Macromolecular dynamics in crowded environments

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.

Mesoscopic model for binary fluids

“…Multiparticle collision dynamics, also known as stochastic rotation dynamics [13], is a particle-based technique for complex fluids that includes thermal fluctuations and hydrodynamic interactions [10]. Multiparticle collision dynamics has proven to be capable of simulating many soft-matter systems, including colloid dynamics [11,14,15], polymer and proteins dynamics [16][17][18][19][20][21], vesicles [22] and reactive systems [23,24]. Multiparticle collision dynamics has also been employed to investigate the properties of chemical reaction in crowded environments; i.e., media containing obstacles [25][26][27].…”

Tubular or Subsurface Morphology of Octabutoxyphthalocyanine upon Self‐Assembly in Polymer Matrices: Effect of the Casting Solvent

“…[8] Polymer diffusion [9] and dynamics [10] under confinement, conformation and molecular mobility of polymers confined in nanochannels [11] (e.g., in urea), and so on have also been studied.…”

“…[7][8][9][10][11][12][13] Studies have been reported on crystallization in ultra thin polymer films [7] and in small nanodomains.…”

Multiscale simulation of molecular processes in cellular environments

“…Hydrodynamic interactions are therefore key to understanding both the motion of proteins in dilute and in crowding conditions. This has been pointed out in seminal theoretical and experimental work [7][8][9][10].…”