A general theory of polymer ejection tested in a quasi two-dimensional space

Hsiao, Pai‐Yi; Chen, Wei-Yei

doi:10.1038/s41598-021-94054-2

Cited by 3 publications

(3 citation statements)

References 55 publications

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“…The process accelerated as the imbalance of surface tension contributed as the driving force. The dependence of the translocation speed on n t could be interpreted as the change in the effective friction as reported for polymers ejected out from a cavity [24,25]. In adopting the HP model of globule, we tried to obtain the friction constant ζ for the given solvent quality.…”

Section: Translocation Times and Their Dispersions: (100) N Sequencesmentioning

confidence: 99%

Translocation of Hydrophobic Polyelectrolytes under Electrical Field: Molecular Dynamics Study

et al. 2023

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We studied the translocation of polyelectrolyte (PE) chains driven by an electric field through a pore by means of molecular dynamics simulations of a coarse-grained HP model mimicking high salt conditions. Charged monomers were considered as polar (P) and neutral monomers as hydrophobic (H). We considered PE sequences that had equally spaced charges along the hydrophobic backbone. Hydrophobic PEs were in the globular form in which H-type and P-type monomers were partially segregated and they unfolded in order to translocate through the narrow channel under the electric field. We provided a quantitative comprehensive study of the interplay between translocation through a realistic pore and globule unraveling. By means of molecular dynamics simulations, incorporating realistic force fields inside the channel, we investigated the translocation dynamics of PEs at various solvent conditions. Starting from the captured conformations, we obtained distributions of waiting times and drift times at various solvent conditions. The shortest translocation time was observed for the slightly poor solvent. The minimum was rather shallow, and the translocation time was almost constant for medium hydrophobicity. The dynamics were controlled not only by the friction of the channel, but also by the internal friction related to the uncoiling of the heterogeneous globule. The latter can be rationalized by slow monomer relaxation in the dense phase. The results were compared with those from a simplified Fokker–Planck equation for the position of the head monomer.

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Section: Translocation Times and Their Dispersions: (100) N Sequencesmentioning

confidence: 99%

Translocation of Hydrophobic Polyelectrolytes under Electrical Field: Molecular Dynamics Study

et al. 2023

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“…As the polymer may be enclosed in a quasi two dimensional nano-container (cavity) for later applications, e.g. inside a channel, the dynamics of polymer translocation into a two dimensional confined space has been investigated [33,43,[53][54][55].…”

Section: Introductionmentioning

confidence: 99%

Translocation of an active polymer into a two dimensional circular nano-container

Rezaie-Dereshgi

Khalilian

Sarabadani

2023

J. Phys.: Condens. Matter

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Translocation dynamics of an active semi-flexible polymer through a nano-pore into a rigid two dimensional circular nano-container has been studied by using Langevin dynamics simulations. The results show that the force exponent $\beta$, for regime of small nano-container radius, i.e. $R \ll R_{\textrm{g}}$, where $R_{\textrm{g}}$ is the gyration radius of the passive semi-flexible polymer in two dimensional free space, is $\beta=-1$, while for large values of $R \gg R_{\textrm{g}}$ the asymptotic value of the force exponent is $\beta \approx -0.93$. The force exponent is defined by the scaling form of the average translocation time $\langle \tau \rangle \propto F_{\textrm{sp}}^{\beta}$, where $F_{\textrm{sp}}$ is the self-propelling force. Moreover, using the definition of the turning number (number of net turns of the polymer configuration) for the polymer inside the cavity, it has been found that at the end of translocation process for small value of $R$ and in the strong force limit the polymer configuration is more regular than the case in which the value of $R$ is large or the force is weak.

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“…This new stage is independent of the two main stages and can be regarded as a nucleation process. The whole theory has been generalized from a three dimensional space to a two-dimensional one, and validated [ 35 ].…”

Section: Introductionmentioning

confidence: 99%

Expansion of Single Chains Released from a Spherical Cavity

Chu

Hsiao

2022

Polymers

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A two-stage model is developed to explain the phenomena of chain expansion, released from a confining cavity. In the first stage, the chain is assumed to expand as a sphere, while in the second stage it expands like a coil. The kinetic equations for the variation of chain size are derived in the two stages by balancing the rate of the free energy change with the rate of the energy dissipation. Langevin dynamics simulations are then performed to examine the theory. We find that the expansion process is dominated by the second stage and the evolution of chain size follows, mainly, the predicted curve for coil expansion, which depends on the chain length and is not sensitive to the confining volume fraction. It permits to define the expansion time for the process. Further study reveals that the chain does undergo a spherical expansion in the first stage with the characteristic time much shorter than the one for the second stage. As a consequence, the first-stage variation of chain size can be regarded as an add-on to the principal curve of expansion designated by the second stage. The scaling behaviors and the associated scaling exponents are analyzed in details. The simulation results well support the theory.

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A general theory of polymer ejection tested in a quasi two-dimensional space

Cited by 3 publications

References 55 publications

Translocation of Hydrophobic Polyelectrolytes under Electrical Field: Molecular Dynamics Study

Translocation of Hydrophobic Polyelectrolytes under Electrical Field: Molecular Dynamics Study

Translocation of an active polymer into a two dimensional circular nano-container

Expansion of Single Chains Released from a Spherical Cavity

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