Accuracy of the blob model for single flexible polymers inside nanoslits that are a few monomer sizes wide

Abstract

The de Gennes' blob model is extensively used in different problems of polymer physics. This model is theoretically applicable when the number of monomers inside each blob is large enough. For confined flexible polymers, this requires the confining geometry to be much larger than the monomer size. In this paper, the opposite limit of polymer in nanoslits with one to several monomers width is studied, using molecular dynamics simulations. Extension of the polymer inside nanoslits, confinement force on the plates, and the effective spring constant of the confined polymer are investigated. Despite the theoretical limitations of the blob model, the simulation results are explained with the blob model very well. The agreement is observed for the static properties and the dynamic spring constant of the polymer. A theoretical description of the conditions under which the dynamic spring constant of the polymer is independent of the small number of monomers inside blobs is given. Our results on the limit of applicability of the blob model can be useful in the design of nanotechnology devices.

Entropic force of cone-tethered polymers interacting with a planar surface

“…Confinement of a polymer chain to a sufficiently small space distorts its shape, leading to a significant reduction in its conformational entropy and thus an increase in its free energy. The effects of confinement on single-polymer conformational statistics has been the subject of numerous theoretical and computational studies, which have examined variety of confinement geometries, including cavities, 1-4 channels, [5][6][7][8][9] slits, [10][11][12][13][14] as well as more complex geometries. 15,16 Most relevant to the present work is the case of a polymer confined to a slit between two parallel hard walls.…”

“…15,16 Most relevant to the present work is the case of a polymer confined to a slit between two parallel hard walls. [11][12][13][14] These studies have characterized the scaling of the molecular dimensions and free energy with respect to confinement dimension, contour length and persistence length. Distinct scaling regimes such as the de Gennes, extended de Gennes and Odijk regimes have been identified, and some predictions have been verified by experiments employing fluorescently labeled DNA molecules confined to nanoslits.…”

A flexible polymer confined inside a cone-shaped nano-channel

“…To date, biological nano-channels have been used for DNA sequencing purposes; while solid-state nano-pores are of interest as a tool for single-molecule studies. 21 and references therein). 12 When DNA passes through the cylindrical part of the a-hemolysin channel, the ionic current through the channel depends on 10-15 nucleotides that reside inside the channel.…”

“…20 Polymers confined near surfaces and inside different geometries such as cylindrical and cone-shaped nano-channels, nano-slits and nano-spheres have been studied (ref. 21 and references therein). Generally, confinement reduces the number of possible configurations of the polymer and causes its entropy to decrease.…”

Torque-Induced Rotational Dynamics in Polymers: Torsional Blobs and Thinning

“…The blob model has been applied to many other equilibrium problems in polymer physics, for instance in modeling dense melts, 10 polyelectrolytes stretched by an applied force, 12,13 polymers and biopolymers confined in nano-channels [14][15][16] and polymers adsorbed to surfaces. 17 The blob model also provides a powerful tool to study polymer dynamics, a paradigmatic example being a polymer pulled by one end [18][19][20][21][22][23] (briefly reviewed in the following section).…”