https://github.com/arinbjornk/dnasupercoil

A model of a DNA supercoiling insulator in a transcription-translation system
https://github.com/arinbjornk/dnasupercoil

biological-simulations dna dna-supercoiling-insulator ieee synthetic-biology transcription-translation

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A model of a DNA supercoiling insulator in a transcription-translation system

• Host: GitHub
• URL: https://github.com/arinbjornk/dnasupercoil
• Owner: arinbjornk
• License: apache-2.0
• Created: 2017-01-28T14:32:32.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2017-01-28T19:53:03.000Z (about 8 years ago)
• Last Synced: 2025-03-05T15:43:11.047Z (about 2 months ago)
• Topics: biological-simulations, dna, dna-supercoiling-insulator, ieee, synthetic-biology, transcription-translation
• Language: Matlab
• Homepage:
• Size: 240 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# DNAsupercoil

A model of a DNA supercoiling insulator in a translation-transcription system.

![A simulation of protein expression](original.png)

The concentration upstream gene is plotted and blue and the downstream gene in red.

### References

1. The base supercoiling model is adapted from:  

  Yeung, Enoch, et al. "Modeling the effects of compositional context on promoter activity in an E. coli extract based transcription-translation system." *Decision and Control (CDC), 2014 IEEE 53rd Annual Conference*. IEEE, 2014.

2. Elastic supercoiling model:  

 Benham, Craig J. "Elastic model of supercoiling." *Proceedings of the National Academy of Sciences* 74.6 (1977): 2397-2401.

### Disclaimer

This code was not been reviewed or tested sufficiently. There is no guarantee that it is correct.

This project is not active, it is just some old code.