Equilibrium organization, conformation, and dynamics of two polymers under box-like confinement.

  title={Equilibrium organization, conformation, and dynamics of two polymers under box-like confinement.},
  author={James M. Polson and Desiree A. Rehel},
  journal={Soft matter},
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as flexible bead-spring chains, and the box has a square cross-section of side length L and a height that is small enough to compress the polymers in that dimension. For sufficiently large L, the system behaviour approaches that of an isolated polymer in a slit… 

Figures from this paper



Segregation of polymers under cylindrical confinement: effects of polymer topology and crowding.

Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement and the conformational free energy, F, of the polymers was measured as a function of the centre-of-mass separation distance, λ, to identify discrepancies between the predicted and measured values of scaling exponents.

Polymer segregation in cylindrical confinement revisited: A three-dimensional free energy landscape.

Interestingly, Brownian dynamics shows that the average induction time t ¯ i n or segregation time t¯ s e decreases monotonically with κ in a power-law dependence if the diffusion coefficient D is fixed, suggesting a distinct mechanism of the induction process which is neither diffusion nor barrier-crossing, in accordance with trajectory analysis by using MD simulations.

Polymer segregation under confinement: free energy calculations and segregation dynamics simulations.

The free energy of the system, F, is measured as a function of the distance between the centers of mass of the polymers, λ, and the effects on the free energy functions of varying the channel diameter D and length L, as well as the polymer length N and bending rigidity κ are examined.

Free energy and segregation dynamics of two channel-confined polymers of different lengths.

This study uses Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere polymers under confinement in a cylindrical channel, and proposes a regime map in which the state of the system is determined by the values of the quantities N_{2}/N{1} and λ/(N_{1}+N_{2})D^{-β}, where N-β are the polymer lengths.

Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity.

A pneumatically-actuated nanofluidic platform that has the capability of dynamically controlling the confinement environment of macromolecules in solution is presented, using pneumatic pressure to deflect a thin nitride lid into a nanoslit, confining molecules in an array of cavities embedded in the slit.

Confinement and crowding control the morphology and dynamics of a model bacterial chromosome.

A polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell that spontaneously adopts a helical shape, which is further compacted by molecular crowders to occupy a nucleoid-like sub-volume of the cell.

Overlapping two self-avoiding polymers in a closed cylindrical pore: Implications for chromosome segregation in a bacterial cell.

  • Youngkyun JungB. Ha
  • Materials Science
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2010
Using molecular-dynamics simulations, longitudinal confinement is shown to have nontrivial effects on segregation dynamics by randomizing and thus slowing down the segregation process, which would otherwise be assisted with entropic forces.

Segregation of polymers in confined spaces

Although the results are restricted to 2D, the basic mechanism of competition between entropy and confinement leading to the minimum is suggestive of an evolutionary driving force for size selection.

Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects

During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly