Polymer translocation: effects of periodically driven confinement.

We study the influence of confinement on the dynamics of translocation of a linear polymer chain in a good solvent through a cone-shaped pore. Using the Langevin dynamics simulations, we calculate both the first attempt time and translocation time as a function of the position of the back wall and apex angle α. As the in vivo confining environment is inherently dynamic, we extended the present study to explore the consequences of a periodically driven back wall and apex angles on the translocation dynamics. Our findings reveal that the translocation time initially decreases as the driving frequency increases, but increases after a certain frequency. The frequency at which the translocation time is found to be minimum is referred to as the resonance activation. Analyzing the distribution of translocation times around this frequency renders interesting information about the translocation process. We further explore the translocation dynamics by calculating the residence time of individual monomers, shedding light on the microscopic aspects of the process.

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.

Self-Assembly of DNA-Grafted Colloids: A Review of Challenges.

DNA-mediated self-assembly of colloids has emerged as a powerful tool to assemble the materials of prescribed structure and properties. The uniqueness of the approach lies in the sequence-specific, thermo-reversible hybridization of the DNA-strands based on Watson-Crick base pairing. Grafting particles with DNA strands, thus, results into building blocks that are fully programmable, and can, in principle, be assembled into any desired structure. There are, however, impediments that hinder the DNA-grafted particles from realizing their full potential, as building blocks, for programmable self-assembly. In this short review, we focus on these challenges and highlight the research around tackling these challenges.

Intrusion of liquids into liquid-infused surfaces with nanoscale roughness.

We present a theoretical study of the intrusion of an ambient liquid into the pores of a nanocorrugated wall w. The pores are prefilled with a liquid lubricant that adheres to the walls of the pores more strongly than the ambient liquid does. The two liquids are modeled as a binary liquid mixture of two species of particles, A and B. The mixture can decompose into a liquid rich in A particles, representing the ambient liquid, and another one rich in B particles, representing the liquid lubricant. The wall is taken to attract the B particles more strongly than the A particles. The ratio w-A/w-B of these interaction strengths is changed in order to tune the contact angle θ_{AB} formed by the A-rich/B-rich liquid interface between the two fluids and a planar wall, composed of the same material as the one forming the pores. We use classical density functional theory in order to capture the effects of microscopic details on the intrusion transition, which occurs as the concentration of the minority component or the pressure in the bulk of the ambient liquid is varied, moving away from bulk liquid-liquid coexistence within the single-phase domain of the A-rich bulk ambient liquid. These liquid structures have been studied as a function of the contact angle θ_{AB} and for various widths and depths of the pores. We also studied the reverse process in which a pore initially filled with the ambient liquid is refilled with the liquid lubricant. The location of the intrusion transition, with respect to its dependence on the contact angle θ_{AB} and the width of the pore, qualitatively follows the corresponding shift of the capillary-coexistence line away from the bulk liquid-liquid coexistence line, as predicted by a macroscopic capillarity model. Quantitatively, the transition found in the microscopic approach occurs somewhat closer to the bulk liquid-liquid coexistence line than predicted by the macroscopic capillarity model. The quantitative discrepancies become larger for narrower cavities. In cases in which the wall is completely wetted by the lubricant (θ_{AB}=0) and for small contact angles, the reverse transition follows the same path as for intrusion; there is no hysteresis. For larger contact angles, hysteresis is observed. The width of the hysteresis increases with increasing contact angle. A reverse transition is not found inside the domain within which the ambient liquid forms a single phase in the bulk once θ_{AB} exceeds a geometry-dependent threshold value. According to the macroscopic capillarity theory, for the considered geometry, this is the case for θ_{AB}>54.7^{∘}. Our computations show, however, that nanoscale effects shift this threshold value to much higher values. This shift increases strongly if the widths of the pores become smaller (below about ten times the diameter of the A and B particles).

Cassie-Wenzel transition of a binary liquid mixture on a nanosculptured surface.

The Cassie-Wenzel transition of a symmetric binary liquid mixture in contact with a nano-corrugated wall is studied. The corrugation consists of a periodic array of nanopits with square cross sections. The substrate potential is the sum over Lennard-Jones interactions, describing the pairwise interaction between the wall particles C and the fluid particles. The liquid is composed of two species of particles, A and B, which have the same size and equal A-A and B-B interactions. The liquid particles interact between each other also via A-B Lennard-Jones potentials. We have employed classical density functional theory to determine the equilibrium structure of binary liquid mixtures in contact with the nano-corrugated surface. Liquid intrusion into the pits is studied as a function of various system parameters such as the composition of the liquid, the strengths of various interparticle interactions, and the geometric parameters of the pits. The binary liquid mixture is taken to be at its mixed-liquid-vapor coexistence. For various sets of parameters the results obtained for the Cassie-Wenzel transition, as well as for the metastability of the two corresponding thermodynamic states, are compared with macroscopic predictions in order to check the range of validity of the macroscopic theories for systems exposed to nanoscopic confinements. Distinct from the macroscopic theory, it is found that the Cassie-Wenzel transition cannot be predicted based on the knowledge of a single parameter, such as the contact angle within the macroscopic theory.

Structures of simple liquids in contact with nanosculptured surfaces.

We present a density functional study of Lennard-Jones liquids in contact with a nanocorrugated wall. The corresponding substrate potential is taken to exhibit a repulsive hard core and a Van der Waals attraction. The corrugation is modeled by a periodic array of square nanopits. We have used the modified Rosenfeld density functional in order to study the interfacial structure of these liquids which with respect to their thermodynamic bulk state are considered to be deep inside their liquid phase. We find that already considerably below the packing fraction of bulk freezing of these liquids, inside the nanopits a three-dimensional-like density localization sets in. If the sizes of the pits are commensurate with the packing requirements, we observe high-density spots separated from each other in all spatial directions by liquid of comparatively very low density. The number, shape, size, and density of these high-density spots depend sensitively on the depth and width of the pits. Outside the pits, only layering is observed; above the pit openings these layers are distorted with the distortion reaching up to a few molecular diameters. We discuss quantitatively how this density localization is affected by the geometrical features of the pits and how it evolves upon increasing the bulk packing fraction. Our results are transferable to colloidal systems and pit dimensions corresponding to several diameters of the colloidal particles. For such systems the predicted unfolding of these structural changes can be studied experimentally on much larger length scales and more directly (e.g., optically) than for molecular fluids which typically call for sophisticated x-ray scattering.

Free-energy functional for freezing transitions: hard-sphere systems freezing into crystalline and amorphous structures.

A free-energy functional that contains both the symmetry-conserved and symmetry-broken parts of the direct pair correlation function has been used to investigate the freezing of a system of hard spheres into crystalline and amorphous structures. The freezing parameters for fluid-crystal transition have been found to be in very good agreement with the results found from simulations. We considered amorphous structures found from molecular dynamics simulations at packing fractions η lower than the glass close packing fraction η(J) and investigated their stability compared to that of a homogeneous fluid. The existence of a free-energy minimum corresponding to a density distribution of overlapping Gaussians centered around an amorphous lattice depicts a deeply supercooled state with a heterogeneous density profile.

Pair correlation functions and a free energy functional for the nematic phase.

In this paper we have presented the calculation of pair correlation functions in a nematic phase for a model of spherical particles with the long-range anisotropic interaction from the mean spherical approximation (MSA) and the Percus-Yevick (PY) integral equation theories. The results found from the MSA theory have been compared with those found analytically by Holovko and Sokolovska [J. Mol. Liq. 82, 161 (1999)]. A free energy functional which involves both the symmetry conserving and symmetry broken parts of the direct pair correlation function has been used to study the properties of the nematic phase. We have also examined the possibility of constructing a free energy functional with the direct pair correlation function which includes only the principal order parameter of the ordered phase and found that the resulting functional gives results that are in good agreement with the original functional. The isotropic-nematic transition has been located using the grand thermodynamic potential. The PY theory has been found to give a nematic phase with pair correlation function harmonic coefficients having all the desired features. In a nematic phase the harmonic coefficient of the total pair correlation function h(x1,x2) connected with the correlations of the director transverse fluctuations should develop a long-range tail. This feature has been found in both the MSA and PY theories.