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Simulation of Single Molecular Bond Rupture in Dynamic Force Spectroscopy

Simulation of Single Molecular Bond Rupture in Dynamic Force Spectroscopy. Prepared for MatSE385 by Fang Li(TAM) Samson Odunuga(MatSE). Phenomenological description of bonds rupture. Probability of being in state 1 at time t. Probability distribution of lifetime

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Simulation of Single Molecular Bond Rupture in Dynamic Force Spectroscopy

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  1. Simulation of Single Molecular Bond Rupturein Dynamic Force Spectroscopy Prepared for MatSE385 by Fang Li(TAM) Samson Odunuga(MatSE)

  2. Phenomenological description of bonds rupture Probability of being in state 1 at time t Probability distribution of lifetime Probability of lifetime within [t, t+dt]

  3. ? , , : Dissociation rate Bell’s Expression Intrinsic dissociation rate Recent Explanation

  4. High loading rate Low loading rate Rupture forces for a non-reversible bond Probability distribution of rupture forces

  5. Modeling the Pulling Experiment V

  6. Z0 Zmin ZFmax E0 Lennard-Jones potential

  7. Overdamped Langevin Equation Browniandisplacement Nanoscopic description of the pulling experiment

  8. Initial Position t=0, Z=Z min, Compute F(z) Move cantilever end Move the particle Measure force Forced in spring is the rupture force No Detached yes Simulate the Pulling Experiment

  9. Dimensionless distance and time Dimensionless loading rate Browniandisplacement Dimensionless description Dimensionless displacement of the particle Scaled Units

  10. Brownian displacement: Random number generation • function ran1 (Bayes et Duham NR pp. 270-271) • I j+1 = I j (mod m) • generates uniform deviates (0, 1] • adjusts against low order correlations • function gasdev (Box-Mueller method NR pp. 279-280) • generates random deviates with standard normal distribution • Transformation p (x) = (22)-1/2 exp-[(x-<x>)2/22] • x = <x> + x’

  11. Single Molecular Bond Rupture

  12. Detachment under low loading rate

  13. Detachment under high loading rate

  14. Mean rupture force V.S loading rates

  15. = z 0 . 1 nm 0 - - = × = 18 2 1 D 10 m s ; T 300K - - = × = × 1 1 km 3 N m ; k 0 . 03 N m c Mean rupture force V.S loading rates

  16. Rupture of Multiple Parallel Molecular Bonds under Dynamic Loading Bell’s Expression Time dependent decrease of the bonds number

  17. Conclusions • The model predicts, as it is observed experimentally, the rupture force measured is an increasing function of the loading rate. • At high loading rate, the rupture force equal to the maximum force corresponding to the LJ potential. • At low loading rate, the thermal fluctuations take an important role in the detachment process.

  18. Acknowledgements Prof. Duane Johnson Prof. Deborah Leckband

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