Dynamical intermediates in the collapse of semiflexible polymers in poor solvents

PACS. 87.15.-v – Biomolecules: structure and physical properties. Abstract. – We investigate, by a Brownian Dynamics (BD) simulation, the collapse of a single, semiflexible or stiff polymer in solution, in the presence of short-range, attractive interactions. In contrast to the mechanism for flexible chains, our results suggest that the collapse occurs via a series of long-lived, metastable intermediates. These intermediates form a well-defined, hierarchical family of conformations. Experiments with DNA condensation have shown similar shapes, which were described as “tennis racquets”. In addition to our primary observation concerning the collapse pathways of stiff filaments, we note that, in the absence of fluctuations (upon annealing), the shape of these intermediates can be calculated exactly in certain limits, and is given by a particular case of Euler’s elastica. This shape is unique up to an overall scale factor determined by the parameters for bending stiffness and short-range attraction. One of the most basic properties of an isolated polymer chain is its size and shape under various solvent conditions [1–3]. For completely flexible chains in good solvent the monomers effectively repel one another, favoring contact with the solvent, and a swollen coil is formed. In poor solvent the monomers attract one another, and an isolated chain forms a compac