Macromolecular dynamics in crowded environments

URL:

https://www.scopus.com/inward/record.uri?eid=2-s2.0-77949576043&doi=10.1063%2f1.3319672&partnerID=40&md5=365e48f0b8833a452e40f20e6a5d75ce

Keywords:

Article, Bulk liquid, Chain length, Chemical bonds, chemical structure, chemistry, Collapse time, Conformations, Dynamical properties, Fluid dynamics, Globular polymers, Globular state, Globular structure, Heterogeneous environments, High volume fraction, Hybrid scheme, Hydrodynamic interaction, Hydrodynamics, Intermolecular forces, Local structure, Macromolecular dynamics, Macromolecules, Models, Molecular, Molecular dynamics, Molecular Dynamics Simulation, Multi-particle collision dynamics, Non-monotonic variation, Obstacle array, Particle Size, polymer, Polymer beads, Polymer chain length, Polymer chains, Polymers, Poor solvents, protein, Proteins, Radius of gyration, solvent, Solvent molecules, Solvents, Time-scales, Titration, Volume fraction

Abstract:

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. © 2010 American Institute of Physics.