1 / 7

Modeling a Molecular Computing Device Using λ-Calculus: A Markov Model Approach

This project presents a molecular computing device modeled using λ-calculus to simulate basic reactions involving DNA sequences. The study is divided into two stages: initial reactions and implementation of a Markov model. Three sets of basic reactions are defined with varying rates, enabling comparative analysis of their effectiveness. Using a defined input of DNA sequences comprised of C and G nucleotides, the model outlines key processes, including reaction initiation, enzyme interaction, and molecule transformation, ultimately tracking the completion time of DNA reactions.

brody
Télécharger la présentation

Modeling a Molecular Computing Device Using λ-Calculus: A Markov Model Approach

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related