BIOMOD Handbook (BIOMOD Handbook)
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BIOMOD Handbook

Pre-release edition

About the Book

The BIOMOD Handbook is an introduction to biomolecular engineering. Topics include molecular self-assembly, structural DNA nanotechnology, DNA computing, and molecular robotics. We've tailored the Handbook for undergraduate students participating in BIOMOD, but concepts and skills may be applicable beyond the scope of the competition, such as in undergraduate-level laboratory courses. The Handbook originated as a translation of a Japanese-language guide by the Molecular Robotics Study Group. All sales proceeds go directly to support the BIOMOD Foundation, a 501(c)(3) non-profit based in California.

About the Editor

Shawn Douglas
Shawn Douglas

Assistant Professor at in the Department of Cellular & Molecular Pharmacology at the University of California, San Francisco.

Lab website:

About the Contributors

Akinori Kuzuya
Akinori Kuzuya
Hisashi Tadakuma
Hisashi Tadakuma

Osaka University

Kei Fujiwara
Kei Fujiwara

Keio University

Ken Komiya
Ken Komiya
Satoshi Murata
Satoshi Murata

Tohoku University

Shinichiro M. Nomura
Shinichiro M. Nomura

Tohoku University

Shogo Hamada
Shogo Hamada

Cornell University

Table of Contents

  • About
    • Support
  • Chapter 1 Let’s go to BIOMOD
    • 1. Welcome to the World of DNA Molecule Design
    • 2. What is BIOMOD?
    • 3. Judging System of BIOMOD
    • 4. Days at the Jamboree
    • 5. Learn from Previous Winners
    • 6. BIOMOD Calendar
    • 7. Tips on Group Work
    • 8. Tips on Website Creation
    • 9. Tips on Making YouTube Video
    • 10. Tips on Presentation in English
    • 11. What You’ll Get From BIOMOD
  • Chapter 2 Before Starting Your Project
    • 12. Subject Matter of Project
    • 13. Types of Brainstorming
    • 14. Design Process
    • 15. How to Collect Information
    • 16. More About Papers
  • Chapter 3 What Does Design of DNA Molecules Make Possible?
    • 17. Structural DNA Nanotechnology: Overview
    • 18. Two-Dimensional DNA Origami
    • 19. Three-Dimensional DNA Origami
    • 20. DNA Tiles
    • 21. DNA-Modified Particles (SNA)
    • 22. DNA Hydrogels
    • 23. DNA Nanomachines and Nanorobots: Overview
    • 24. DNA Tweezers
    • 25. DNA Walker
    • 26. DNA Nanomachines
    • 27. Autonomous DNA Reaction Systems
    • 28. DNA Computing: Overview
    • 29. DNA Logic Gates
    • 30. DNAzyme Logic Gates
    • 31. Entropy-Driven Gate
    • 32. Seesaw Gate
    • 33. DNA Toolbox
    • 34. DNA-Based Finite State Machine
    • 35. Traveling Salesman Problem
  • Chapter 4 Basic Textbook Knowledge
    • 36. Importance of Multidisciplinary Knowledge: Overview
    • 37. Thermodynamics
    • 38. Free Energy and Chemical Equilibrium
    • 39. Reaction Kinetics
    • 40. Molecular Structure of DNA
    • 41. Thermodynamics of DNA Hybridization
    • 42. Strand Displacement
    • 43. Secondary Structures of DNA
    • 44. DNA Synthesis
  • Chapter 5 Techniques/Materials to Boost DNA
    • 45. Enzymes
    • 46. Polymerase Reactions
    • 47. Restriction Enzymes
    • 48. Artificial Bases
    • 49. Non-Watson-Crick Structure
    • 50. Protein Motors
    • 51. FRET and Molecular Beacons
    • 52. Artificial Cell and Liposome (and Some Related Topics)
  • Chapter 6 Software Techniques
    • 53. Basic Software Programs: Overview
    • 54. Document/Table/Graph Preparation
    • 55. Preparation of Presentation Slides
    • 56. Figure Preparation
    • 57. 3D Animation
    • 58. Image Processing
    • 59. Video Editing
    • 60. Numerical Analysis Library
    • 61. Software for Molecular Design of DNA
    • 62. DNA Secondary Structure Prediction
    • 63. Sequence Design
    • 64. Design of DNA Origami
    • 65. Simulation of DNA Origami
    • 66. Molecular Modeling of DNA
    • 67. Simulation of DNA Logic Gate

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