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

Past engineered biological memory & logic devices/systems

Some engineered biological memory & logic systems

Rationale

Scaling to larger applications with more states and deeper sequential logics is a future need. Systems whose output depends on input history are necessary for sophisticated computation and information storage. Memory is common in systems that control functions such as development. Memory may confer fitness advantage for synthetic systems that exist and compete in the living world. (reference: Arkin, Ham 2008)

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

Of particular interest to us

• 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