Related papers: Changing the mechanical unfolding pathway of FnIII…
Although known that single domain proteins fold and unfold by parallel pathways, demonstration of this expectation has been difficult to establish in experiments. Unfolding rate, $k_\mathrm{u}(f)$, as a function of force $f$, obtained in…
Heterostructures of two-dimensional (2D) layered materials with selective compositions play an important role in creating novel functionalities. Effective interface coupling between 2D ferromagnet and electronic materials would enable the…
We present a theoretical and numerical study of Fourier space triad phase dynamics in one-dimensional stochastically forced Burgers equation at Reynolds number $\mathrm{Re} \approx 2.7 \times 10^4$. We demonstrate that Fourier triad phases…
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…
Recent years have seen tremendous progress in experimental techniques to create uniaxial strain. Motivated by these advances we investigate the effect of uniaxial strain on LaMnO$_3$ employing ab-initio dynamical mean-field theory, and put…
Mechanical unfolding trajectories, generated by applying constant force in optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of the group I intron unfold reversibly. We use coarse-grained Go-like models for RNA…
Mechanical displacement in commonly used piezoelectric materials is typically restricted to linear or biaxial in nature and to a few percent of the material dimensions. Here, we show that free-standing BaTiO$_3$ membranes exhibit…
Creating new interfacial magnetic states with desired functionalities is attractive for fundamental studies and spintronics applications. The emergence of interfacial magnetic phases demands the fabrication of pristine interfaces and the…
Interfacial magnetism stimulates the discovery of giant magnetoresistance and spin-orbital coupling across the heterointerfaces, facilitating the intimate correlation between spin transport and complex magnetic structures. Over decades,…
The Metropolis Monte Carlo (MC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins - a model…
Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative…
A simple model for the force-dependent unwinding and rewinding rates of the nucleosome inner turn is constructed and quantitatively compared to the results of recent measurements [A. H. Mack et al., J. Mol. Biol. 423, 687 (2012)]. First, a…
The evolution of a crack front under mixed mode loading (I+III) is studied using a phase field model in 3 dimensions with no stress boundary conditions. As previously observed experimentally in gels, there is a relaxation toward a geometry…
Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…
The unfolding of a polymer below the $\theta$ point when pulled by an external force is studied both in d=2 on the lattice and in $d=3$ off lattice. A ground state analysis of finite length chains shows that the globule unfolds via multiple…
Self-positioned nanomembranes such as rolled-up tubes and wrinkled thin films have been potential systems for a variety of applications and basic studies on elastic properties of nanometer-thick systems. Although there is a clear driving…
We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting…
Using coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of $f_S$ and the loading rate ($r_f$). The simulations and theoretical analysis have been done without and with the handles that are explicitly…
We discuss steady state crack growth in the spirit of a free boundary problem. It turns out that mode I and mode III situations are very different from each other: In particular, mode III exhibits a pronounced transition towards unstable…