Force-extension behavior of folding polymers.

A novel approach in geometrical-mechanical analysis of plain woven fabrics; Initial load-extension behavior

Monte Carlo simulation for single RNA unfolding by force.

Using polymer elastic theory and known RNA free energies, we construct a Monte Carlo algorithm to simulate the single RNA folding and unfolding by mechanical force on the secondary structure level. For the constant force ensemble, we simulate the force-extension curves of the P5ab, P5abc deltaA, and P5abc molecules in equilibrium. For the constant extension ensemble, we focus on the mechanical ...

Exploring the folding pattern of a polymer chain in a single crystal by combining single-molecule force spectroscopy and steered molecular dynamics simulations.

Understanding the folding pattern of a single polymer chain within its single crystal will shed light on the mechanism of crystallization. Here, we use the combined techniques of atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations to study the folding pattern of a polyethylene oxide (PEO) chain in its single crystal. Our...

Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes.

The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated by using single-molecule force-clamp experiments by attaching semiflexible polymers to the ends of hairpins, have been used to infer their folding landscapes. Using simulations and theory, we study the effect of the dynamics of the attached h...

Thermodynamics of force-dependent folding and unfolding of small protein and nucleic acid structures.

In this paper, we outline the theoretical framework for understanding the equilibrium force-dependent folding and unfolding transitions of protein domains and small nucleic acid structures, both having small rigid folded structures and highly flexible unfolded polymeric chain conformations. A complete statistical description of the state described by the probability function ρ(ξ)(n,x), is obtai...