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

Piili, Joonas; Suhonen, Pauli; Linna, Riku

doi:10.1103/physreve.95.052418

Cited by 12 publications

(20 citation statements)

References 33 publications

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“…Truncating the tail channel of the virion or increasing the solvent temperature accelerates the evolution of ejection [36]. Other effects that are able to affect the ejection include the chain rigidity [34,[37][38][39], the solvent quality [40,41], the hydrodynamics [36,42], the electrostatics [36,43], the pore dimension [44][45][46], and so on. These effects have been the main topics of investigation in the past two decades.…”

Section: Introductionmentioning

confidence: 99%

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

Hsiao

2020

Polymers

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A two-stage model is developed in order to understand the scaling behaviors of single polymers ejecting from a spherical cavity through a nanopore. The dynamics of ejection is derived by balancing the free energy change with the energy dissipation during a process. The ejection velocity is found to vary with the number of monomers in the cavity, m, as mz1/(Nx1D3z1) at the confined stage, and it turns to be m−z2 at the non-confined stage, where N is the chain length and D the cavity diameter. The exponents are shown to be z1=(3ν−1)−1, z2=2ν and x1=1/3, with ν being the Flory exponent. The profile of the velocity is carefully verified by performing Langevin dynamics simulations. The simulations further reveal that, at the starting point, the decreasing of m can be stalled for a good moment. It suggests the existence of a pre-stage that can be explained by using the concept of a classical nucleation theory. By trimming the pre-stage, the ejection time are properly studied by varying N, D, and ϕ0 (the initial volume fraction). The scaling properties of the nucleation time are also analyzed. The results fully support the predictions of the theory. The physical pictures are given for various ejection conditions that cover the entire parameter space.

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Section: Introductionmentioning

confidence: 99%

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

Hsiao

2020

Polymers

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“…The ejection time was deduced to scale asymptotically asat the osmotic driven stage. Simulations, on the other hand, revealed that translocation behaviors can be altered by the details of the escape pore [16,17], the cavity [18,19], the solvent [20,21], the chain stiffness [19,22], etc. Despite of the varieties, universalities can be still traced.…”

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confidence: 99%

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

Huang

Hsiao

2019

Phys. Rev. Lett.

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Langevin dynamics simulations are performed to investigate ejection dynamics of spherically confined flexible polymers through a pore. By varying the chain length N and the initial volume fraction φ0 of the monomers, two scaling behaviors for the ejection velocity v on the monomer number m in the cavity are obtained: v ∼ m 1.25 φ 1.25 0 /N 1.6 for large m and v ∼ m −1.4 as m is small. A robust scaling theory is developed by dividing the process into the confined and the non-confined stages, and the dynamical equation is derived via the study of energy dissipation. After trimming the prior stage related to the escape of the head monomer across the pore, the evolution of m is shown to be well described by the scaling theory. The ejection time exhibits two proper scaling behaviors:and N 2+y 2 under the large and small φ0-or N -conditions, respectively, where y1 = 1/3, y2 = 1 − ν, and ν is the Flory exponent.Translocation of biopolymers via small pores is a very important biological process; it allows exchange of large biomolecules, such as DNA, RNA and proteins, between different cellular compartments [1]. When passing through the pores, the conformation of biomolecules is significantly changed in order to fit with the pores which have typically the size of few monomers. It creates a large entropic barrier and therefore, driving forces such as chemical potential gradient are generally required to effectuate a translocation [2][3][4]. In this study, we focus on a special type of driving: polymer translocation induced by spatial confinement. A vital example is the ejection of a DNA molecule from a virus capsid to a bacteria cell [1,5]. Application examples in nanotechnology include trapping single DNA in a nanocage on a membrane [6], transportation of DNA between nanotraps [7], gene therapy using engineered protein shells as the transfection vectors [8,9], and so on. These topics require fundamental understanding of packing or ejecting a biopolymer into or from a closed shell.Muthukumar [10,11] has studied polymer ejection by considering it as a nucleation problem, and predicted that the ejection time scaleswhere N is the number of monomers, φ 0 is the volume fraction (vf) of the monomers prior to ejection, and ν is the Flory exponent. Using the scaling theory and Monte Carlo simulations, Cacciuto and Luijten (CL) [12,13] argued that the ejection time should be τ ∼ N 1+ν φ −1/(3ν−1) 0 for a polymer escaped from a spherical cavity. It was issued from the Kantor and Kardar's expression τ ∼ N 1+ν /∆µ [14] by setting the chemical potential difference ∆µ to the estimated free energy per monomer F/N ∼ φ 1/(3ν−1) 0 . The exponent 1 + ν depicted a lower-bound time scale for the polymer to diffuse unimpededly over its size. Sakaue and Yoshinaga (SY) [15] pointed out that ∆µ should decrease with the process. They studied ejec- * Corresponding author, email: pyhsiao@mx.nthu.edu.tw tion dynamics by balancing the free energy change with the dissipation of the mechanical energy near the pore. The ejection time was deduced to scale ...

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“…In addition to SRD, we use Langevin dynamics (LD) to model solvent in force measurements and polymer packaging due to its superior computational efficiency. In [15] we showed that LD and SRD without hydrodynamics yield similar results. LD follows the Langevin equation…”

Section: B the Solvent And Polymer Dynamicsmentioning

confidence: 57%

“…Using our general simulation model, we will study the ejection process for polymers of different bending rigidity. In our previous studies on capsid ejection of flexible polymers we showed that the ejection dynamics is governed by the force the polymer beads inside the capsid exert on the bead at the pore entrance [14,15]. As will be seen, this result cannot be generalized to semiflexible polymer chains.…”

Section: Introductionmentioning

confidence: 93%

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Rigidity-induced scale invariance in polymer ejection from capsid

2017

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While the dynamics of a fully flexible polymer ejecting a capsid through a nanopore has been extensively studied, the ejection dynamics of semiflexible polymers has not been properly characterized. Here we report results from simulations of ejection dynamics of semiflexible polymers ejecting from spherical capsids. Ejections start from strongly confined polymer conformations of constant initial monomer density. We find 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. The cumulative waiting time t(s), that is, the time at which a monomer s exits the capsid the last time, shows a clear change when increasing the polymer rigidity κ. The major part of an ejecting polymer is driven out of the capsid by internal pressure. At the final stage the polymer escapes the capsid by diffusion. For the driven part there is a crossover from essentially exponential growth of t with s of the fully flexible polymers to a scale-invariant form. In addition, a clear dependence of t on polymer length N_{0} was found. These findings combined give the dependence t(s)∝N_{0}^{0.55}s^{1.33} for the strongly rigid polymers. This crossover in dynamics where κ acts as a control parameter is reminiscent of a phase transition. This analogy is further enhanced by our finding a perfect data collapse of t for polymers of different N_{0} and any constant κ.

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

Cited by 12 publications

References 33 publications

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

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

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

Rigidity-induced scale invariance in polymer ejection from capsid

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