In this paper, the stability characteristics of single-walled carbon nanotubes (SWCNTs) under the action of axial load are investigated. To this end, a nonlocal Flügge shell model is developed to accommodate the small length scale effects. The analytical Rayleigh-Ritz method with beam functions is applied to the variational statement derived from the Flügge-type buckling equations. Molecular dy...

The phosphate-binding loop (P-loop) is a conserved sequence motif found in mononucleotide-binding proteins. Little is known about the structural dynamics of this region and its contribution to the observed nucleotide binding properties. Understanding the underlying design principles is of great interest for biomolecular engineering applications. We have used rapid-kinetics measurements in vitro...

G-quadruplexes are attractive drug targets in cancer therapy. Understanding the mechanisms of the binding-unbinding processes involving biomolecules and molecular recognition is essential for designing new drugs of G-quadruplexes. We performed steered molecular dynamics and umbrella sampling simulations to investigate the molecular mechanism and kinetics of ligand unbinding processes of the bas...

In this paper, the stability characteristics of single-walled carbon nanotubes (SWCNTs) under the action of axial load are investigated. To this end, a nonlocal Flügge shell model is developed to accommodate the small length scale effects. The analytical Rayleigh-Ritz method with beam functions is applied to the variational statement derived from the Flügge-type buckling equations. Molecular dy...

Oxime drugs translocate through the 20 Å active-site gorge of acetylcholinesterase in order to liberate the enzyme from organophosphorus compounds' (such as tabun) conjugation. Here we report bidirectional steered molecular dynamics simulations of oxime drug (Ortho-7) translocation through the gorge of tabun intoxicated enzyme, in which time dependent external forces accelerate the translocatio...