User:Lance Martin: Difference between revisions
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*[http://www.pnas.org/content/88/24/10983.abstract Chemical implementation of Turing machine] | *[http://www.pnas.org/content/88/24/10983.abstract Chemical implementation of Turing machine] | ||
[[Image:Process.jpg|thumb|right|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== | ==Past engineered biological memory & logic devices/systems== |
Revision as of 09:49, 6 April 2009
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Projects
Electronic counter review
Gemini
Simulation
Computational modeling notebook
Genetic switches: methylation & feedback regulation
Recombination switches
Assorted items of interest
James Ferrell
- Timekeeping (James Ferrell)
- Feedback loops (James Ferrell)
Biological computation
- Arkin: computation in biochemical networks
- Chemical implementation of finite state machine
- Chemical implementation of Turing machine
Basic construction / design principles
- Summary of reviews by
- Voight, Endy, Arkin
Computational modeling to aid design
- Review of
- Collins toggle switch
- Elowitz repressilator
Past engineered biological memory & logic devices/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
- Harvard/BU 2004 iGem Int/Xis inversion switch & counter
- Their final presentation
- My notes on this work
- DNA methylation switch