Macromolecular dynamics in crowded environments

被引:22
|
作者
Echeverria, Carlos [1 ,2 ]
Kapral, Raymond [2 ]
机构
[1] Univ Nacl Expt Tachira, Lab Fis Aplicada & Computac, San Cristobal 5001, Venezuela
[2] Univ Toronto, Chem Phys Theory Grp, Dept Chem, Toronto, ON M5S 3H6, Canada
来源
JOURNAL OF CHEMICAL PHYSICS | 2010年 / 132卷 / 10期
基金
加拿大自然科学与工程研究理事会;
关键词
diffusion; hydrodynamics; liquid structure; macromolecules; molecular configurations; molecular dynamics method; polymer solutions; MULTIPARTICLE COLLISION DYNAMICS; ANOMALOUS DIFFUSION; TRANSLATIONAL DIFFUSION; MOLECULAR-DYNAMICS; COMPLEX FLUIDS; POLYMER-CHAIN; CONFINEMENT; SIMULATION; CYTOPLASM; HYDRODYNAMICS;
D O I
10.1063/1.3319672
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
The structural and dynamical properties of macromolecules in confining or crowded environments are different from those in simple bulk liquids. In this paper, both the conformational and diffusional dynamics of globular polymers are studied in solutions containing fixed spherical obstacles. These properties are studied as a function of obstacle volume fraction and size, as well as polymer chain length. The results are obtained using a hybrid scheme that combines multiparticle collision dynamics of the solvent with molecular dynamics that includes the interactions among the polymer monomers and between the polymer beads and obstacles and solvent molecules. The dynamics accounts for hydrodynamic interactions among the polymer beads and intermolecular forces with the solvent molecules. We consider polymers in poor solvents where the polymer chain adopts a compact globular structure in solution. Our results show that the collapse of the polymer chain to a compact globular state is strongly influenced by the obstacle array. A nonmonotonic variation in the radius of gyration with time is observed and the collapse time scale is much longer than that in simple solutions without obstacles. Hydrodynamic interactions are important at low obstacle volume fractions but are screened at high volume fractions. The diffusion of the globular polymer chain among the obstacles is subdiffusive in character on intermediate time scales where the dynamics explores the local structure of the heterogeneous environment. For large polymer chains in systems with high obstacle volume fractions, the chain adopts bloblike conformations that arise from trapping of portions of the chain in voids among the obstacles.
引用
收藏
页数:9
相关论文
共 50 条
  • [31] Mesoscale hydrodynamics via stochastic rotation dynamics: Comparison with Lennard-Jones fluid
    Petersen, Matt K.
    Lechman, Jeremy B.
    Plimpton, Steven J.
    Grest, Gary S.
    in't Veld, Pieter J.
    Schunk, P. R.
    JOURNAL OF CHEMICAL PHYSICS, 2010, 132 (17):
  • [32] Entropic transport in a crowded medium
    Arango-Restrepo, A.
    Rubi, J. M.
    JOURNAL OF CHEMICAL PHYSICS, 2020, 153 (03):
  • [33] Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments
    Nawrocki, Grzegorz
    Karaboga, Alp
    Sugita, Yuji
    Feig, Michael
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2019, 21 (02) : 876 - 883
  • [34] Anomalous Dynamics in Macromolecular Liquids
    Guenza, Marina G.
    POLYMERS, 2022, 14 (05)
  • [35] Surface Charge- and Space-Dependent Transport of Proteins in Crowded Environments of Nanotailored Posts
    Choi, Chang Kyoung
    Fowlkes, Jason D.
    Retterer, Scott T.
    Siuti, Piro
    Iyer, Sukanya
    Doktycz, Mitchel J.
    ACS NANO, 2010, 4 (06) : 3345 - 3355
  • [36] Effects of soft interactions and bound mobility on diffusion in crowded environments: a model of sticky and slippery obstacles
    Stefferson, Michael W.
    Norris, Samantha L.
    Vernerey, Franck J.
    Betterton, Meredith D.
    Hough, Loren E.
    PHYSICAL BIOLOGY, 2017, 14 (04)
  • [37] Mechanism of Facilitated Diffusion during a DNA Search in Crowded Environments
    Krepel, Dana
    Gomez, David
    Klumpp, Stefan
    Levy, Yaakov
    JOURNAL OF PHYSICAL CHEMISTRY B, 2016, 120 (43): : 11113 - 11122
  • [38] Formation of protein complexes in crowded environments - From in vitro to in vivo
    Phillip, Yael
    Schreiber, Gideon
    FEBS LETTERS, 2013, 587 (08) : 1046 - 1052
  • [39] Conformation and dynamics of an active filament in crowded media
    Yan, Ran
    Tan, Fei
    Wang, Jingli
    Zhao, Nanrong
    JOURNAL OF CHEMICAL PHYSICS, 2023, 158 (11):
  • [40] Gelsolin-mediated actin filament severing in crowded environments
    Heidings, James B.
    Demosthene, Bryan
    Merlino, Theresa R.
    Castaneda, Nicholas
    Kang, Ellen H.
    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2020, 532 (04) : 548 - 554