Unravelling looping efficiency of stochastic Cosserat polymers

TL;DR

This paper develops analytical methods to compute looping probabilities of stochastic Cosserat polymers, like DNA, revealing high cyclization probabilities in stiff regimes and providing efficient approximations validated by simulations.

Contribution

It introduces a novel analytical framework using path integrals and Gaussian approximations for Cosserat rods, improving understanding of looping in short, stiff polymers.

Findings

High cyclization probabilities in stiff regimes due to shear and extension effects

Analytical approximations align well with Monte Carlo simulations

Path integral approach offers new insights into Goldstone modes in polymer looping

Abstract

Understanding looping probabilities, including the particular case of ring-closure or cyclization, of fluctuating polymers (eg DNA) is important in many applications in molecular biology and chemistry. In a continuum limit the configuration of a polymer is a curve in the group SE(3) of rigid body displacements, whose energy can be modelled via the Cosserat theory of elastic rods. Cosserat rods are a more detailed version of the classic wormlike-chain (WLC) model, which we show to be more appropriate in short-length scale, or stiff, regimes, where the contributions of extension and shear deformations are not negligible and lead to noteworthy high values for the cyclization probabilities (or J-factors). Characterizing the stochastic fluctuations about minimizers of the energy by means of Laplace expansions in a (real) path integral formulation, we develop efficient analytical approximations for the two cases of full looping, in which both end-to-end relative translation and rotation are prescribed, and of marginal looping probabilities, where only end-to-end translation is prescribed. For isotropic Cosserat rods, certain looping boundary value problems admit non-isolated families of critical points of the energy due to an associated continuous symmetry. For the first time, taking inspiration from (imaginary) path integral techniques, a quantum mechanical probabilistic treatment of Goldstone modes in statistical rod mechanics sheds light on J-factor computations for isotropic rods in the semi-classical context. All the results are achieved exploiting appropriate Jacobi fields arising from Gaussian path integrals, and show good agreement when compared with intense Monte Carlo simulations for the target examples.