Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics.

  title={Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics.},
  author={Joonas Piili and Pauli Suhonen and Riku Linna},
  journal={Physical review. E},
  volume={95 5-1},
We use stochastic rotation dynamics (SRD) to examine the dynamics of the ejection of an initially strongly confined flexible polymer from a spherical capsid with and without hydrodynamics. The results obtained using stochastic rotation dynamics (SRD) are compared to similar Langevin simulations. Inclusion of hydrodynamic modes speeds up the ejection but also allows the part of the polymer outside the capsid to expand closer to equilibrium. This shows as higher values of radius of gyration when… 

Scaling Behaviors of a Polymer Ejected from a Cavity through a Small Pore.

The evolution of m is shown to be well described by the scaling theory and the ejection time exhibits two proper scaling behaviors: N^{(2/3ν)+y_{1}}ϕ_{0}^{-(2/ 3ν)} and N^{2+y_{2}} under the large and small ϕ_0} or N conditions, respectively.

Dynamics of driven translocation of semiflexible polymers.

It is shown that for realistic f_{d} translocation dynamics is to a large extent, but not completely, determined by the polymer's elastic length measured in number of Kuhn segments, which is elastically so short that the finite-length dynamics outlined here applies.

Quantification of tension to explain bias dependence of driven polymer translocation dynamics.

The results corroborate the theoretical prediction by Sakaue's theory that there should not be bias dependence of β for asymptotically long polymers and show that monomer crowding at the pore exit cannot have a measurable effect on translocation dynamics under realistic conditions.

Scaling Theory of a Polymer Ejecting from a Cavity into a Semi-Space

A two-stage model developed in order to understand the scaling behaviors of single polymers ejecting from a spherical cavity through a nanopore suggests the existence of a pre-stage that can be explained by using the concept of a classical nucleation theory.

Diffusion of a Ring Threaded on a Linear Chain

A mesoscopic simulation is applied to investigate the effects of hydrodynamic interactions and axial chains on the dynamics of threaded rings. The hydrodynamic interactions significantly speed up the

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.

E 97 , 062413 ( 2018 ) Dynamics of driven translocation of semiflexible polymers

This material is protected by copyright and other intellectual property rights, and duplication or sale of all or part of any of the repository collections is not permitted, except that material may be duplicated by you for your research use or educational purposes in electronic or print form.

Rigidity-induced scale invariance in polymer ejection from capsid.

It is found that, unlike for fully flexible polymers, for semiflexible polymers the force measured at the pore does not show a direct relation to the instantaneous ejection velocity.



Polymer ejection from strong spherical confinement.

  • J. PiiliR. Linna
  • Physics
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2015
It is shown that the time for an individual monomer to eject grows exponentially with the number of ejected monomers, and that the superlinear dependence obtained for polymers amenable to computer simulations results from a finite-size effect due to the final retraction of polymers' tails from capsids.

Dynamics of polymer ejection from capsid.

The high-resolution data show that the capsid ejection for both pores, analogously to polymer translocation, can be characterized as a multiplicative stochastic process that is dominated by small-scale transitions.

Driven polymer translocation in good and bad solvent: Effects of hydrodynamics and tension propagation.

By measuring the effective friction in a setup where a polymer in free solvent is pulled by a constant force at the end, it is found that hydrodynamics does speed up collective polymer motion in the bad solvent even more effectively than in the good solvent.

Effect of Temperature and Capsid Tail on the Packing and Ejection of Viral DNA

The effect of including the tail on the dynamics of a charged polymer, in particular, is rather significant: more packing fraction is facilitated at higher temperatures due to more ordered polymer configuration inside the capsid.

Langevin dynamics simulations of genome packing in bacteriophage.

L Langevin dynamics simulations are used to study the process by which a coarse-grained DNA chain is packaged within an icosahedral container and suggest that packing in general does not proceed in the deterministic fashion of the inverse-spool model, but rather is stochastic in character.

Polymer packaging and ejection in viral capsids: shape matters.

The results suggest that phages may have evolved to be roughly spherical in shape to optimize the speed of genome ejection, which is the first stage in infection.

Criteria for minimal model of driven polymer translocation.

A minimal model where dynamics is completely excluded is constructed to show that close alignment with a full translocation model can be achieved, and suggests that contribution due to fluctuations is important.

Knot-controlled ejection of a polymer from a virus capsid.

A numerical study of the effect of knotting on the ejection of flexible and semiflexible polymers from a spherical, viruslike capsid suggests that this process has the biological advantage of unknotting the DNA before it enters a cell.

Dynamics of polymer decompression: expansion, unfolding, and ejection.

The dynamics of polymer decompression from a compact state to swollen conformation can be formally described as nonlinear diffusion and a scheme called uniform approximation is shown to be useful to get a physical insight involved.

Mesoscopic Multi-particle Collision Model for Fluid Flow and Molecular Dynamics

Several aspects of modeling dynamics at the mesoscale level are discussed: (1) The construction of a mesoscopic description of fluid dynamics. The mesoscale dynamics consists of free streaming