We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show that the sedimentation coefficient s, related to the terminal velocity of the knotted polymers, increases linearly with the average crossing number n(c) of the corresponding ideal knot. This provides direct computational confirmation of this relation, postulated on the basis of sedimentation experiments by Rybenkov et al. [J. Mol. Biol. 267, 299 (1997)]. Such a relation was previously shown to hold with simulations for knot electrophoresis. We also show that there is an accurate linear dependence of s on the inverse of the radius of gyration R(g)(-1), more specifically with the inverse of the R(g) component that is perpendicular to the direction along which the polymer sediments. When the polymer sediments in a slab, the walls affect the results appreciably. However, R(g)(-1) remains to a good precision linearly dependent on n(c). Therefore, R(g)(-1) is a good measure of a knot's complexity.
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http://dx.doi.org/10.1103/PhysRevE.87.012728 | DOI Listing |
Angew Chem Int Ed Engl
January 2025
Shanghai Key Lab of Chemical Assessment and Sustainability, School of Chemical Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
The synthesis of crystalline covalent organic frameworks (COFs) has in principle relied on reversible dynamic chemistry. A general method to synthesize irreversibly bonded COFs is urgently demanded for driving the COF chemistry to a new era. Here we report a universal two-step method for the straightforward synthesis of irreversibly amide-linked COF (AmCOF) membranes by autocatalytic interfacial polymerization (AIP).
View Article and Find Full Text PDFJ Chem Phys
December 2024
Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA.
Molecular dynamics calculations have been used to explore the influence of knots on the strength of a polymer strand. In particular, the mechanism of breaking 31, 41, 51, and 52 prime knots has been studied using two very different models to represent the polymer: (1) the generic coarse-grained (CG) bead model of polymer physics and (2) a state-of-the-art machine learned atomistic neural network (NN) potential for polyethylene derived from electronic structure calculations. While there is a broad overall agreement between the results on the influence of the pulling rate on chain rupture based on the CG and atomistic NN models, for the simple 31 and 41 knots, significant differences are found for the more complex 51 and 52 knots.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Johannes Gutenberg-Universität, Institut für Physik, Mainz, Germany.
Sci Adv
November 2024
National Laboratory of Solid State Microstructures and School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China.
Macromolecules can gain special properties by adopting knotted conformations, but engineering knotted macromolecules is a challenging task. Here, we unexpectedly find that knots can be efficiently generated in active polymer systems. When one end of an actively reptative polymer is anchored, it undergoes continual self-knotting as a result of intermittent giant conformation fluctuations and the outward reptative motion.
View Article and Find Full Text PDFBiomacromolecules
December 2024
Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
We prepared biocompatible elastic fibers with high porosity and high tensile strength from poly[()-3-hydroxybutyrate--4-hydroxybutyrate], which is a microbial polyester that can be produced from renewable carbon resources by isothermal crystallization. It was possible to control the pore size by adjusting the isothermal crystallization time. Most of the pores were approximately less than 10 μm in diameter, did not penetrate, and were distributed discontinuously throughout the fibers.
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