Browsing by Subject "Polymer physics"

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Electrostatics of polymer translocation through membrane nanopores in electrolyte solutions
(2021-02) Mohamed, Ghada Mahmoud Abdullah
The transport of polymers across membranes in electrolyte solutions happens in most biological systems and is necessary for cells to function. Moreover, the poly-mer translocation process has proven to be very important in experiments and applications as well, providing a rich source of information about the polymer’s size and composition [1], [2], making the polymer translocation procedure a po-tential sequencing method that is eﬃcient, cheap, and quick [3], [4]. However, no consensus on the theoretical understanding of the translocation mechanism has been reached yet [3], leaving it a major challenge for theoretical modelling due to its steric, hydrodynamic, and electrostatic interactions [2], [5]. Here, we calculate the electrostatic energy cost of the translocating polymer in both the approach and translocation phases and investigate the dependence of the poly-mer’s grand potential on diﬀerent model tunable parameters. In the case of neu-tral membranes, low permittivity carbon-based membranes repel the approaching polymer with energy magnitude between ∼ 11 kBT and ∼ 27 kBT , while high permittivity engineered membranes attract the approaching polymer with almost the same energy magnitude. This behavior can be attributed to polymer image-charge interactions, which become ampliﬁed with low permittivity membranes. In strong salt solutions, the membrane exhibits a repulsive barrier that turns to a metastable well in dilute solutions. In pure solvents, the metastable well becomes a deep, stable well that traps the polymer in the pore for some time, where the translocation phase is mainly governed by the attractive trans-cis side interac-tion. For weakly charged membranes, the membrane charge attraction wins over the image-charge repulsion, leading to an attractive minimum at zt ≈ −1 nm followed by a repulsive barrier at lt = L/2 while for stronger membrane charges, the attractive well turns to a metastable point followed by an attractive, stable well. These results suggest that, in translocation experiments, DNA motion can be controlled by tuning the system parameters, such as the solution concentration or the membrane charge.
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Molecular investigation of polyelectrolyte hydrogel under mechanical deformation
(2023-07) Rafique, Muzaffar
Polyelectrolyte hydrogels are fascinating materials that can produce electromechanical responses when they are electrically or mechanically deformed. However, the accurate molecular origins of such phenomenon are still unknown, even though it is often ascribed to the change in condensation of counterion levels or alteration of ionic conditions in the pervaded volume of the hydrogel. We used all-atom molecular dynamics (MD) simulations to investigate this behavior by utilizing a polyacrylic acid (PAA) hydrogel immersed in an explicit polar solvent as our model system. In the atomistic MD simulation, we investigated the swelling behavior of polyelectrolyte hydrogels, traditionally computed through the equilibrium of chemical potential and pressure between the system and reservoir. However, we discovered that achieving the equilibrium swelling state was non-trivial, as faster relaxation of the simulation box resulted in lower swelling ratios, while slower relaxation led to larger swelling ratios. To address this challenge, we employed theoretical calculations with a Gaussian state as the reference to estimate the hydrogel’s swelling ratio effectively. In our computational study, we investigated the response of PAA polyelectrolyte hydrogel from weak to highly swollen (i.e., between 60 to 90% solvent content) when subjected to uniaxial mechanical compression and extension. Our primary aim is to compute the condensed counterions at different deformations at the microscopic level. We found out that condensation of counterion shows highly non-monotonic behavior when they are mechanically deformed, with an overall increase in total counterion condensation when the PAA hydrogel is uniaxially compressed or stretched. However, this effect diminishes for weakly swollen gel because a large fraction of counterions are already condensed on the polyelectrolyte polymer. Upon closer examination, we found that counterion condensation increases along the stretched chains in the hydrogel. on the one hand, this increase reaches to maximum value for certain deformation ratios after that, we see a decline in the condensation of counterions when the hydrogel chains are stretched further. On the other hand, we see a very minimal increase in condensation when the hydrogel is compressed, and chains are collapsed state. We also analyzed the single polyelectrolyte chains, which also displayed a qualitatively similar response. This observation gives us insight that polymer chain conformations affect the distribution of counterions in the gel. We further investigated the counterion condensation behavior for polyelectrolyte solutions at their critical concentration level. However, we don’t see any deformation-dependent counterion condensation. This suggests the importance of hydrogel topology, which constrains the polyelectrolyte chain ends and leads to the observed behavior. These extensive molecular dynamics simulations shed light on the interesting and heterogeneous behavior of counterion condensation when the hydrogel is deformed, showing a rich electrostatic response behavior. These findings contribute significantly to the understanding of the underlying behavior of mechanically deformed polyelectrolyte hydrogels.