User:Lance Martin

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Projects

Electronic counter review

Electronic counter notebook

Gemini

Gemini notebook

Simulation

Computational modeling notebook

Genetic switches: methylation & feedback regulation

Genetic switches notebook

Recombination switches

Review of recombinases

Assorted items of interest

A biological bit

James Ferrell

• Timekeeping (James Ferrell)
  • Toggle switch at heart of circadian timekeeping
  • Cell cycle and its switches
• Feedback loops (James Ferrell)
  • Interlinked positive and negative feedback loops
  • Systems level dissection of the cell cycle

Biological computation

• Arkin: computation in biochemical networks
• Chemical implementation of finite state machine
• Chemical implementation of Turing machine

Design process

Basic construction / design principles

• Summary of reviews by
  • Voight, Endy, Arkin

Media: Principles.ppt

Computational modeling to aid design

• Review of
  • Collins toggle switch
  • Elowitz repressilator

Media:Modeling.ppt

Some engineered biological memory & logic systems

Prior work: implementing recombinase switches

• Ham & Arkin inversion switch
  • Media:Ham&Arkin.ppt
• Harvard/BU 2004 iGem Int/Xis inversion switch & counter
  • Their final presentation
    • Media:iGem.ppt
  • Notes on this work
    • Media:iGemLance.ppt

Challenges

• No spatial addressing of signals in biological systems
• Many heterogeneous parts implemented, resulting in:
  • Heterogeneity of device physics across circuits
  • Complex properties, making design and modeling hard
  • Large outlays of DNA real-estate may be necessary
  • Large energetic loads on host state