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
  • [1] Diffusion in crowded biological environments: applications of Brownian dynamics
    Dlugosz, Maciej
    Trylska, Joanna
    BMC BIOPHYSICS, 2011, 4
  • [2] Structure and dynamics of water in crowded environments slows down peptide conformational changes
    Lu, Cheng
    Prada-Gracia, Diego
    Rao, Francesco
    JOURNAL OF CHEMICAL PHYSICS, 2014, 141 (04):
  • [3] Alignment of Colloidal Rods in Crowded Environments
    Calabrese, Vincenzo
    Varchanis, Stylianos
    Haward, Simon J.
    Shen, Amy Q. .
    MACROMOLECULES, 2022, 55 (13) : 5610 - 5620
  • [4] Dynamics in Crowded Environments: Is Non-Gaussian Brownian Diffusion Normal?
    Kwon, Gyemin
    Sung, Bong June
    Yethiraj, Arun
    JOURNAL OF PHYSICAL CHEMISTRY B, 2014, 118 (28): : 8128 - 8134
  • [5] Langevin Dynamics Simulation on the Diffusivity of Polymers in Crowded Environments with Immobile Nanoparticles
    Hua, Dao-Yang
    Khan, Raja Azhar Ashraaf
    Luo, Meng-Bo
    MACROMOLECULES, 2022, 55 (23) : 10468 - 10478
  • [6] Water Dynamics in Cytoplasm-Like Crowded Environment Correlates with the Conformational Transition of the Macromolecular Crowder
    Verma, Pramod Kumar
    Kundu, Achintya
    Ha, Jeong-Hyon
    Cho, Minhaeng
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2016, 138 (49) : 16081 - 16088
  • [7] Macromolecular diffusion in crowded media beyond the hard-sphere model
    Blanco, Pablo M.
    Lluis Garces, Josep
    Madurga, Sergio
    Mas, Francesc
    SOFT MATTER, 2018, 14 (16) : 3105 - 3114
  • [8] Translational and rotational dynamics of a self-propelled Janus probe in crowded environments
    Theeyancheri, Ligesh
    Chaki, Subhasish
    Samanta, Nairhita
    Goswami, Rohit
    Chelakkot, Raghunath
    Chakrabarti, Rajarshi
    SOFT MATTER, 2020, 16 (36) : 8482 - 8491
  • [9] Effects of confinement on models of intracellular macromolecular dynamics
    Chow, Edmond
    Skolnick, Jeffrey
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (48) : 14846 - 14851
  • [10] Protein Aggregation in Crowded Environments
    White, Duncan A.
    Buell, Alexander K.
    Knowles, Tuomas P. J.
    Welland, Mark E.
    Dobson, Christopher M.
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2010, 132 (14) : 5170 - 5175