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CS411: Non-Standard Computing

Unit 2: Molecular Computation   The first part of this unit covers the structure and manipulation of DNA for computational purposes.  Then, we discuss the development of biocomputers and biologically derived materials to perform computational functions.  In order to understand biocomputers better, we list some elementary concepts and building blocks of supramolecular chemistry.  The last part of the unit shows a video about the workings of a DNA computer.  

Unit 2 Time Advisory
This unit will take approximately 13 hours to complete.

☐    Subunit 2.1: 3 hours

☐    Subunit 2.2: 3 hours

☐    Subunit 2.3: 3 hours

☐    Subunit 2.4: 3 hours

☐    Unit 2 Assessment: 1 hour

Unit2 Learning Outcomes
Upon successful completion of this unit, the student will be able to:

  • Describe DNA for computational purposes, and list the operations of DNA.
  • Describe the advantages of DNA-based computers.
  • Explain the technological hurdles of DNA computation.
  • Explain the differences between bio-electronic, biochemical, and biomechanical computers.
  • Explain the basic concepts and building blocks of supramolecular chemistry.

2.1 DNA-Based Computation   - Reading: G. Sweety Peter’s “DNA-Based Computation” Link: G. Sweety Peter‘s “DNA-Based Computation” (HTML)
 
Instructions: Read the webpage to learn about the structure and manipulation of DNA, about the operations of DNA sequences, and about DNA computing models.  Make sure you understand the shortcomings of DNA computation.  This reading covers subunits 2.1.1 through 2.1.5.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

2.1.1 The Structure and Manipulation of DNA   2.1.2 Operations of DNA Sequences   2.1.3 The Case for DNA Computing   2.1.4 Models and Formats of DNA Computation   2.1.5 Pitfalls of DNA Computing   2.2 Biocomputers   - Reading: Wikipedia: “Biocomputers” Link: Wikipedia: “Biocomputers” (PDF)
 
Instructions: Read this webpage to learn about the development of biocomputers and biologically derived materials to perform computational functions.  Pay particular attention to the differences among bio-electronic, biochemical, and biomechanical computers.  This reading covers subunits 2.2.1 through 2.2.7.
 
Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML).  You can find the original Wikipedia version of this article here (HTML).

2.2.1 Scientific Background   2.2.2 Biochemical Computers   2.2.3 Biomechanical Computers   2.2.4 Bioelectronic Computers   2.2.5 Engineering Biocomputers   2.2.6 Economical Benefit of Biocomputers   2.2.7 Notable Advancements in Biocomputer Technology   - Reading: Biocomputers The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

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2.3 Supramolecular Systems   - Reading: Wikipedia: “Supramolecular Chemistry” Link: Wikipedia: “Supramolecular Chemistry” (PDF)
 
Instructions: Read this webpage to learn about the concepts and building blocks of supramolecular chemistry.  Please pay particular attention to section five “Applications,” which provides examples of how supramolecular chemistry is used.  This reading covers subunits 2.3.1 through 2.3.3.
 
Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML).  You can find the original Wikipedia version of this article here (HTML).

2.3.1 Concepts in Supramolecular Chemistry   2.3.2 Building Blocks of Supramolecular Chemistry   2.3.3 Applications   2.4 Bio-molecular Computing of Finite-State Automata   - Assessment: The Saylor Foundation's "CS411: Unit 2 Quiz" The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

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  • Web Media: Videolectures.net: Yasubumi Sakakibara’s “Bio-Molecular Computing of Finite-State Automata” Link: Videolectures.net: Yasubumi Sakakibara’s "Bio-Molecular Computing of Finite-State Automata" (YouTube)
     
    Instructions: Watch this video to learn what a DNA computer is and to see some examples of how a DNA computer works.  Please take notes as you watch the video and review portions of the video as necessary to make sure you understand each concept.  This should take approximately 3 hours of study time.
     
    Terms of Use:  This video is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. It is attributed to videolectures.net and the original version can be found here.