Different pathways in mechanical unfolding/folding cycle of a single semiflexible polymer

Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations

We study the conformational dynamics within homopolymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength ε and the globule size N (G) is observed. We find two distinct dynamical regimes: a liquid-like regime (for ε < ε(s) with fast internal dynamics and a solid-like regime (for ε > ε(s) with slow internal dynamics. The cohesion strength ε(s) of this freezing transition depends on N (G) . Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with ε and scales extensive in N (G) . This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.

Linear viscoelasticity of a single semiflexible polymer with internal friction

The linear viscoelastic behaviors of single semiflexible chains with internal friction are studied based on the wormlike-chain model. It is shown that the frequency dependence of the complex compliance in the high frequency limit is the same as that of the Voigt model. This asymptotic behavior appears also for the Rouse model with internal friction. We derive the characteristic times for both the high frequency limit and the low frequency limit and compare the results with those obtained by Khatri et al.

Internal friction and nonequilibrium unfolding of polymeric globules

The stretching response of a single collapsed homopolymer is studied using Brownian dynamic simulations. The irreversibly dissipated work is found to be dominated by internal friction effects below the collapse temperature, and the internal viscosity grows exponentially with the effective cohesive strength between monomers. These results explain friction effects of globular DNA and are relevant for dissipation at intermediate stages of protein folding.

Folding and unfolding kinetics of a single semiflexible polymer

We investigate theoretically the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decreases with an increase in the number of monomers in the collapsed domain, suggesting that the main contribution to dissipation is from the motion of the domain. In the unfolding transition, the dynamic scaling exponents 1/8 and 1/4 were determined for the disentanglement and relaxation steps, respectively. We performed Langevin dynamics simulations to test our theory. It is found that our theory is in good agreement with simulations. We also propose the kinetics of the transitions in the presence of a hydrodynamic interaction.

Core-shell structures in single flexible-semiflexible block copolymers: Finding the free energy minimum for the folding transition

We investigate the folding transition of a single diblock copolymer consisting of a semiflexible and a flexible block. We obtain a Saturn-shaped core-shell conformation in the folded state, in which the flexible block forms a core and the semiflexible block wraps around it. We demonstrate two distinctive features of the core-shell structures: (i) The kinetics of the folding transition in the copolymer are significantly more efficient than those of a semiflexible homopolymer. (ii) The core-shell structure does not depend on the transition pathway.