No Arabic abstract
The flow and deformation of macromolecules is ubiquitous in nature and industry, and an understanding of this phenomenon at both macroscopic and microscopic length scales is of fundamental and practical importance. Here we present the formulation of a general mathematical framework, which could be used to extract, from scattering experiments, the molecular relaxation of deformed polymers. By combining and modestly extending several key conceptual ingredients in the literature, we show how the anisotropic single-chain structure factor can be decomposed by spherical harmonics and experimentally reconstructed from its cross sections on the scattering planes. The resulting wavenumber-dependent expansion coefficients constitute a characteristic fingerprint of the macromolecular deformation, permitting detailed examinations of polymer dynamics at the microscopic level. We apply this approach to survey a long-standing problem in polymer physics regarding the molecular relaxation in entangled polymers after a large step deformation. The classical tube theory of Doi and Edwards predicts a fast chain retraction process immediately after the deformation, followed by a slow orientation relaxation through the reptation mechanism. This chain retraction hypothesis, which is the keystone of the tube theory for macromolecular flow and deformation, was critically examined by analyzing the fine features of the two-dimensional anisotropic spectra from small-angle neutron scattering by entangled polystyrenes. It is shown that the unique scattering patterns associated with the chain retraction mechanism were not experimentally observed. This result calls for a fundamental revision of the current theoretical picture for nonlinear rheological behavior of entangled polymeric liquids.
Drawing an analogy to the paradigm of quasi-elastic neutron scattering, we present a general approach for quantitatively investigating the spatiotemporal dependence of structural anisotropy relaxation in deformed polymers by using small-angle neutron scattering. Experiments and non-equilibrium molecular dynamics simulations on polymer melts over a wide range of molecular weights reveal that their conformational relaxation at relatively high momentum transfer $Q$ and short time can be described by a simple scaling law, with the relaxation rate proportional to $Q$. This peculiar scaling behavior, which cannot be derived from the classical Rouse and tube models, is indicative of a surprisingly weak direct influence of entanglement on the microscopic mechanism of single-chain anisotropy relaxation.
Evolving structure and rheology across Kuhn scale interfaces in entangled polymer fluids under flow play a prominent role in processing of manufactured plastics, and have numerous other applications. Quantitative tracking of chain conformation statistics on the Kuhn scale is essential for developing computational models of such phenomena. For this purpose, we formulate here a two-scale/two-mode model of entangled polymer chains under flow. Each chain is partitioned by successive entanglements into strands that are in one of two modes: entangled or dangling. On the strand scale, conformation statistics of ideal (non-interacting) strands follows a differential evolution equation for the second moment of its end-to-end distance. The latter regulates persistent random walks sampling conformation statistics of ideal entangled strands on the Kuhn scale, as follows from a generalized Green-Kubo relation and the Maximum Entropy Principle. We test it numerically for a range of deformation rates at the start-up of simple elongational and shear flows. A self-consistent potential, representing segmental interactions, modifies strand conformation statistics on the Kuhn scale, as it renormalizes the parameters controlling the persistent random walk. The generalized Green-Kubo relation is then inverted to determine how the second moment of the strand end-to-end distance is changed by the self-consistent potential. This allows us to devise a two-scale propagation scheme for the statistical weights of subchains of the entangled chain. The latter is used to calculate local volume fractions for each chemical type of Kuhn segments in entangled chains, thus determining the self-consistent potential.
We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are represented as freely diffusing beads which, upon encountering the substrate, bind to it through a short-ranged attractive potential. When bound, motors and polymer beads experience an equal and opposite active force, directed tangential to the polymer; this leads to motion of the motors along the polymer contour. The inclusion of explicit motors differentiates our model from other recent active polymer models. We study, by means of Langevin dynamics simulations, the effect of the motor activity on both the conformational and dynamical properties of the substrate. We find that activity leads, in addition to the expected enhancement of polymer diffusion, to an effective reduction of its persistence length. We discover that this effective softening is a consequence of the emergence of double-folded branches, or hairpins, and that it can be tuned by changing the number of motors or the force they generate. Finally, we investigate the effect of the motors on the probability of knot formation. Counter-intuitively our simulations reveal that, even though at equilibrium a more flexible substrate would show an increased knotting probability, motor activity leads to a marked decrease in the occurrence of knotted conformations with respect to equilibrium.
We study the conformational properties of charged polymers in a solvent in the presence of structural obstacles correlated according to a power law $sim x^{-a}$. We work within the continuous representation of a model of linear chain considered as a random sequence of charges $q_i=pm q_0$. Such a model captures the properties of polyampholytes -- heteropolymers comprising both positively and negatively charged monomers. We apply the direct polymer renormalization scheme and analyze the scaling behavior of charged polymers up to the first order of an $epsilon=6-d$, $delta=4-a$-expansion.
We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by a special three body interaction and impacts on the behaviour both locally and non-locally. When thick polymers undergo compaction due to an attractive self-interaction, we find a new type of phase transition between a compact phase and a swollen phase at zero temperature on increasing the thickness. In the vicinity of this transition, short tubes form space filling helices and sheets as observed in protein native state structures. Upon increasing the chain length, or the number of chains, we numerically find a crossover from secondary structure motifs to a quite distinct class of structures akin to the semi-crystalline phase of polymers or amyloid fibers in polypeptides.