Numerical simulation of the electrophoretic transport of a biopolymer through a synthetic nano-pore

Simulation of Natural Convection in a Concentric Hexagonal Annulus Using the Lattice Boltzmann Method Combined with the Smoothed Profile Method

This research work presents results obtained from the simulation of natural convection inside a concentric hexagonal annulus by using the lattice Boltzmann method (LBM). The fluid flow (pressure and velocity fields) inside the annulus is evaluated by LBM and a finite difference method (FDM) is used to get the temperature filed. The isothermal and no-slip boundary conditions (BC) on the hexagonal edges are treated with a smooth profile method (SPM). At first, for validating the present simulation technique, a standard benchmarking problem of natural convection inside a cold square cavity with a hot circular cylinder is simulated. Later, natural convection simulations inside the hexagonal annulus are carried out for different values of the aspect ratio, AR (ratio of the inner and outer hexagon sizes), and the Rayleigh number, Ra. The simulation results are presented in terms of isotherms (temperature contours), streamlines, temperature, and velocity distributions inside the annulus. The results show that the fluid flow intensity and the size and number of vortex pairs formed inside the annulus strongly depend on AR and Ra values. Based on the concentric isotherms and weak fluid flow intensity at the low Ra, it is observed that the heat transfer inside the annulus is dominated by the conduction mode. However, multiple circulation zones and distorted isotherms are observed at the high Ra due to the strong convective flow. To further access the accuracy and robustness of the present scheme, the present simulation results are compared with the results given by the commercial software, ANSYS-Fluent®. For all combinations of AR and Ra values, the simulation results of streamlines and isotherms patterns, and temperature and velocity distributions inside the annulus are in very good agreement with those of the Fluent software.

Effect of Nanopore Length on the Translocation Process of a Biopolymer: Numerical Study

In this study, we simulate the electrophoretic motion of a bio-polymer through a synthetic nanopore in the presence of an external bias voltage by considering the hydrodynamic interactions between the polymer and the fluid explicitly. The motion of the polymer is simulated by 3D Langevin dynamics technique by modeling the polymer as a worm-like-chain, while the hydrodynamic interactions are incorporated by the lattice Boltzmann equation. We report the simulation results for three different lengths of the nanopore. The translocation time increases with the pore length even though the electrophoretic force on the polymer is the same irrespective of the pore length. This is attributed to the fact that the translocation velocity of each bead inside the nanopore decreases with the pore length due to the increased fluid resistance force caused by the increase in the straightened portion of the polymer. We confirmed this using a theoretical formula.