validate the approaches.

    Original Description:

    Original Title

    Talk

    Copyright

    © Attribution Non-Commercial (BY-NC)

    Available Formats

    PPT, PDF, TXT or read online from Scribd

    Did you find this document useful?

    Is this content inappropriate?

    Report this Document
    This document discusses techniques for making DNA tile self-assembly more error resilient by modifying the tile design. It presents the original approach of using error checking pads on the tiles, which reduces the error rate from ε to ε^2. A new compact approach is introduced using a "two-way overlay" scheme where one mismatch causes at least one more mismatch, again reducing the error rate from ε to ε^2 without increasing the assembly size. A "three-way overlay" scheme is proposed to reduce the error rate further from ε to ε^3 by ensuring one mismatch causes at least two more mismatches. Simulation results validate the approaches.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPT, PDF, TXT or read online from Scribd
    Flag for inappropriate content
    Download as ppt, pdf, or txt
    13 views22 pages

    Compact Error Resilient Computational DNA Tiling Assemblies: John Reif, Sudheer Sahu, Peng Yin

    Uploaded by

    shoshank655
    This document discusses techniques for making DNA tile self-assembly more error resilient by modifying the tile design. It presents the original approach of using error checking pads on the tiles, which reduces the error rate from ε to ε^2. A new compact approach is introduced using a "two-way overlay" scheme where one mismatch causes at least one more mismatch, again reducing the error rate from ε to ε^2 without increasing the assembly size. A "three-way overlay" scheme is proposed to reduce the error rate further from ε to ε^3 by ensuring one mismatch causes at least two more mismatches. Simulation results validate the approaches.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPT, PDF, TXT or read online from Scribd
    Flag for inappropriate content
    Download as ppt, pdf, or txt
    of 22

    Compact Error Resilient Computational DNA Tiling Assemblies

    John Reif, Sudheer Sahu, Peng Yin


    Department of Computer Science, Duke University
    2

    Self-Assembly of DNA Tiles

    • Perform universal computation.

    • Manufacture patterned nanostructures from smaller unit


    nanostructures.
    Assembly of Binary Counter (Winfree)

    Computational tiles

    Seed tile

    Frame tiles

    Binary counter
    Errors in Self-Assembly of DNA Tiles

    • Binding rules are not strict.

    • A tile might get assembled to a binding site where it was


    not supposed to go.
    Example of a Computational Error

    Computational tiles

    Seed tile

    Error!

    Frame tiles
    How to Decrease Errors?

    • Errors can be arbitrarily decreased by


    – Decreasing concentration of tiles.
    – Increasing binding strengths.
    – Drawback : Reduce speed.

    • Another approach:
    – Change the logical design of the tiles.
    Error Resilient Tilings by Winfree

    Original tiles:

    Error resilient tiles:

    (Excerpted from Winfree 03)

    • Error rate  => 2


    • Assembly size increased by 4
    Original tiles: A B C

    Error resilient tiles: AB BC


    Original tiles: A B C

    Error resilient tiles: AB BC


    Original tiles: A B C

    Error resilient tiles: AB BC

    Error checking
    pads
    A Computational Tile
    Compact Error Resilient Construction

    • Wholeness of pad: Single pad per side.


    One Mismatch causes more Mismatch

    Case 1
    One Mismatch causes more Mismatch

    Case 2
    One Mismatch causes more Mismatch

    Case 3
    One Mismatch causes more Mismatch

    Case 4
    Result of Compact Error Resilient Scheme

    • We saw:
    – Two way overlay scheme.
    – One mismatch caused at least one more mismatch.
    – Error is reduced from  to 2.

    • Next we will see:


    – Three way overlay scheme.
    – One mismatch will cause at least two more mismatches.
    – Error will reduce from  to 3.
    Compact Error Resilient Tiles (3-way overlay)

    Reduce Error from  to 3


    Examples of Error Resilient Assembly
    Examples of Error Resilient Assembly
    Computer Simulation (Xgrow, Winfree)

    Three way overlay

    Winfree 3x3 construction

    Winfree 2x2 construction

    Two way overlay

    No error correction
    Conclusions

    • Assembly size not increased.


    • Two way overlay: error rate (5%) => 2(0.25%).
    • Three way overlay: error rate  (5%) => 3 (0.0125%).
    • Open question: error rate  => k ?

    You might also like