Monte Carlo study of the translocation of a polymer chain through a hole

Nowicki, Waldemar; Nowicka, Grażyna

doi:10.1016/j.eurpolymj.2009.10.012

Cited by 7 publications

(9 citation statements)

References 56 publications

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“…For instance, it is not useful to discuss the crossover in dynamics emerging upon increasing the polymer stiffness, which may be made more complicated for our systems as the average distance between charged monomers belonging to the escaped polymer head is higher than for their absorbed counterparts. This should lower both the Coulomb energy and the rigidity of the escaped part, thus modulating the intensity of the thermodynamic force . Besides, the Helmholtz energy profile for the translocation of star polymers through a pore may be different from the one for linear species, and it may also be modulated by how the ionization of monomers inside the pore responds to the additional entropic constraint.…”

Section: General Discussion and Conclusionmentioning

confidence: 99%

Absorbed weak polyelectrolytes: Impact of confinement, topology, and chemically specific interactions on ionization, conformation free energy, counterion condensation, and absorption equilibrium

Tagliabue

Izzo

Mella

2019

J Polym Sci B Polym Phys

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Absorption of weak polyelectrolytes impacts on properties such as ionization, conformations, and counterion (CI) condensation that are important in several areas of applied and fundamental science. We used a weak polyelectrolyte model and Monte Carlo simulations to investigate how the mentioned properties depend on pH or the size of a spherical cavity (SC) permeable to CIs but not to polyelectrolytes; the latter have either linear or starlike topologies and may be allowed to form charged hydrogen bonds (c H-bonds) between ionized and neutral monomers. Average ionization decreases upon increasing the number of arms at a constant number of monomers; it instead increases with the arm length in large SC due to CI screening. The way SC size, c H-bonds, and pH values interrelate to define ionization is instead more complicate due to arm pairing or clustering when c H-bonds are possible. These induce oscillations in the arm local ionization and impact on both monomer and CI distributions in the complete simulation cell in a way that also depends on polymer topology. The impact of ionization on the confinement free energy is also estimated; this highlighted that c H-bonding may enhance absorption compared with neutral chains.

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Section: General Discussion and Conclusionmentioning

confidence: 99%

Absorbed weak polyelectrolytes: Impact of confinement, topology, and chemically specific interactions on ionization, conformation free energy, counterion condensation, and absorption equilibrium

Tagliabue

Izzo

Mella

2019

J Polym Sci B Polym Phys

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“…[29] The corresponding rate constants can be derived from ap air of differential equations, Equations (7) and (8) (Figure 3d-e;s ee the Supporting Information for am ore detailed discussion). [30] dlnðr 1in-½L1&TC Þ dt the ratios of singly,doubly and triply interlocked pseudorotaxanev ersus timea t298 K; c) the ratioso fs ingly,doubly andtriply interlocked pseudorotaxanes at equilibrium at 293-313K;d )the ratioso fd oubly and triply interlocked pseudorotaxanesw ere fitted accordingt oE quation (8), which gave the gradient as k C 23 and the y-intercept as k C 32 ;e)the ratios of singly and doubly interlocked pseudorotaxanesw ere fitteda ccording to Equation (7), which gave the gradienta s k C 21 and the y-intercept as k C 12 ;f)Eyring plotf or the rate constants k C 12 , k C 21 ,k C 23 ,and k C 32 .…”

Section: Analysis Of the Formation Of 3in-[l1andtc]mentioning

confidence: 99%

“…Several mechanisms have been proposed for the translocation of polypeptides, such as ratcheting and pushing mechanisms . However, a clear understanding of how the structural features of the channel and threading molecule and their interaction features would affect the translocation is still missing . To improve the fundamental understanding of the various controlling factors of translocation in channels or pores with specific spatial architectures, it is desirable to identify experimental systems in which the complexity arising from the rich chemical detail of biological molecules is minimized.…”

Section: Introductionmentioning

confidence: 99%

Self‐Assembly of a [2]Pseudorotaxane by an Inchworm‐Motion Mechanism

Meng

Wang

Xiang

et al. 2016

Chemistry A European J

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The threading of biomolecules through pores or channels in membranes is important to validate the physiological activities of cells. To aid understanding of the controlling factors required for the translocation in space with confined size and distorted conformation, it is desirable to identify experimental systems with minimized complexity. We demonstrate the mechanism of a linear guest L1 threading into a tris(crown ether) host TC with a combinational distorted cavity to form a triply interlocked [2]pseudorotaxane 3in-[L1⊂TC]. An inchworm-motion mechanism is proposed for the process. For the forward-threading steps that lead to the formation of higher-order interlocked species, guest L1 must adopt a bent conformation to find the next crown ether cavity. Two simplified models are applied to investigate the self-assembly dynamic of 3in-[L1⊂TC]. Kinetic NMR spectroscopic and molecular dynamics (MD) studies show that formation of the singly penetrated species is fast, whereas formation of the doubly and triply threaded species is several orders of magnitude slower. During threading the freedom of both the guest L1 and host TC gradually decrease due to their interactions. This results in a significant entropy effect for the threading dynamic, which is also observed for the threading of a biomolecular chain through a channel.

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“…For large polymer densities at the surface, the chains form a structure called the polymer “brush,” whereas they adopt a “mushroom” conformation at low densities. Studies of the conformations of chains that are end-grafted to convex and concave interfaces [8, 9] are relevant to issues such as the deformation of a bacteria cell membrane by an attached chain [10], the application of a macromolecule as a localized pressure microtool [11], or the micromanipulation of individual polymer molecules using AFM [12]. …”

Section: Introductionmentioning

confidence: 99%

Conformational entropy of a polymer chain grafted to rough surfaces

et al. 2012

Self Cite

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A polymer molecule (represented by a statistical chain) end-grafted to a topologically rough surface was studied by static MC simulations. A modified self-avoiding walk on a cubic lattice was used to model the polymer in an athermal solution. Different statistical models of surface roughness were applied. Conformational entropies of chains attached to uncorrelated Gaussian, Brownian, and fractional Brownian surfaces were calculated. Results were compared with the predictions of a simple analytical model of a macromolecule end-grafted to a fractal surface.FigureVisualization of SAW generated by the (023) algorithm on a 3D cubic latticeElectronic supplementary materialThe online version of this article (doi:10.1007/s00894-012-1546-5) contains supplementary material, which is available to authorized users.

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Monte Carlo study of the translocation of a polymer chain through a hole

Cited by 7 publications

References 56 publications

Absorbed weak polyelectrolytes: Impact of confinement, topology, and chemically specific interactions on ionization, conformation free energy, counterion condensation, and absorption equilibrium

Absorbed weak polyelectrolytes: Impact of confinement, topology, and chemically specific interactions on ionization, conformation free energy, counterion condensation, and absorption equilibrium

Self‐Assembly of a [2]Pseudorotaxane by an Inchworm‐Motion Mechanism

Conformational entropy of a polymer chain grafted to rough surfaces

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