Related papers: Direction dependent mechanical unfolding and Green…
We study the tilt dependence of the pinning-depinning transition for an interface described by the anisotropic quenched Kardar-Parisi-Zhang equation in 2+1 dimensions, where the two signs of the nonlinear terms are different from each…
We numerically investigate the electronic transport properties between two mesoscopic graphene disks with a twist by employing the density functional theory coupled with non-equilibrium Green's function technique. By attaching two graphene…
How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…
We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding/refolding force distributions of an RNA hairpin pulled at different loading rates using…
We show that the critical behavior of a driven interface, depinned from quenched random impurities, depends on the isotropy of the medium. In anisotropic media the interface is pinned by a bounding (conducting) surface characteristic of a…
The thesis examines in detail the folding and unfolding processes of a number of proteins including hbSBD, DDLNF4, single and multi Ubiquitin. Using simplified coarse-grained off-lattice Go model and CD experiments we have shown the…
Mechatronic systems have increasingly stringent performance requirements for motion control, leading to a situation where many factors, such as position-dependency, cannot be neglected in feedforward control. The aim of this paper is to…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
A feed-forward neural network is demonstrated to efficiently unfold the energy distribution of protons and alpha particles passing through passive material. This model-independent approach works with unbinned data and does not require…
Using self-organized polymer models, we predict mechanical unfolding and refolding pathways of ribo-zymes, and the green fluorescent protein. In agreement with experiments, there are between six and eight unfolding transitions in the…
A shearing interferometer is presented which uses polarization control to shear the wavefront and to modulate the interference pattern. The shear is generated by spatial walk-off in a birefringent crystal. By adjusting the orientation of…
The interrogation of a sensor based on a highly birefringent film irradiated by an incident beam whose polarization is oriented 45o with respect to the normal film axes is shown to display exceptional features and resolve some outstanding…
The trajectory of light rays propagating through a nonuniformly moving anisotropic medium is determined by considering the Fresnel drag experienced by the wave at each point along the ray. By showing that symmetries in the velocity field…
We explicitly show the connection between the protein folding problem and spin glass transition. This is then used to identify appropriate quantities that are required to describe the transition. A possible way of observing the spin glass…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
A pinned-free beam in axial fluid flow, subjected to feedback-based actuation at the pinned end, is investigated. The actuation may be a moment or a prescribed angle and it is proportional to the state (curvature, slope, or displacement) of…