Biomod/2011/UTAustin/Hook'em Hybridizers:Tools: Difference between revisions

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Few systems work the first time they are built, and a nanoscale molecular machine is no different. Given that the kinetics of DNA interactions are well studied, we proposed that it should be possible to completely simulate our system. A number of important questions can be answered about our system using simulation. For example, we could ask what the optimal concentrations of threshold strands and gate strands are to ensure that our machine functions.
Few systems work the first time they are built, and a nanoscale molecular machine is no different. Given that the kinetics of DNA interactions are well studied, we proposed that it should be possible to simulate our counter system computationally. A number of important questions can be answered about our system using simulation. For example, we could ask what the optimal concentrations of threshold strands and gate strands are to ensure that our machine functions.


There exist software tools for simulating nucleic acid systems. Notably, Nupack and Visual DSD are both good options for many system applications. However, neither was able to completely simulate our system adequately. Hence, we developed TripleSim.
There exist software tools for simulating nucleic acid systems. Notably, Nupack and Visual DSD are both good options for many system applications. However, neither was able to completely simulate our system adequately. Hence, we developed TripleSim.

Revision as of 23:42, 2 November 2011

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Tools

Few systems work the first time they are built, and a nanoscale molecular machine is no different. Given that the kinetics of DNA interactions are well studied, we proposed that it should be possible to simulate our counter system computationally. A number of important questions can be answered about our system using simulation. For example, we could ask what the optimal concentrations of threshold strands and gate strands are to ensure that our machine functions.

There exist software tools for simulating nucleic acid systems. Notably, Nupack and Visual DSD are both good options for many system applications. However, neither was able to completely simulate our system adequately. Hence, we developed TripleSim.

TripleSim is a

  • unpSeuddoknotted
  • Secondary
  • Structures
  • Simulator

Like Visual DSD, TripleSim uses dynamic compilation to discover the "most important" reaction pathways through a system.


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