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Stochastic Displacement

Stochastic Displacement. Daniel Vitek. Overview. Overview Non-Stochastic Model Changes General Ideas Sample Space. Non-Stochastic Model. Deterministic displacement generation Disregarded the “borderline conditions” (Ponnala, et al. 2006). Overview Non-Stochastic Model Changes

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Stochastic Displacement

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  1. Stochastic Displacement Daniel Vitek

  2. Overview

  3. Overview Non-Stochastic Model Changes General Ideas Sample Space Non-Stochastic Model • Deterministic displacement generation • Disregarded the “borderline conditions” (Ponnala, et al. 2006)

  4. Overview Non-Stochastic Model Changes General Ideas Sample Space Changes • Incorporated probability based on: • Displacement • tRNA Availability

  5. Overview Non-Stochastic Model Changes General Ideas Sample Space General Ideas • Concept of “cycles” • Old concept of Nloop • Increment for each Nloop • Sinusoidal probability function of displacement • Function of tRNA availability

  6. Overview Non-Stochastic Model Changes General Ideas Sample Space Sample Space • For each cycle: • Stay in current frame • Shift to +1 frame • Reloop

  7. Mathematics

  8. Mathematics Flow Chart Probabilities Weight Value of n Flow Chart Calculate Probabilities Increment Displacement No Randomly Choose a Possibility Reloop abc or bcd Move by a Codon Check For Stop Codon Yes Done

  9. Mathematics Flow Chart Probabilities Weight Value of n Probabilities

  10. Mathematics Flow Chart Probabilities Weight Value of n Weight

  11. Mathematics Flow Chart Probabilities Weight Value of n Weight

  12. Mathematics Flow Chart Probabilities Weight Value of n Value of n • Normalization from N (Nloop)

  13. Sample Graphs

  14. Sample Graphs prfB rpmB arnA prfB

  15. Sample Graphs prfB rpmB arnA prfB

  16. Sample Graphs prfB rpmB arnA rpmB

  17. Sample Graphs prfB rpmB arnA rpmB

  18. Sample Graphs prfB rpmB arnA arnA

  19. Sample Graphs prfB rpmB arnA arnA

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