In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very low thermodynamic stability, especially when the contact map used is too sparse. We consider six different structure-based models and show that allowing for a ...

Stirring of fluid with moving rods is necessary in many practical applications to achieve homogeneity. These rods are topological obstacles that force stretching of fluid elements. The resulting stretching and folding is commonly observed as filaments and striations, and is a precursor to mixing. In a space-time diagram, the trajectories of the rods form a braid, and the properties of this brai...

Unfolding of proteins by forced stretching with atomic force microscopy or laser tweezer experiments complements more classical techniques using chemical denaturants or temperature. Forced unfolding is of particular interest for proteins that are under mechanical stress in their biological function. For beta-sandwich proteins (a fibronectin type III and an immunoglobulin domain), both of which ...

The stretching response of a single collapsed homopolymer is studied using Brownian dynamic simulations. The irreversibly dissipated work is found to be dominated by internal friction effects below the collapse temperature, and the internal viscosity grows exponentially with the effective cohesive strength between monomers. These results explain friction effects of globular DNA and are relevant...

The Gō-like models of proteins are constructed based on the knowledge of the native conformation. However, there are many possible choices of a Hamiltonian for which the ground state coincides with the native state. Here, we propose to use experimental data on protein stretching to determine what choices are most adequate physically. This criterion is motivated by the fact that stretching proce...

We define metrics on Culler-Vogtmann space, which are an analogue of the Teichmüller metric and are constructed using stretching factors. In fact the metrics we study are related, one being a symmetrised version of the other. We investigate the basic properties of these metrics, showing the advantages and pathologies of both choices. We show how to compute stretching factors between marked metr...

RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpreted by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induc...

Tenascin, an important extracellular matrix protein, is subject to stretching force under physiological conditions and plays important roles in regulating the cell–matrix interactions. Using the recently developed single molecule force–ramp spectroscopy, we investigated the unfolding– folding kinetics of a recombinant tenascin fragment TNfnALL. Our results showed that all the 15 FnIII domains i...

Spontaneous folding of a polypeptide chain into a knotted structure remains one of the most puzzling and fascinating features of protein folding. The folding of knotted proteins is on the timescale of minutes and thus hard to reproduce with atomistic simulations that have been able to reproduce features of ultrafast folding in great detail. Furthermore, it is generally not possible to control t...