A Sticker-Based Model for DNA Computation

Slides:

Advertisements

Similar presentations

Ashish Goel, 1 A simple analysis Suppose complementary DNA strands of length U always stick, and those of length L never stick (eg:

Advertisements

Strict Self-Assembly of Discrete Sierpinski Triangles James I. Lathrop, Jack H. Lutz, and Scott M. Summers Iowa State University © James I. Lathrop, Jack.

Self-Assembly with Geometric Tiles ICALP 2012 Bin FuUniversity of Texas – Pan American Matt PatitzUniversity of Arkansas Robert Schweller (Speaker)University.

Solution of a 20-Variable 3-SAT Problem on a DNA Computer R. S. Briach, N. Chelyapov, C. Johnson, P. W. K. Rothemund, L. Adleman 발표자 : 문승현.

1 SODA January 23, 2011 Temperature 1 Self-Assembly: Deterministic Assembly in 3D and Probabilistic Assembly in 2D Matthew CookUniversity of Zurich and.

Cell and Microbial Engineering Laboratory Solution of a 20-Variable 3-SAT Problem on a DNA Computer Ravinderjit S. Braich, Nickolas.

DNA Computing By Thierry Metais

DNA Computer ~ 回顧 Leonard M. Adleman 之研究化工系 F 洪仕馨.

Self-Assembly Ho-Lin Chen Nov Self-Assembly is the process by which simple objects autonomously assemble into complexes. Geometry, dynamics,

Reducing Tile Complexity for Self-Assembly Through Temperature Programming Midwest Theory Day, December 10, 2006 Based on paper to appear in SODA 2006.

Topics in Biological Physics Design and self-assembly of two-dimensional DNA crystals Benny Gil 16/12/08 Fig3.a.

Complexities for Generalized Models of Self-Assembly Gagan Aggarwal Stanford University Michael H. Goldwasser St. Louis University Ming-Yang Kao Northwestern.

Reducing Tile Complexity for Self-Assembly Through Temperature Programming Symposium on Discrete Algorithms SODA 2006 January 23, 2006 Robert Schweller.

Ashish Goel Stanford University Joint work with Len Adleman, Holin Chen, Qi Cheng, Ming-Deh Huang, Pablo Moisset, Paul.

Section 8.4: Transcription.

1 Proceedings of the 24 th Annual ACM-SIAM Symposium on Discrete Algorithms January, 2013 Fuel Efficient Computation in Passive Self-Assembly Robert SchwellerUniversity.

JM - 1 Introduction to Bioinformatics: Lecture XVI Global Optimization and Monte Carlo Jarek Meller Jarek Meller Division of Biomedical.

OCR GCSE Computing © Hodder Education 2013 Slide 1 OCR GCSE Computing Chapter 2: Binary Logic.

Algorithmic self-assembly for nano-scale fabrication Erik Winfree Computer Science Computation & Neural Systems and The DNA Caltech DARPA NSF NASA.

Notes on the optimal encoding scheme for self-assembly Days 10, 11 and 12 Of Comp Sci 480.

Horn Clause Computation by Self-Assembly of DNA Molecules Hiroki Uejima Masami Hagiya Satoshi Kobayashi.

Branching in Biological Models of Computation Blair Andres-Beck, Vera Bereg, Stephanie Lee, Mike Lindmark, Wojciech Makowiecki Mike Lindmark, Wojciech.

An Introduction to Algorithmic Tile Self-Assembly.

1 David DotyCalifornia Institute of Technology Matthew J. PatitzUniversity of Texas Pan-American Dustin ReishusUniversity of Southern California Robert.

Copyright © 2007 Pearson Education, Inc. Publishing as Pearson Prentice Hall Areas in the Plane Section 7.2.

Towards Autonomous Molecular Computers Towards Autonomous Molecular Computers Masami Hagiya, Proceedings of GP, Nakjung Choi

Demonstration of a universal surface DNA computer Nucleic Acids Research, 2004, Vol. 32, Xingping Su and Lloyd M. Smith Presented by Je-Keun.

Molecular Computation and Splicing Systems J.H.M. Dassen, Summarized by Dongmin Kim

1 35 th International Colloquium on Automata, Languages and Programming July 8, 2008 Randomized Self-Assembly for Approximate Shapes Robert Schweller University.

DNA Computing Guided by: Ms. Leena Patel Computer Engineering Prepared by: Devharsh Trivedi

1 January 18, 2010 Shape Replication through Self-Assembly and Rnase Enzymes Zachary AbelHarvard University Nadia BenbernouMassachusetts Institute of Technology.

Number Systems Decimal Can you write 12,045 in expanded form? Base? Allowable digits for each place?

DNA Strand Algebracuits 1 Luca Cardelli, Strand Algebras for DNA Computing, DNA 15 Conference, 2009.

How do Computers Work ?.

Computational and Experimental Design of DNA Devices

continued on next slide

Introduction to Tiling Assembly

Molecular Computation

Programmable DNA Lattices: Design Synthesis & Applications

continued on next slide

continued on next slide

Thirteenth International Meeting on DNA Computers

Paul Rothemund’s Scaffolded DNA Origami Method

Self-Assembly of Shapes at Constant Scale Using Repulsive Forces

HOW NATURE BEAT US TO THE SUPERCOMPUTER MARTIN HANZEL

Tiing Error Correction & ExperimentsChen

DNA Self-Assembly Robert Schweller Northwestern University

From Gene to Protein.

Strict Self-Assembly of Discrete Sierpinski Triangles

Molecular computing: Does DNA compute?

JSPS Project on Molecular Computing (presentation by Masami Hagiya)

Self-Assembly Ho-Lin Chen Nov

Molecular Computing Leonard Adleman Laboratory for Molecular Science

Self-Assembly of Any Shape with

DNA Hybridization Catalysts and Catalyst Circuits

Complexities for the Design of Self-Assembly Systems

DNA & Chromosome Notes.

The Power of Nondeterminism in Self-Assembly

4/6 Objective: Explain the steps and key players in transcription.

Algorithms for Robust Self-Assembly

4/2 Objective: Explain the steps and key players in transcription.

Homework 1 (May 31) Material covered: Episodes 1 and 2

continued on next slide

Condor: BLAST Tuesday, Dec 7th, 10:45am

DNA polymerase adds new nucleotides to 3’-OH; DNA strands grow 5'3'

Codes Let’s show you how DNA can use codes to make proteins:

Finite Field Arithmetic using Self-Assembly of DNA Tilings

continued on next slide

Presentation transcript:

A Sticker-Based Model for DNA Computation Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N. V., Goodman, M. F., Rothemund, P. W. K., & Adleman, L. M. (1998). A Sticker-Based Model for DNA Computation. Journal of Computational Biology, 5(4), 615–629. doi:10.1089/cmb.1998.5.615 Slides by Reem Mokhtar 1

Sticker(s) Model memory complexes = bit string: Memory strand (N bases) Sticker strands (M bases * K regions) 1 = on: memory strand region with hybridized sticker strand 0 = off: memory strand region wthout sticker strand Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N. V., Goodman, M. F., Rothemund, P. W. K., & Adleman, L. M. (1998). A Sticker-Based Model for DNA Computation. Journal of Computational Biology, 5(4), 615–629. doi:10.1089/cmb.1998.5.615 2

Sticker(s) Model Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N. V., Goodman, M. F., Rothemund, P. W. K., & Adleman, L. M. (1998). A Sticker-Based Model for DNA Computation. Journal of Computational Biology, 5(4), 615–629. doi:10.1089/cmb.1998.5.615 3

Sticker(s) Model Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N. V., Goodman, M. F., Rothemund, P. W. K., & Adleman, L. M. (1998). A Sticker-Based Model for DNA Computation. Journal of Computational Biology, 5(4), 615–629. doi:10.1089/cmb.1998.5.615 4

Sticker(s) Model Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N. V., Goodman, M. F., Rothemund, P. W. K., & Adleman, L. M. (1998). A Sticker-Based Model for DNA Computation. Journal of Computational Biology, 5(4), 615–629. doi:10.1089/cmb.1998.5.615 5