Compression of a confined semiflexible polymer under direct and oscillating fields

被引:2
|
作者
Radhakrishnan, Keerthi [1 ]
Singh, Sunil P. [1 ]
机构
[1] Indian Inst Sci Educ & Res, Dept Phys, Bhopal 462066, Madhya Pradesh, India
关键词
MULTIPARTICLE COLLISION DYNAMICS; LONG DNA-MOLECULES; KNOTTING PROBABILITY; NUCLEIC-ACID; SIMULATION; KNOTS; ENTANGLEMENT; POLYELECTROLYTES; ELECTROPHORESIS; HYDRODYNAMICS;
D O I
10.1103/PhysRevE.108.014501
中图分类号
O35 [流体力学]; O53 [等离子体物理学];
学科分类号
070204 ; 080103 ; 080704 ;
摘要
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long biopolymers tend to collapse under an external field, which is contrary to the previously reported stretching of the chain. In this work, we capture the compression of a confined semiflexible polymer under direct and oscillating fields using a coarse-grained computer simulation model in the presence of long-range hydrodynamics. In the case of a semiflexible polymer chain, the inhomogeneous hydrodynamic drag from the center to the periphery of the coil couples with the chain bending to cause a swirling movement of the chain segments, leading to structural intertwining and compaction. Contrarily, a flexible chain of the same length lacks such structural deformation and forms a well-established tadpole structure. While bending rigidity profoundly influences the chain's folding favorability, we also found that subject to the direct field, chains in stronger confinements exhibit substantial compaction, contrary to the one in moderate confinements or bulk where such compaction is absent. However, an alternating field within an optimum frequency can effectuate this compression even in moderate or no confinement. This field-induced collapse is a quintessential hydrodynamic phenomenon, resulting in intertwined knotted structures even for shorter chains, unlike other spontaneous knotting experiments where it happens exclusively for longer chains.
引用
收藏
页数:11
相关论文
共 50 条
  • [1] Buckling a Semiflexible Polymer Chain under Compression
    Pilyugina, Ekaterina
    Krajina, Brad
    Spakowitz, Andrew J.
    Schieber, Jay D.
    POLYMERS, 2017, 9 (03):
  • [2] Semiflexible polymers under external fields confined to two dimensions
    Lamura, A.
    Winkler, R. G.
    JOURNAL OF CHEMICAL PHYSICS, 2012, 137 (24):
  • [3] Semiflexible polymer confined in closed spaces
    Sakaue, Takahiro
    MACROMOLECULES, 2007, 40 (14) : 5206 - 5211
  • [4] Semiflexible polymer confined to a spherical surface
    Spakowitz, AJ
    Wang, ZG
    PHYSICAL REVIEW LETTERS, 2003, 91 (16) : 166102 - 166102
  • [5] CONFINED SEMIFLEXIBLE POLYMER-CHAINS
    HENDRICKS, J
    KAWAKATSU, T
    KAWASAKI, K
    ZIMMERMANN, W
    PHYSICAL REVIEW E, 1995, 51 (03): : 2658 - 2661
  • [6] Stretching strongly confined semiflexible polymer chain
    王记增
    李润华
    Applied Mathematics and Mechanics(English Edition), 2014, 35 (10) : 1233 - 1238
  • [7] Microstructure and viscoelasticity of confined semiflexible polymer networks
    M. M. A. E. Claessens
    R. Tharmann
    K. Kroy
    A. R. Bausch
    Nature Physics, 2006, 2 : 186 - 189
  • [8] Stretching strongly confined semiflexible polymer chain
    Wang, Ji-zeng
    Li, Run-hua
    APPLIED MATHEMATICS AND MECHANICS-ENGLISH EDITION, 2014, 35 (10) : 1233 - 1238
  • [9] Stretching strongly confined semiflexible polymer chain
    Ji-zeng Wang
    Run-hua Li
    Applied Mathematics and Mechanics, 2014, 35 : 1233 - 1238
  • [10] Exact solution for the force-extension relation of a semiflexible polymer under compression
    Kurzthaler, Christina
    Franosch, Thomas
    PHYSICAL REVIEW E, 2017, 95 (05)