Universality in conformations and transverse fluctuations of a semi-flexible polymer in a crowded environment

Abstract

We study universal aspects of polymer conformations and transverse fluctuations for a single swollen chain characterized by a contour length $L$ and a persistence length $\ell_p$ in two dimensions (2D) and in three dimensions (3D) in the bulk, as well as in the presence of excluded volume (EV) particles of different sizes occupying different volume fractions. In the absence of the EV particles we extend the previously established universal scaling relations in 2D (A. Huang, A. Bhattacharya, and K. Binder, J. Chem. 140, 214902 (2014)) to include 3D and demonstrate that the scaled end-to-end distance $\langle R_N^2\rangle/(2 L\ell_p)$ and the scaled transverse fluctuation $\sqrt{\langle{l_{\perp}^2}\rangle}/{L}$ as a function of $L/\ell_p$ collapse onto the same master curve, where $\langle R_N^2\rangle$ and $\langle{l_{\perp}^2\rangle}$ are the mean-square end-to-end distance and transverse fluctuations. However, unlike in 2D, where the Gaussian regime is absent due to extreme dominance of the EV interaction, we find the Gaussian regime is present, albeit very narrow in 3D. The scaled transverse fluctuation in the limit $L/\ell_p \ll 1$ is independent of the physical dimension and scales as $\sqrt{\langle{l_{\perp}^2}\rangle}/{L} \sim (L/\ell_p)^{ζ-1}$, where $ζ= 1.5$ is the roughening exponent. For $L/\ell_p \gg 1$ the scaled fluctuation scales as $\sqrt{\langle{l_{\perp}^2}\rangle}/{L} \sim (L/\ell_p)^{ν-1}$, where $ν$ is Flory exponent for the corresponding spatial dimension ($ν_{2D}=0.75$, and $ν_{3D}=0.58$). When EV particles are added into the system, our results indicate that the crowding density either does not or only weakly affects the universal scaling relations. We discuss the implications of these results in living matter by showing the experimental result for a dsDNA onto the master plot.