Suppression of thermally activated escape by heating

The problem of thermally activated escape over a potential barrier is solved by means of path integrals for one-dimensional reaction dynamics with very general time dependences. For a suitably chosen but still quite simple static potential landscape, the net escape rate may be substantially reduced by temporally increasing the temperature above its unperturbed constant level.Comment: 4 pages, 2 figure

Optimal evaluation of single-molecule force spectroscopy experiments

The forced rupture of single chemical bonds under external load is addressed. A general framework is put forward to optimally utilize the experimentally observed rupture force data for estimating the parameters of a theoretical model. As an application we explore to what extent a distinction between several recently proposed models is feasible on the basis of realistic experimental data sets.Comment: 4 pages, 3 figures, accepted for publication in Phys. Rev.

On the Lubensky-Nelson model of polymer translocation through nanopores

We revisit the one-dimensional stochastic model of Lubensky and Nelson [Biophys. J 77, 1824 (1999)] for the electrically driven translocation of polynucleotides through alpha-hemolysin pores. We show that the model correctly describes two further important properties of the experimentally observed translocation time distributions, namely their spread (width) and their exponential decay. The resulting overall agreement between theoretical and experimental translocation time distributions is thus very good

Hidden multiple bond effects in dynamic force spectroscopy

In dynamic force spectroscopy, a (bio-)molecular complex is subjected to a steadily increasing force until the chemical bond breaks. Repeating the same experiment many times results in a broad distribution of rupture forces, whose quantitative interpretation represents a formidable theoretical challenge. In this study we address the situation that more than a single molecular bond is involved in one experimental run, giving rise to multiple rupture events which are even more difficult to analyze and thus are usually eliminated as far as possible from the further evaluation of the experimental data. We develop and numerically solve a detailed model of a complete dynamic force spectroscopy experiment including a possible clustering of molecules on the substrate surface, the formation of bonds, their dissociation under load, and the post processing of the force extension curves. We show that the data, remaining after elimination of obvious multiple rupture events, may still contain a considerable number of "hidden" multiple bonds, which are experimentally indistinguishable from "true" single bonds, but which have considerable effects on the resulting rupture force statistics and its consistent theoretical interpretation.Comment: 31 pages, 7 figure

Escape processes far from thermal equilibrium : path integrals and force spectroscopy

Getfert S. Escape processes far from thermal equilibrium : path integrals and force spectroscopy. Bielefeld (Germany): Bielefeld University; 2009.Thermally activated escape over a potential barrier is ubiquitous in physical, biological, chemical, and technical processes and its understanding of paramount importance. For example, single-molecule force spectroscopy experiments, and a number of other physical systems are governed by thermally activated transitions out of a metastable state under the action of a steadily increasing external force. This allows to observe the chemical dissociation of two biomolecules at the single-molecule level. In the first part of this work, we address the problem of theoretically modeling and interpreting these experiments. In the second part of this thesis, the technique of path integration is employed to develop an approximation to the instantaneous escape rate that applies to arbitrarily modulated potentials and temperatures. As such systems are far from thermal equilibrium, the physics is not restricted by the second law of thermodynamics and interesting effects can occur. Using our new approximation, several of these effects are discussed and demonstrated

Thermally activated escape far from equilibrium: A unified path-integral approach

Getfert S, Reimann P. Thermally activated escape far from equilibrium: A unified path-integral approach. CHEMICAL PHYSICS. 2010;375(2-3):386-398.Thermally activated escape over potential barriers is addressed for systems driven out of equilibrium by time-dependent forces, temperatures, or dissipation coefficients of rather general type. Particular examples are periodic perturbations, single pulses, and the initial convergence towards Kramers rate in a time-independent set up. The general problem is treated within one common, unifying path-integral approach in the simplest case of an overdamped, one-dimensional model dynamics. As an application, the following quite astonishing effect is demonstrated: for a suitably chosen, but still quite simple static potential landscape, the net escape rate may be substantially reduced by temporally increasing the temperature above its unperturbed, constant level. (C) 2010 Elsevier B.V. All rights reserved

Opposite translocation of long and short oligomers through a nanopore

Getfert S, Töws T, Reimann P. Opposite translocation of long and short oligomers through a nanopore. Physical Review E. 2013;87(6): 62710.We consider elongated cylindrical particles, modeling, e. g., DNA fragments or nanorods, while they translocate under the action of an externally applied voltage through a solid state nanopore. Particular emphasis is put on the concomitant potential energy landscape encountered by the particle on its passage through the pore due to the complex interplay of various electrohydrodynamic effects beyond the realm of small Debye lengths. We find that the net potential energy difference across the membrane may be of opposite sign for short and long particles of equal diameters and charge densities (e. g., oligomers). Thermal noise thus leads to biased diffusion through the pore in opposite directions. By means of an additional membrane gate electrode it is even possible to control the specific particle length at which this transport inversion occurs

Refined procedure of evaluating experimental single-molecule force spectroscopy data

Fuhrmann A, Anselmetti D, Ros R, Getfert S, Reimann P. Refined procedure of evaluating experimental single-molecule force spectroscopy data. PHYSICAL REVIEW E. 2008;77(3):31912.Dynamic force spectroscopy is a well-established tool to study molecular recognition in a wide range of binding affinities on the single-molecule level. The theoretical interpretation of these data is still very challenging and the models describe the experimental data only partly. In this paper we reconsider the basic assumptions of the models on the basis of an experimental data set and propose an approach of analyzing and quantitatively evaluating dynamic force spectroscopy data on single ligand-receptor complexes. We present our procedure to process and analyze the force-distance curves, to detect the rupture events in an automated manner, and to calculate quantitative parameters for a biophysical characterization of the investigated interaction