Driven translocation of a semiflexible polymer through a conical channel in the presence of attractive surface interactions

Crowding induced switching of polymer translocation by the amalgamation of entropy and osmotic pressure

The translocation of polymers is omnipresent in inherently crowded biological systems. We investigate the dynamics of polymer translocation through a pore in free and crowded environments using Langevin dynamics simulation. We observed a location-dependent translocation rate of monomers showcasing counterintuitive behavior in stark contrast to the bead velocity along the polymer backbone. The free energy calculation of asymmetrically placed polymers indicates a critical number of segments to direct receiver-side translocation. For one-sided crowding, we have identified a critical crowding size revealing a nonzero probability of translocation toward the crowded-side. Moreover, we have observed that shifting the polymer toward the crowded-side compensates for one-sided crowding, yielding an equal probability akin to a crowder-free system. In two-sided crowding, a slight variation in crowder size and packing fraction induces a polymer to switch its translocation direction. These conspicuous yet counter-intuitive phenomena are rationalized by minimalistic theoretical arguments based on osmotic pressure and radial entropic forces.

Gain reversal in the translocation dynamics of a semiflexible polymer through a flickering pore

We study the driven translocation of a semiflexible polymer through an attractive extended pore with a periodically oscillating width. Similar to its flexible counterpart, a stiff polymer translocates through an oscillating pore more quickly than a static pore whose width is equal to the oscillating pore's mean width. This efficiency quantified as a gain in the translocation time, highlights a considerable dependence of the translocation dynamics on the stiffness of the polymer and the attractive nature of the pore. The gain characteristics for various polymer stiffness exhibit a trend reversal when the stickiness of the pore is changed. The gain reduces with increasing stiffness for a lower attractive strength of the pore, whereas it increases with increasing stiffness for higher attractive strengths. Such a dependence leads to the possibility of a high degree of robust selectivity in the translocation process.

Polymer translocation: Effects of confinement

We investigate the influence of varying confinement on the dynamics of polymer translocation through a cone-shaped channel. For this, a linear polymer chain is modeled using self-avoiding walks on a square lattice. The cis side of a cone-shaped channel has a finite volume, while the trans side has a semi-infinite space. The confining environment is varied either by changing the position of the back wall while keeping the apex angle fixed or altering the apex angle while keeping the position of the back wall fixed. In both cases, the effective space ϕ, which represents the number of monomers in a chain relative to the total number of accessible sites within the cone, is reduced due to the imposed confinement. Consequently, the translocation dynamics are affected. We analyze the entropy of the confined system as a function of ϕ, which exhibits nonmonotonic behavior. We also calculate the free energy associated with the confinement as a function of a virtual coordinate for different positions of the back wall (base of the cone) along the conical axis for various apex angles. Employing the Fokker-Planck equation, we calculate the translocation time as a function of ϕ for different solvent conditions across the channel. Our findings indicate that the translocation time decreases as ϕ increases, but it eventually reaches a saturation point at a certain value of ϕ. Moreover, we highlight the possibility of controlling the translocation dynamics by manipulating the solvent quality across the channel. Furthermore, our investigation delves into the intricacies of polymer translocation through a cone-shaped channel, considering both repulsive and neutral interactions with the channel wall. This exploration unveils nuanced dynamics and sheds light on the factors that significantly impact translocation within confined channels.

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.