Simulation of Single Molecular Bond Rupture in Dynamic Force Spectroscopy

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Simulation of Single Molecular Bond Rupturein
Dynamic Force Spectroscopy

• Prepared for MatSE385 by
• Fang Li(TAM)
• Samson Odunuga(MatSE)

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Phenomenological description of bonds rupture
Probability of being in state 1 at time t
Probability distribution of lifetime Probability
of lifetime within t, tdt
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Dissociation rate
Bells Expression
Intrinsic dissociation rate
Recent Explanation
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Rupture forces for a non-reversible bond
Probability distribution of rupture forces
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Modeling the Pulling Experiment
V
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Lennard-Jones potential
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Nanoscopic description of the pulling experiment
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Simulate the Pulling Experiment
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Dimensionless description
Dimensionless displacement of the particle
Scaled Units
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Brownian displacement Random number generation

• function ran1 (Bayes et Duham NR pp. 270-271)
• I j1 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-ltxgt)2/2?2
• x ltxgt ?x

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Single Molecular Bond Rupture
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Detachment under low loading rate
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Detachment under high loading rate
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Mean rupture force V.S loading rates
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Mean rupture force V.S loading rates
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Rupture of Multiple Parallel Molecular Bonds
under Dynamic Loading
Bells Expression
Time dependent decrease of the bonds number
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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.

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Acknowledgements

• Prof. Duane Johnson
• Prof. Deborah Leckband