Nonequilibrium dynamics of polymer translocation and straightening

Abstract

When a flexible polymer is sucked into a localized small hole, the chain can initially respond only locally and the sequential nonequilibrium processes follow in line with the propagation of the tensile force along the chain backbone. We analyze this dynamical process by taking the nonuniform stretching of the polymer into account both with and without hydrodynamics interactions. Earlier conjectures on the absorption time are criticized and new formulae are proposed together with time evolutions of relevant dynamical variables.

Dynamics of Polymer Decompression: Expansion, Unfolding, and Ejection

“…However, the origin of this scaling is unclear. Indeed, it was proposed as a translocation time of a polymer driven by strong and constant ∆µ [20], which would be asymptotically valid in the limit of the strong driving force [21]. In the present case of the ejection, ∆µ is far below such an asymptote and gradually decreases with the process advanced.…”

“…In contrast, in the ejection process from a closed cavity, both the elastic modulus and the driving force are dictated by the mesh size ξ. In the former case, the entire chain cannot respond to the ejection force acting on a particular monomer residing at the pore immediately, and the highly nonequilibrium process of the front evolution associated with the tension propagation along the chain would occur [21], while in the latter, the pressure drop is transmitted not along the chain, but radially from the pore. These differences in the underlying physics are indeed a consequence of the different confinement regimes [13,14].…”

Driven translocation of a polymer: Fluctuations at work

“…This scenario has been treated within the linear response theory (that is, for relatively weak driving forces) and the corresponding memory function has been derived explicitly [7,8]. For arbitrary strong driving forces, an interesting approach based on the notion of tensile force propagation along the chain backbone has been suggested by Sakaue [9][10][11]. Sakaue's idea has been used and worked out very recently in other theoretical treatments [12,13].…”

“…It is important to determine the origin of this inconsistency since apparently there is something missing in the aforementioned theoretical consideration which gives room for speculations. For example, in a paper by Ikonen et al [12], the model based on the idea of tensile force propagation [9][10][11] and the role of pore-polymer friction has been numerically investigated. The authors argue that the theoretical value for the exponent, α = 1 + ν, may be seen only for very long chains whereas for the chain lengths used in real experiments or simulations the effective exponent α could be approximately 20% smaller.…”

“…Recently [13] we suggested a theoretical description based on the tensile (Pincus) blob picture of a pulled chain and the notion of a tensile force propagation, introduced by Sakaue [9][10][11]. Assuming that the local driving force is matched by a drag force of equal magnitude, (i.e., in a quasistatic approximation), we derived an equation of motion for the tensile front position.…”