Numerical study of pattern formation in compliant surfaces scraped by a rigid tip.

The emergence of surface patterns on the surfaces of compliant materials subject to plowing wear is a complex problem which can be quantitatively characterized, e.g., on polymer surfaces scraped by an atomic force microscope (AFM) tip.

Thermal versus mechanical unfolding in a model protein.

Force spectroscopy techniques are often used to learn about the free energy landscape of single biomolecules, typically by recovering free energy quantities that, extrapolated to zero force, are compared to those measured in bulk experiments. However, it is not always clear how the information obtained from a mechanically perturbed system can be related to the information obtained using other denaturants since tensioned molecules unfold and refold along a reaction coordinate imposed by the force, which is not likely to be meaningful in its absence. Here, we explore this dichotomy by investigating the unfolding landscape of a model protein, which is unfolded first mechanically through typical force spectroscopy-like protocols and next thermally.

Plowing-Induced Structuring of Compliant Surfaces.

The structures produced by a sharp tip scraping a compliant surface are modeled in the illustrative case of scan patterns formed by a series of parallel lines. This is made possible by a modified version of the Prandtl model for stick-slip friction, with an interaction energy landscape replicating the morphology of the evolving surface. As a result, a ripple motif emerges with a tilt angle increasing linearly with the distance between the scan lines, except for the region close to the left boundary of the scanned area, where the ripples are oriented at 90°.

Time Strengthening of Crystal Nanocontacts.

We demonstrate how an exponentially saturating increase of the contact area between a nanoasperity and a crystal surface, occurring on time scales governed by the Arrhenius equation, is consistent with measurements of the static friction and lateral contact stiffness on a model alkali-halide surface at different temperatures in ultrahigh vacuum. The "contact ageing" effect is attributed to atomic attrition and is eventually broken by thermally activated slip of the nanoasperity on the surface. The combination of the two effects also leads to regions of strengthening and weakening in the velocity dependence of the friction, which are well-reproduced by an extended version of the Prandtl-Tomlinson model.

A physical picture for mechanical dissociation of biological complexes: from forces to free energies.

Single-molecule force spectroscopy is a powerful technique based on the application of controlled forces to macromolecules. In order to relate the measured response of the molecule to its equilibrium and dynamic properties, a suitable physical picture of the involved process is necessary. In this work, we introduce a plausible model for mechanical unbinding of some molecular complexes, based on a novel free energy profile.

Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters.

The identification of protein binding sites in promoter sequences is a key problem to understand and control regulation in biochemistry and biotechnological processes. We use a computational method to analyze promoters from a given genome. Our approach is based on a physical model at the mesoscopic level of protein-DNA interaction based on the influence of DNA local conformation on the dynamics of a general particle along the chain.

Quantum chaos in an ultrastrongly coupled bosonic junction.

The semiclassical and quantum dynamics of two ultrastrongly coupled nonlinear resonators cannot be explained using the discrete nonlinear Schrödinger equation or the Bose-Hubbard model, respectively. Instead, a model beyond the rotating wave approximation must be studied. In the semiclassical limit this model is not integrable and becomes chaotic for a finite window of parameters.

Noise-induced enhancement of stability in a metastable system with damping.

The mean first passage time of a Brownian particle from an initial unstable state in a metastable system with damping is investigated. The system is analyzed in the low to high damping regime, and the role played by the damping parameter is studied. We observe the noise enhanced stability effect for all the initial unstable states under study and for all values of the damping parameter γ investigated.

Translocation time of periodically forced polymer chains.

In this work we study the presence of both a minimum and clear oscillations in the frequency dependence of the translocation time of a polymer described as a unidimensional Rouse chain driven by a spatially localized oscillating linear potential. The observed oscillations of the mean translocation time arise from the synchronization between the very mean translocation time and the period of the external force. We have checked the robustness of the frequency value for the minimum translocation time by changing the damping parameter, finding a very simple relationship between this frequency and the correspondent translocation time.