Eur. Phys. J. E (2010) 32: 273-279
https://doi.org/10.1140/epje/i2010-10626-y

Regular Article

Shape transition of semi-flexible macromolecules confined in channel and cavity

Polymer Institute, Slovak Academy of Sciences, 842 36, Bratislava, Slovakia

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Received: 13 April 2010
Accepted: 17 June 2010
Published online: 27 July 2010

Abstract

Stiff macromolecules entrapped in channels or in spherical cavities undergo a shape transition on increasing confinement as shown by our investigation using molecular simulations. In channels this weak-to-strong confinement transition leads to extended conformations without the hairpin-like back-folding. In cavities, on decrease of cavity radius, the semi-flexible chain in a disordered state starts to self-organize into the torus. As a common rule for both types of confinement the transition to the ordered structures is observed when the radius of cavity and cylindrical channel reaches the lower bound of macromolecular flexibility given by the average typical radius of curvature of the chain, which is approximately equal to the persistence length of the macromolecular chain. This simple geometric rule finds its application in various confinement situations of stiff bio-macromolecules either in micro-channel experiments or in real biophysical situation, such as DNA in viral capsid.