Abstract
We consider semiflexible chains governed by preferred curvature and twist and their flexural and twist moduli. These filaments possess a helical rather than straight three-dimensional (3D) ground state and we call them helical filaments (H-filament). Depending on the moduli, the helical shape may be smeared by thermal fluctuations. Secondary superhelical structures are expected to form on top of the specific local structure of biofilaments, as is documented for vimentin. We study confinement and adsorption of helical filaments utilizing both a combination of numerical simulations and analytical theory. We investigate overall chain shapes, transverse chain fluctuations, loop and tail distributions, and energy distributions along the chain together with the mean square average height of the monomers . The number fraction of adsorbed monomers serves as an order parameter for adsorption. Signatures of adsorbed helical polymers are the occurrence of 3D helical loops/tails and spiral or wavy quasi-flat shapes. None of these arise for the Worm-Like-Chain, whose straight ground state can be embedded in a plane.
Highlights
When a large macromolecule is attracted towards an adsorbing wall by a short range surface force field acting along its contour, cooperative adsorption can take place [1]
Helical loops/tails and spiral or wavy quasi-flat shapes. None of these arise for the Worm-Like-Chain, whose straight ground state can be embedded in a plane
The molecules considered here have helical radii larger than the filament diameter and are called superhelical filaments (Figure 1). This is different from double-stranded DNA in the B-form [6] and the Holmes helix of actin [7]
Summary
When a large macromolecule is attracted towards an adsorbing wall by a short range surface force field acting along its contour, cooperative adsorption can take place [1]. Actin [19] and vimentin [20] filaments were studied under double confinement in microfluidics channels and manifest shapes unexpected for WLCs. The more precise images of vimentin have delivered data that have been successfully fitted [21] by the helical filament model. When F-actin is confined close to a wall by depleting agents, short circular actin filaments are detected with a much larger abundance than expected from the WLC model [22,23] Adsorption is a competition between gain in interaction energy upon flattening into the surface potential and cost of confinement free energy to do so In this contribution, we study the equilibrium characteristics of an adsorbed helical filament combining numerical simulations and analytical theory.
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