Related papers: Tightening the knot in phytochrome by single molec…
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 interpretated by…
The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…
Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed…
Single-molecule FRET is widely used to study helicases by detecting distance changes between a fluorescent donor and an acceptor anchored to overhangs of a forked DNA duplex. However, it has lacked single-base pair (1-bp) resolution…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
Mechanically induced protein unfolding in the force-clamp apparatus is shown, in a coarse-grained model of ubiquitin, to have lognormal statistics above a treshold force and exponential below it. Correspondingly, the mean unfolding time is…
Amino acids are essential to all life. However, our understanding of some aspects of their intrinsic structure, molecular chemistry, and electronic structure is still limited. In particular the nature of amino acids in their crystalline…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
We investigate the sliding strength of thin filaments in frictional contact with a translating cylinder, perpendicular to the filaments' axes, in knotted (clove hitch) and unknotted (capstan) configurations. Recent work reported superlinear…
Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
We develop a theoretical description of the topological disentanglement occurring when torus knots reach the ends of a semi-flexible polymer under tension. These include decays into simpler knots and total unknotting. The minimal number of…
We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the…
We present a theoretical analysis of the structural and mechanical properties of the 30-nm chromatin fiber. Our study is based on the two-angle model introduced by Woodcock et al. (Woodcock, C. L., S. A. Grigoryev, R. A. Horowitz, and N.…
We propose a simple approach, based on the minimization of the total (entropic plus unfolding) energy of a two-state system, describing the stretch-induced unfolding of macromolecules (proteins, silks, nanopolymers, DNA/RNA). The model is…
We report here that atomic force microscope (AFM) in frictional force mode can be used to detect onset of chain scission and crosslinking in polymeric and macromolecular samples upon irradiation. A systematic investigation to detect chain…
One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive…