Polymer translocation through nanopore into active bath

Translocation Dynamics of an Active Filament through a Long-Length Scale Channel

Active filament translocation through a confined space is crucial for diverse biological processes. By using Langevin dynamics simulations, we investigate the translocation dynamics of an axially self-propelled chain through a channel. First, results show a suggestive reciprocal scaling of translocation time versus active force. Second, in the case of a long channel, we demonstrate a very intriguing nonmonotonic change of translocation time with increasing channel width. The driving force shows a similar trend, providing a consistent picture to understand the unexpected channel width effect. In particular, in a moderately broad channel, the disordered chain conformation results in a loss of driving force and thus inhibits translocation dynamics. Chain adsorption might occur in a wide channel, which accounts for a facilitated translocation. Lastly, we connect the translocation process to tension propagation (TP). A modified TP picture is proposed to interpret the waiting time distribution. Our work highlights the new phenomenology owing to the crucial interplay of activity and spacial confinement, which drives the translocation dynamics, going beyond the traditional entropic barrier scenario.

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

Rectification of polymer translocation through nanopores by nonchiral and chiral active particles

We study translocation of a flexible polymer chain through a membrane pore under the influence of active forces and steric exclusion using Langevin dynamics simulations within a minimal two-dimensional model. The active forces on the polymer are imparted by nonchiral and chiral active particles that are introduced on one side or both sides of a rigid membrane positioned across the midline of a confining box. We show that the polymer can translocate through the pore to either side of the dividing membrane in the absence of external forcing. Translocation of the polymer to a given side of the membrane is driven (hindered) by an effective pulling (pushing) exerted by the active particles that are present on that side. The effective pulling results from accumulation of active particles around the polymer. This crowding effect signifies persistent motion of active particles causing prolonged detention times for them close to the confining walls and the polymer. The effective pushing that hinders the translocation, on the other hand, results from steric collisions that occur between the polymer and active particles. As a result of the competition between these effective forces, we find a transition between two rectified cis-to-trans and trans-to-cis translocation regimes. This transition is identified by a sharp peak in the average translocation time. The effects of active particles on the transition is studied by analyzing how the translocation peak is regulated by the activity (self-propulsion) strength of these particles, their area fraction, and chirality strength.

Effects of active crowder size and activity-crowding coupling on polymer translocation

Polymer translocation in complex environments is crucially important to many biological processes in life. In the present work, we adopted two-dimensional Langevin dynamics simulations to study the forced and unbiased polymer translocation dynamics in active and crowded media. The translocation time and probability are analyzed in terms of active force F_a, volume fraction φ and also the crowder size. The non-trivial active crowder size effect and activity-crowding coupling effect as well as the novel mechanism of unbiased translocation between two active environments with different active particle sizes are clarified. Firstly, for forced translocation, we reveal an intriguing non-monotonic dependence of the translocation time on the crowder size in the case of large activity. In particular, crowders of intermediate size similar to the polymer segment are proven to be the most favorable for translocation. Moreover, a facilitation-inhibition crossover of the translocation time with increasing volume fraction is observed, indicating a crucial activity-crowding coupling effect. Secondly, for unbiased translocation driven by different active crowder sizes, the translocation probability demonstrates a novel turnover phenomenon, implying the appearance of an opposite directional preference as the active force exceeds a critical value. The translocation time in both directions decreases monotonically with the active force. The asymmetric activity effect together with the entropic driving scenario provides a reasonable picture for the peculiar behavior observed in unbiased translocation.

Pore shapes effects on polymer translocation

We translocated polymers through pores of different shapes and interaction patterns in three dimensions by Langevin molecular dynamics. There were four simple cylindrical pores of the same length but with different diameters. The results showed that even though decreasing the pore diameter would always decrease the translocation velocity, it was strongly dependent on the shape of the increased pore diameter. Although increasing the pore diameter made the translocation faster in simple cylindrical pores, it was complicated in different pore shapes, e.g. increasing the diameter in the middle decreased the translocation velocity. Investigating polymer shapes through the translocation process and comparing the shapes by the cumulative waiting time for different pore structures reveals the non-equilibrium properties of translocation. Moreover, polymer shape parameters such as gyration radius, polymer center of mass, and average aspect ratio help us to distinguish different pore shapes and/or different polymers.

Non-monotonic dependence of polymer chain dynamics on active crowder size

Configuration dynamics of flexible polymer chains is of ubiquitous importance in many biological processes. Here, we investigate a polymer chain immersed in a bath of size-changed active particles in two dimensional space using Langevin dynamics simulations. Particular attention is paid to how the radius of gyration R_g of the polymer chain depends on the size σ_c of active crowders. We find that R_g shows nontrivial non-monotonic dependence on σ_c: The chain first swells upon increasing σ_c, reaching a fully expanded state with maximum R_g, and then, R_g decreases until the chain collapses to a compact coil state if the crowder is large enough. Interestingly, the chain may oscillate between a collapse state and a stretched state at moderate crowder size. Analysis shows that it is the competition between two effects of active particles, one stretching the chain from inside due to persistence motion and the other compressing the chain from outside, that leads to the non-monotonic dependence. Besides, the diffusion of the polymer chain also shows nontrivial non-monotonic dependence on σ_c. Our results demonstrate the important interplay between particle activity and size associated with polymer configurations in active crowding environments.