Nonequilibrium dynamics of single polymer molecules: Relaxation close to and far from equilibrium

Hanke, Felix; Kreuzer, H. J.

doi:10.1002/qua.21120

Cited by 3 publications

(2 citation statements)

References 23 publications

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“…For all pulling speeds investigated, transitions with width β of order unity are sufficiently fast to maintain equilibrium throughout the calculation (or experiment): taking the limit β → 0 does not affect the results presented in section 3.2. In order to accurately estimate the pulling speeds at which nonequilibrium effects would be observed in the extension of titin WLC segments, the precise value of (and also of w 0 ) for the transitions in unfolded titin chains would have to be obtained from relaxation times [31]. Unfortunately these measurements have not yet been done for titin.…”

Section: The Stretching Of Wlc Segments Occurs In Equilibriummentioning

confidence: 99%

Stretching and unfolding of multidomain biopolymers: a statistical mechanics theory of titin

Staple¹,

Payne

Reddin

et al. 2009

Phys. Biol.

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Single-molecule manipulation has allowed the forced unfolding of multidomain proteins. Here we develop a theory that not only explains these experiments, but also points out a number of difficulties in their interpretation and makes suggestions for further experiments. Our theory is valid for essentially any molecule that can be unfolded in the AFM: as an example we present force-extension curves for the unfolding of both titin and RNA hairpins. For titin we reproduce force-extension curves, the dependence of break force on pulling speed, and break-force distributions, and also validate two common experimental views: unfolding titin Ig domains can be explained as stepwise increases in contour length, and increasing force peaks in native Ig sequences represent a hierarchy of bond strengths.

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Section: The Stretching Of Wlc Segments Occurs In Equilibriummentioning

confidence: 99%

Stretching and unfolding of multidomain biopolymers: a statistical mechanics theory of titin

Staple¹,

Payne

Reddin

et al. 2009

Phys. Biol.

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“…In the isometric ensemble the position of the chain ends is employed as a control parameter, fixing also the end-to-end distance, while in the isotensional case the control parameter is represented by the force applied on one loose end. The conditions under which the equivalence between these two ensembles can be obtained have been investigated in many works, both from a theoretical point of view [21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40] and by means of computer simulations [41,42,43,44,45,46,47,48,49,50]. Some of the authors concluded that ensembles are equivalent in the infinitely long chain limit for a Gaussian chain, [30,47] as well as for a generic chain [21] and toy lattice chain models [21,35,36].…”

Section: Introductionmentioning

confidence: 99%

Ensemble inequivalence in single-molecule experiments

2009

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In bulk systems the calculation of the main thermodynamic quantities leads to the same expectation values in the thermodynamic limit, regardless of the choice of the statistical ensemble. Single linear molecules can be still regarded as statistical systems, where the thermodynamic limit is represented by infinitely long chains. The question of equivalence between different ensembles is not at all obvious and has been addressed in the literature, with sometimes contradicting conclusions. We address this problem by studying the scaling properties of the ensemble difference for two different chain models as a function of the degree of polymerization. By characterizing the scaling behavior of the difference between the isotensional (Gibbs) and isometric (Helmholtz) ensembles in the transition from the low-stretching to the high-stretching regime, we show that ensemble equivalence cannot be reached for macroscopic chains in the low force regime, and we characterize the transition from the inequivalence to the equivalence regime.

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

2008

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In the force-ramp mode of the atomic force microscope, the force with which a macromolecule is stretched is increased linearly in time by properly controlling the motion of the cantilever through a feedback loop. Using a master equation approach for the coupled cantilever-macromolecule system, we mimic such a feedback loop, to study nonequilibrium effects in the measurements of force-extension curves and fluctuations. In particular, it is shown that the fluctuations are the same for force-ramp experiments and for the more commonly used constant velocity experiments. Thus the exact same statistics suffice for the explanation of either experiment. Specific results are presented for the stretching of Dextran.

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Nonequilibrium dynamics of single polymer molecules: Relaxation close to and far from equilibrium

Cited by 3 publications

References 23 publications

Stretching and unfolding of multidomain biopolymers: a statistical mechanics theory of titin

Stretching and unfolding of multidomain biopolymers: a statistical mechanics theory of titin

Ensemble inequivalence in single-molecule experiments

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

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