Dynamics of single-molecule force-ramp experiments: The role of fluctuations

Staple, Douglas B.; Hanke, Felix; Kreuzer, H. J.

doi:10.1103/physreve.77.021801

Cited by 4 publications

(6 citation statements)

References 13 publications

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“…1)) so that in the case of a single molecule desorption experiment only a really strong adsorption energy is essential. This limit has been discussed in the recent papers by Jagota et al [17][18][19][20] and Kreuzer et al [21][22][23] Here we consider this problem in a slightly more general form. In doing so we distinguish between two different models: with frictionless-and strong-friction substrates, as indicated in Fig.…”

Section: Equilibrium Theory In the Strong Adsorption Casementioning

confidence: 92%

“…This limit has been discussed in the recent papers by Jagota et al [17][18][19][20] and Kreuzer ey al. [21][22][23]. Here we consider this problem in a slightly more general form.…”

Section: Equilibrium Theory At the Strong Adsorption Casementioning

confidence: 99%

“…This case has been considered in Refs. [17,18,[21][22][23] and is based on the assumption that the force resisting sliding is sufficiently small, i.e., the cantilever tip and the contact point c are both placed along the same z-axis (see Fig. 1 (left panel)).…”

Section: A Frictionless Substratementioning

confidence: 99%

“…The nonequilibrium theory of forced desorption has been developed by Kreuzer et al [21][22][23] on the basis of the master equation approach for the cases of constant velocity and forceramp modes in an AFM experiment. The authors assumed that the detachment of individual monomers represents a fast process as compared to the removal of all monomers.…”

Section: Introductionmentioning

confidence: 99%

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Force spectroscopy of polymer desorption: theory and molecular dynamics simulations

et al. 2014

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Forced detachment of a single polymer chain, strongly adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics (MD) simulations with a Langevin thermostat. The suggested approach makes it possible to go beyond the limitations of the conventional Bell-Evans model. We observe a series of characteristic force spikes when the pulling force is measured against the cantilever displacement during detachment at constant velocity vc (displacement control mode) and find that the average magnitude of this force increases as vc increases. The probability distributions of the pulling force and the end-monomer distance from the surface at the moment of the final detachment are investigated for different adsorption energies ε and pulling velocities vc. Our extensive MD simulations validate and support the main theoretical findings. Moreover, the simulations reveal a novel behavior: for a strong-friction and massive cantilever the force spike pattern is smeared out at large vc. As a challenging task for experimental bio-polymer sequencing in future we suggest the fabrication of a stiff, super-light, nanometer-sized AFM probe.

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Section: Equilibrium Theory In the Strong Adsorption Casementioning

confidence: 92%

“…This limit has been discussed in the recent papers by Jagota et al [17][18][19][20] and Kreuzer ey al. [21][22][23]. Here we consider this problem in a slightly more general form.…”

Section: Equilibrium Theory At the Strong Adsorption Casementioning

confidence: 99%

Section: A Frictionless Substratementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Force spectroscopy of polymer desorption: theory and molecular dynamics simulations

et al. 2014

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“…Therefore we ought maybe to describe this as a 'pseudo'-force ramp experiment. For the detailed definition of the force ramp experiment, see [27,28].…”

Section: Introductionmentioning

confidence: 99%

A new atomic force microscope force ramp technique using digital force feedback control reveals mechanically weak protein unfolding events

Kawakami¹,

Smith²

2008

Nanotechnology

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We have developed a new force ramp modification of the atomic force microscope (AFM) which can control multiple unfolding events of a multi-modular protein using software-based digital force feedback control. With this feedback the force loading rate can be kept constant regardless the length of soft elastic linkage or number of unfolded polypeptide domains. An unfolding event is detected as a sudden drop in force, immediately after which the feedback control reduces the applied force to a low value of a few pN by lowering the force set point. Hence the remaining folded domains can relax and the subsequent force ramp is applied to relaxed protein domains identically in each case. We have applied this technique to determine the kinetic parameters x(u), which is the distance between the native state and transition state, and α(0), which is the unfolding rate constant at zero force, for the mechanical unfolding of a pentamer of I27 domains of titin. In each force ramp the unfolding probability depends on the number of folded domains remaining in the system and we had to take account of this effect in the analysis of unfolding force data. We obtained values of x(u) and α(0) to be 0.28 nm and 1.02 × 10(-3) s(-1), which are in good agreement with those obtained from conventional constant velocity experiments. This method reveals unfolding data at low forces that are not seen in constant velocity experiments and corrects for the change in stiffness that occurs with most mechanical systems throughout the unfolding process to allow constant force ramp experiments to be carried out. In addition, a mechanically weak structure was detected, which formed from the fully extended polypeptide chain during a force quench. This indicates that the new technique will allow studies of the folding kinetics of previously hidden, mechanically weak species.

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