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Modeling a Molecular Computing Device Using -Calculus Semester Project

Modeling a Molecular Computing Device Using -Calculus Semester Project. Ya ’ ara Goldschmidt Department of Applied Math – Bioinformatics June 2001. First Stage: Basic Reactions Second Stage: The Markov model. eTI. T + I  TI. eTFok. breakTI. T + Fok  TFok. breakTFok.

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Modeling a Molecular Computing Device Using -Calculus Semester Project

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  1. Modeling a Molecular Computing Device Using -CalculusSemester Project Ya’ara Goldschmidt Department of Applied Math – Bioinformatics June 2001

  2. First Stage: Basic Reactions • Second Stage: The Markov model.

  3. eTI T + I  TI eTFok breakTI T + Fok  TFok breakTFok eTIFok TI + Fok  TIFok breakTIFok eITFok TFok + I  TIFok breakITFok eNS TIFok  T + Fok + Inew Basic Reactions • There are 3 sets of basic reactions, each with different rates(According to Kobi’s request – so he can test which is the best one,They are at the folders called: rateSet1, rateSet2, rateSet3). I – input (DNA) T – Transition State (DNA) Fok – Nuclease (Enzyme)

  4. Implementation of the Markov Model • Input: • DNA sequence of C and G (of length N>3). • # copies of the DNA sequence • # Transition molecules. • # FokI molecules • Output: • The time each DNA molecule finished reacting (was left with no letters)

  5. GGC GCC GCG GGG G CGG CGC CCC CCG C Implementation of the Model • Transition molecules: • There are 16 possible transitions: 8 possible triplets of C and G, and for each one the next letter can be either C or G. C G

  6. Implementation of the Model • The process: • First 3 letters are inspected, according to the fourth letter, the right transition molecule will react with the input DNA molecule, and create (with the fokI enzyme) a new Input molecule. • The new molecule is the same as its previous one, but lacks its first letter. • The process repeats until the last letter is reached and consumed. • NOTE: all steps until the creation of a new DNA molecule are reversible !

  7. Results • 10 Input molecules • 30 Transition molecules of each type. • 100 FokI molecules

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