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

  title={Segregation of polymers under cylindrical confinement: effects of polymer topology and crowding.},
  author={James M. Polson and Deanna R. M. Kerry},
  journal={Soft matter},
  volume={14 30},
Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of the centre-of-mass separation distance, λ. We examined the scaling of the free energy functions with the polymer length, the length and diameter of the confining cylinder, the polymer topology (i.e. linear vs. ring polymers), and the packing fraction and size… 
10 Citations

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

Brownian dynamics and Monte Carlo simulations are used to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity and the static and dynamical behaviour differs significantly from that previously observed for confinement of two polymers to a narrow channel.

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.

Adherent Moving of Polymers in Spherical Confined Binary Semiflexible Ring Polymer Mixtures

Based on the coarse-grained model, we used molecular dynamics methods to calculate and simulate a semiflexible long ring–semiflexible short ring blended polymer system confined in a hard sphere. We

Segregation of ring polyelectrolytes in nano-channel.

  • W. Nowicki
  • Physics
    The Journal of chemical physics
  • 2019
A segregation process of two ring polyions in the confined environment, represented by a tight nanopore, has been investigated by means of the nonequilibrium Monte Carlo method on the lattice.

First-in-class matrix anti-assembly peptide prevents staphylococcal biofilm in vitro and in vivo

It is demonstrated that capsicumicine strongly prevents methicillin-resistant S. epidermidis biofilm via a new extracellular “matrix anti-assembly” mechanism of action.

Capsicumicine, a New Bioinspired Peptide from Red Peppers Prevents Staphylococcal Biofilm In Vitro and In Vivo via a Matrix Anti-Assembly Mechanism of Action

Insight is provided into an antibiofilm strategy based on the development of capsicumicine, a natural peptide that strongly controls biofilm formation by Staphylococcus epidermidis, the most prevalent pathogen in device-related infections.

Capsicumine: a new peptide from red peppers turns out to be a powerful antibiofilm agent and displays a new mechanism of action, matrix anti-assembly

It is demonstrated that capsicumicine prevents methicillin-resistant Staphylococcus epidermidis adhesion as well as biofilm establishment and maintenance via a new extracellular matrix anti-assembly (MAA) mechanism of action.

Piston Compression of Semiflexible Ring Polymers in Channels

Polymer translocation into cavities: Effects of confinement geometry, crowding, and bending rigidity on the free energy.

This work describes the confinement free energy for a flexible polymer in cavities with constant cross-sectional area A for various cavity shapes (cylindrical, rectangular, and triangular) and examines the effects of crowding agents inside the cavity.

Free Energy of a Folded Semiflexible Polymer Confined to a Nanochannel of Various Geometries

Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with



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.

Polymer segregation under confinement: Influences of macromolecular crowding and the interaction between the polymer and crowders.

Using Langevin dynamics simulations, it is found that the segregation time increases with increasing the volume fraction of crowders due to the slower chain diffusion in crowded environments, and the attractive interaction between the polymer and a small number of crowder can significantly facilitate the chain segregation.

Polymer translocation into and out of an ellipsoidal cavity.

  • J. Polson
  • Physics
    The Journal of chemical physics
  • 2015
It is found that both polymer ejection and insertion are faster for ellipsoidal cavities than for spherical cavities, and the discrepancy is likely due to out-of-equilibrium conformational behaviour that is not accounted for in the FP approach.

Simulation study of the polymer translocation free energy barrier.

It is proposed that the theoretical models developed here can be used to make quantitatively accurate predictions of translocation free energy functions for very long polymers using simulation data acquired for short polymers.

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

Free Energy of a Folded Polymer under Cylindrical Confinement

Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its

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.

Polymer translocation dynamics in the quasi-static limit.

This work uses a multiple-histogram method and the Fokker-Planck formalism to calculate the variation of the free energy with Q, a coordinate used to quantify the degree of translocation in a quasi-static regime of polymer-nanopore friction.

A polymer in a crowded and confined space: effects of crowder size and poly-dispersity.

This work studies how a flexible chain molecule can be compacted by crowding particles with variable sizes in a (cell-like) cylindrical space and shows that with smaller crowding agents the compaction occurs at a lower volume fraction but at a larger concentration such that doubling their size is equivalent to increasing their concentration fourfold.

Entropic Segregation of Ring Polymers in Cylindrical Confinement

Entropic forces tend to demix polymers in confinement, which has been argued to at least facilitate DNA segregation in cylindrical bacteria. Ring polymers as found in modern bacteria such as