Helical Conformations of Semiflexible Polymers Confined between Two Concentric Cylinders

Spiral and helical formation of passive and active polymers with stiffness heterogeneity in a spherical cavity

Biomolecules usually adopt ubiquitous circular structures which are important for their functionality. Based on three-dimensional Langevin dynamics simulations, we investigate the conformational change of a polymer confined in a spherical cavity. Both passive and active polymers with either homogeneous or heterogeneous stiffness are analyzed in a comparative manner. For a homogeneous chain, continuous rigidity along the backbone promotes a flat spiral expanding along the cavity surface, while activity-induced softening results in a less-ordered spiral structure. Stiffness heterogeneity basically plays a destructive role in spiral formation. However, as the chain is endowed with activity, the heterogeneity effect depends on the stiffness of the front edge of the chain. As the head is rigid, the flat spiral largely holds, whereas such a structure easily loses as the head is flexible. More intriguingly, a short flexible head induces a distinct compact helix in the interior of the cavity. Under low friction conditions, the prominent inertial effect leads to the break-up of both spiral and helix. In the presence of crowding, the flat spiral close to the surface keeps its stability, while the compact helix inside tends to be dissolved. Our results decipher the significant effects of activity, rigidity, confinement and crowding on modulating polymer conformations, which provides a deeper insight about mechanisms for circular structure formation of biopolymers in crowded environments.

Structure and dynamics of an active polymer adsorbed on the surface of a cylinder

The structure and dynamics of an active polymer on a smooth cylindrical surface are studied by Brownian dynamics simulations. The effect of an active force on the polymer adsorption behavior and the combined effect of chain mobility, length N, rigidity κ, and cylinder radius, R, on the phase diagrams are systemically investigated. We find that complete adsorption is replaced by the irregular alternative adsorption/desorption process at a large driving force. Three typical (spiral, helix-like, and rod-like) conformations of the active polymer are observed, dependent on N, κ, and R. Dynamically, the polymer shows rotational motion in the spiral state, snake-like motion in the intermediate state, and straight translational motion without turning back in the rod-like state. In the spiral state, we find that the rotation velocity ω and the chain length follow a power-law relation ω ∼ N^-0.42, consistent with the torque-balance theory of general Archimedean spirals. And the polymer shows super-diffusive behavior along the cylinder for a long time in the helix-like and rod-like states. Our results highlight that the mobility, rigidity, and curvature of surface can be used to regulate the polymer behavior.

Confinement-driven organization of a histone-complexed DNA molecule in a dense array of nanoposts

The first step in the controlled storage of lengthy DNA molecules is to keep DNA molecules separated while integrated in micrometer-sized space. Herein, we present hybrid Monte Carlo simulations of a histone-complexed DNA (hcDNA) molecule confined in a dense array of nanoposts. Depending on the nanopost dimension, a single, 8.7 kilobase pair hcDNA molecule was either localized and elongated in a single inter-post space surrounded by four nanoposts or spread over several inter-post spaces through passages between two neighboring nanoposts. The conformational change of a hcDNA molecule is interpreted in terms of competitive effects of confinements in the inter-post and passage spaces. We propose that, by elaborately designing nanopost arrays, the competitive confinement effects can be adjusted such that each hcDNA molecule is localized in a single inter-post space, and thereby multiple hcDNA molecules can be physically separated from each other while stored together in the nanopost array.

Structural phases of adsorption for flexible polymers on nanocylinder surfaces

By means of generalized-ensemble Monte Carlo simulations, we investigate the thermodynamic behavior of a flexible, elastic polymer model in the presence of an attractive nanocylinder. We systematically identify the structural phases that are formed by competing monomer-monomer and monomer-substrate interactions. The influence of the relative surface attraction strength on the structural phases in the hyperphase diagram, parameterized by cylinder radius and temperature, is discussed as well. In the limiting case of the infinitely large cylinder radius, our results coincide with previous outcomes of studies of polymer adsorption on planar substrates.