Effect of simple shear on knotted polymer coils and globules

被引：0
作者：
Milchev, Andrey [1 ]
Schmitt, Maurice P. [2 ]
Virnau, Peter [2 ]
机构：
[1] Bulgarian Acad Sci, Inst Phys Chem, Sofia 1113, Bulgaria
[2] Johannes Gutenberg Univ Mainz, Inst Phys, Mainz, Germany
来源：
JOURNAL OF CHEMICAL PHYSICS | 2024年 / 161卷 / 22期
关键词：
DYNAMICS SIMULATIONS; DNA; COLLAPSE; PROBABILITY; SOLVENT; CHAINS; MODEL; STATE; SOFT;
D O I：
10.1063/5.0236904
中图分类号：
O64 [物理化学（理论化学）、化学物理学];
学科分类号：
070304 ; 081704 ;
摘要：
We explore the effect of Couette flow on knotted linear polymer chains with extensive molecular dynamics simulations. Hydrodynamic interactions are accounted for using multi-particle collision dynamics. The polymer chain, originally containing a simple trefoil knot at rest, is described by a coarse-grained bead-spring model in a coil or globular state. We demonstrate that under shear existing loosely localized knots in polymer coils typically tighten to several segments beyond a certain shear rate threshold. At large shear rates, the polymer undergoes a tumbling-like motion during which knot sizes can fluctuate. In contrast, sheared knotted globules unwind into a convoluted pearl-necklace structure of sub-globules that folds back onto itself and in which knot types change over time.
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页数：8
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共 62 条
  • [1] Micheletti C., Marenduzzo D., Orlandini E., Polymers with spatial or topological constraints: Theoretical and computational results, Phys. Rep., 504, pp. 1-73, (2011)
  • [2] Tubiana L., Et al., Topology in soft and biological matter, Phys. Rep., 1075, pp. 1-137, (2024)
  • [3] Arsuaga J., Vazquez M., Trigueros S., Sumners D.W., Roca J., Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids, Proc. Natl. Acad. Sci. U. S. A., 99, pp. 5373-5377, (2002)
  • [4] Arsuaga J., Vazquez M., McGuirk P., Trigueros S., Sumners D.W., Roca J., DNA knots reveal a chiral organization of DNA in phage capsids, Proc. Natl. Acad. Sci. U. S. A., 102, pp. 9165-9169, (2005)
  • [5] Marenduzzo D., Orlandini E., Stasiak A., Sumners D.W., Tubiana L., Micheletti C., DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting, Proc. Natl. Acad. Sci. U. S. A., 106, pp. 22269-22274, (2009)
  • [6] Plesa C., Verschueren D., Pud S., van der Torre J., Ruitenberg J.W., Witteveen M.J., Jonsson M.P., Grosberg A.Y., Rabin Y., Dekker C., Direct observation of DNA knots using a solid-state nanopore, Nat. Nanotechnol., 11, pp. 1093-1097, (2016)
  • [7] Kumar Sharma R., Agrawal I., Dai L., Doyle P.S., Garaj S., Complex DNA knots detected with a nanopore sensor, Nat. Commun., 10, (2019)
  • [8] Taylor W.R., A deeply knotted protein structure and how it might fold, Nature, 406, pp. 916-919, (2000)
  • [9] Virnau P., Mirny L.A., Kardar M., Intricate knots in proteins: Function and evolution, PLoS Comput. Biol., 2, (2006)
  • [10] Potestio R., Micheletti C., Orland H., Knotted vs. unknotted proteins: Evidence of knot-promoting loops, PLoS Comput. Biol., 6, (2010)
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