Suresh Alapati

Numerical and theoretical study on the mechanism of biopolymer translocation process through a nano-pore

We conducted a numerical study on the translocation of a biopolymer from the cis side to the trans side of a membrane through a synthetic nano-pore driven by an external electric field in the presence of hydrodynamic interactions (HIs). The motion of the polymer is simulated by 3D Langevin dynamics technique using a worm-like chain model of N identical beads, while HI between the polymer and fluid are incorporated by the lattice Boltzmann equation. The translocation process is induced by electrophoretic force, which sequentially straightens out the folds of the initial random configuration of the polymer chain on the cis side. Our simulation results on translocation time and velocity are in good quantitative agreement with the corresponding experimental ones when the surface charge on the nano-pore and the HI effect are considered explicitly. We found that the translocation velocity of each bead inside the nano-pore mainly depends upon the length of the straightened portion of the polymer in forced motion near the pore. We confirmed this by a theoretical formula. After performing simulations with different pore lengths, we observed that translocation velocity mainly depends upon the applied potential difference rather than upon the electric field inside the nano-pore.

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

We employed a hybrid approach to study numerically the translocation of a biopolymer through an artificial nano-pore driven by an external electric field in the presence of an explicit solvent. The motion of the polymer is simulated by the 3D Langevin dynamics technique. The hydrodynamic interactions (HI) between the polymer and the fluid are taken into account by the lattice Boltzmann equation. Our polymer chain model representing the double-stranded DNA was first validated by comparing the diffusion coefficient obtained from the numerical results with the experimental and theoretical results. Then, we conducted numerical simulations of the biopolymers translocation process by applying a theoretical formula for the net electrophoretic force acting on the part of the polymer residing in the pore. We compared quantitatively the translocation times and the velocities of different DNA lengths with the corresponding experimental results. Our simulation results are in good agreement with the experimental ones when the HI are considered explicitly.

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.

Use of lattice Boltzmann method to simulate interaction between fluid flow and particle motion in small scales

N simulation of interaction between fluid flow and particle motion demands sophisticated algorithms due to the motion of particles and difficulty in creating the grid system. We developed, during past decades, numerical solution methods to tackle this problem and applied the methods to several branches of engineering applications of small scales. The method is based on the Lattice Boltzmann Method (LBM). In this presentation, we demonstrate three kinds of numerical solutions provided by the methods. First, we developed the simulation code for the problem of translocation of a biopolymer through a nano–pore driven by an external electric field. A theoretical formula is also used to calculate the net electrophoretic force acting on the part of the polymer residing inside the pore. Next, we simulated the motion of microscopic artificial swimmer. The swimmer consists of an artificial filament composed of super–paramagnetic beads connected by elastic linkers and an externally oscillating magnetic field is used to actuate the filament, and we have found that there is an optimum sperm number at which the filament swims with maximum velocity. Then, we computed the fluid flow generated inside a micro -channel by an array of beating elastic cilia. We have found that there exists a maximum flow rate at an optimum sperm number. We also simulated the motion of particles caused by fluid flow of cilia actuation.T Magnus effect is the phenomenon whereby a rotating body experiences an asymmetric force due to its rotation. Historically researchers (Benjamin Robins and Gustav Magnus) investigated this effect using spherical bodies. A simplified investigation later followed by limiting attention to two dimensions, reducing the sphere to a circle was performed. Potential flow theory was capable of describing this situation by superposing a uniform stream upon a collocated doublet/vortex flow. Integrating Euler’s equation along the surface of the resulting “rotating” circle yielded an asymmetric force. Experimental verification of this theoretical result was undertaken by approximating the two dimensional circle by a circular cylinder that spanned either a water or wind tunnel. Potential flow theory was taken by Ludwig Prandtl and expanded to describe the lifting flow about a three dimensional surface. Prandtl and his colleague Max Munk used this theory to derive the optimum distribution of vortex flow (hence, circulation) along the span of a lifting body. The elliptical distribution is the optimum in order to reduce induced drag. Given that optimum, Munk was able to solve for the optimum chord distribution for a fixed wing. The extension from two dimensional to three dimensional investigation for airfoils/fixed wings has outpaced that for rotating bodies. The majority of the work on rotating bodies to date has remained two dimensional. The author has taken the optimum circulation distribution and applied it to a rotating cylindrical body. The theoretically optimum three dimensional geometry has been derived and will herein be described.Like most accredited mechanical engineering programs, the undergraduate curriculum at California State University Chico includes a required course in Finite Element Analysis (FEA). Historically, the primary focus of the class has been the underlying theory of the method and its formulation from fundamental governing equations with little to no instruction in commercial software designed specifically for the purpose. Students were taught the traditional theoretical methods (Stiffness, Galerkin, Virtual Work, Castigliano, etc.) and were given assignment problems with rigorous hand-work such as assembling stiffness matrices. They were taught computer based solution methods through non-specific computational software such as Excel and MATLAB®. Feedback from advisory boards, capstone project sponsors, senior exit surveys, and other evidence clearly indicated a problem with the curriculum’s approach to finite element analysis. While program graduates were well versed in the theory of the method, there was strong evidence that they were not skilled its proper application via commercial FEA software, a very common task in the workplace. Observations included poorly posed problems, unnecessary computational rigor, meaningless results, or indeed the inability to obtain a solution at all. In response, the FEA course was redesigned to include basic instruction in the proper use of commercial FEA software while still maintaining sufficient theory for understanding the inherent assumptions and limitations of the method. Segments of theory-based discussion and traditional assignments are now followed with exploration of the same concepts in the context of commercial software. Emphasis is placed on its proper use, underlying assumptions, limitations, and validity of results.

Mixing in a Microchannel by using Induced-charge Electro-osmosis

Abstract. This paper presents an experimental study on the performance of a micro-mixer using AC elec-tro-osmotic flow. The microchannel is made of PDMS for the side and top walls and glass patterned withITO for the bottom wall. We first investigated the effect of the applied potential as well as the frequencyon the slip velocity. We have found that the slip velocity is roughly proportional to the applied voltagein line with the Helmholtz-Smoluchowski equation and there is an optimum frequency at which the slipvelocity becomes maximized. To find the optimum parameters for mixing device we tested our devicefor various design parameters. It turned out that the best mixing effect is obtained approximately whenthe electrode angle is 30 o , electrode width 200µm, and the frequency of power supply 700 Hz. Key Words: AC Electro-osmosis flow(교류전기삼투 유동), Flow visualization(유동가시화 ), Mixing index(혼합지수 ), Optimum design(최적설계) 1. Introduction Lab-on-chips receive increasing attention in view oftheir possibility of practical applications in broad areassuch as biology and chemistry. Lab-on-chips arecomposed of micro-size mechanical and electricalsystems which enable pumping, mixing, separation,sequencing, reaction and even cell growth.Characterized by very low Reynolds numbers, thesystem encounters difficulty in mixing of fluids. Inorder to enhance mixing, various ideas have beenproposed in the literature. Cha et al.