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Register a new userThe conformation of a semiflexible filament in a quenched random potential
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Motivated by the observation of the storage of excess elastic free energy - (prestress) -- in cross linked semiflexible networks, we consider the problem of the conformational statistics of a single semiflexible polymer in a quenched random potential. The random potential, which represents the effect of cross linking to other filaments is assumed to have a finite correlation length $xi$ and mean strength $V_{0}$. We examine statistical distribution of curvature in filament with thermal persistence length $ell_{P}$ and length $L_0$ in the limit that $ell_{P} gg L_0$. We compare our theoretical predictions to finite element Brownian dynamics simulations. Lastly we comment on the validity of replica field techniques in addressing these questions.
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We study the effect of quenched randomness in the arc-length dependent spontaneous curvature of a wormlike chain under tension. In the weakly bending approximation in two dimensions, we obtain analytic results for the force-elongation curve and the width of transverse fluctuations. We compare quenched and annealed disorder and conclude that the former cannot always be reduced to a simple change in the stiffness of the pure system. We also discuss the effect of a random transverse force on the stretching response of a wormlike chain without spontaneous curvature.
We examine the nonequilibrium production of topological defects -- braids -- in semiflexible filament bundles under cycles of compression and tension. During these cycles, the period of compression facilitates the thermally activated pair production of braid/anti-braid pairs, which then may separate when the bundle is under tension. As result, appropriately tuned alternating periods of compression and extension should lead to the proliferation of braid defects in a bundle so that linear density of these pairs far exceeds that expected in thermal equilibrium. Secondly, we examine the slow extension of braided bundles under tension, showing that their end-to-end length creeps nonmonotonically under a fixed force due to braid deformation and the motion of the braid pair along the bundle. We conclude with a few speculations regarding experiments on semiflexible filament bundles and their networks.
Single-filament tracing has been a valuable tool to directly determine geometrical and mechanical properties of entangled polymer networks. However, systematically verifying how the stiffness of the tracer filament or its molecular interactions with the surrounding network impacts the measurement of these parameters has not been possible with the established experimental systems. Here, we use mechanically programmable DNA nanotubes embedded in crosslinked and entangled F-actin networks, as well as in synthetic DNA networks, in order to measure fundamental, structural network properties like tube width and mesh size with respect to the stiffness of the tracers. While we confirm some predictions derived from models based purely on steric interactions, our results indicate that these models should be expanded to account for additional inter-filament interactions, thus describing the behavior of real polymer networks.
We construct a dynamical field theory for noninteracting Brownian particles in the presence of a quenched Gaussian random potential. The main variable for the field theory is the density fluctuation which measures the difference between the local density and its average value. The average density is spatially inhomogeneous for given realization of the random potential. It becomes uniform only after averaged over the disorder configurations. We develop the diagrammatic perturbation theory for the density correlation function and calculate the zero-frequency component of the response function exactly by summing all the diagrams contributing to it. From this exact result and the fluctuation dissipation relation, which holds in an equilibrium dynamics, we find that the connected density correlation function always decays to zero in the long-time limit for all values of disorder strength implying that the system always remains ergodic. This nonperturbative calculation relies on the simple diagrammatic structure of the present field theoretical scheme. We compare in detail our diagrammatic perturbation theory with the one used in a recent paper [B. Kim, M. Fuchs and V. Krakoviack, J. Stat. Mech. (2020) 023301], which uses the density fluctuation around the uniform average, and discuss the difference in the diagrammatic structures of the two formulations.
We present a model for semiflexible polymers in Hamiltonian formulation which interpolates between a Rouse chain and worm-like chain. Both models are realized as limits for the parameters. The model parameters can also be chosen to match the experimental force-extension curve for double-stranded DNA. Near the ground state of the Hamiltonian, the eigenvalues for the longitudinal (stretching) and the transversal (bending) modes of a chain with N springs, indexed by p, scale as lambda_lp ~ (p/N)^2 and lambda_tp ~ p^2(p-1)^2/N^4 respectively for small p. We also show that the associated decay times tau_p ~ (N/p)^4 will not be observed if they exceed the orientational time scale tau_r ~ N^3 for an equally-long rigid rod, as the driven decay is then washed out by diffusive motion.
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