Free energy of a macromolecule in a confined domain

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.

Confinement and partitioning of a single polymer chain in a dense array of nanoposts

We present a Brownian dynamics simulation study on the confinement and partitioning of a single, flexible polymer chain in a dense array of nanoposts with different sizes and separations, especially, when the volume of an interstitial space formed among four nanoposts is less than the volume of the polymer chain. As the interstitial volume decreases by either increasing the nanopost diameter or decreasing the separation between nanoposts, the chain conformation becomes elongated in the direction parallel to the nanoposts. Interestingly, however, the degree of chain elongation varies in a non-monotonic fashion as the interstitial volume decreases while keeping the passage width between two nanoposts constant at a small value. We calculate the free energy of chain partitioning over several interstitial spaces from the partitioning probability, and find that the non-monotonic dependence of the chain elongation results from an interplay between the confinement-driven chain elongation along the direction parallel to the nanoposts and the chain spreading perpendicular to the nanoposts by partitioning chain segments over several interstitial spaces. These results present the possibility of utilizing a dense array of nanoposts as a template to control polymer conformations.

Confinement free energy of flexible polyelectrolytes in spherical cavities

A weakly charged flexible polyelectrolyte chain in a neutral spherical cavity is analyzed by using self-consistent field theory within an explicit solvent model. Assuming the radial symmetry for the system, it is found that the confinement of the chain leads to creation of a charge density wave along with the development of a potential difference across the center of cavity and the surface. We show that the solvent entropy plays an important role in the free energy of the confined system. For a given radius of the spherical cavity and fixed charge density along the backbone of the chain, solvent and small ion entropies dominate over all other contributions when chain lengths are small. However, with the increase in chain length, chain conformational entropy and polymer-solvent interaction energy also become important. Our calculations reveal that energy due to electrostatic interactions plays a minor role in the free energy. Furthermore, we show that the total free energy under spherical confinement is not extensive in the number of monomers. Results for the osmotic pressure and mean activity coefficient for monovalent salt are presented. We demonstrate that fluctuations at one-loop level lower the free energy and corrections to the osmotic pressure and mean activity coefficient of the salt are discussed. Finite size corrections are shown to widen the range of validity of the fluctuation analysis.