Immersed Molecular Electrokinetic Finite Element Method for the Analysis of Pathogen Screening Nanotip Sensor.

摘要

The primary goal of this thesis was to develop a unique and predictive simulation technique capable of modeling electric field guided assembly of biomolecules such as DNA and viruses at room temperatures where thermal fluctuations must be considered. The newly proposed immersed molecular electrokinetic finite element method (IMEFEM), for the first time, couples electrokinetics with fluctuating hydrodynamics to study the motion and deformation of flexible objects immersed in a suspending medium under an applied electric field. The force induced on an arbitrary object due to an electric field is calculated based on the continuum electromechanics and Maxwell stress tensor (MST). The thermal fluctuations were included in the Navier-Stokes fluid equations via random stress terms. Fluctuating forces acting on the particle were coupled through the fluid-structure interaction (FSI) force calculated within the surrounding fluctuating medium.;The development of the new framework initiated with the immersed finite element method, which was employed previously to analyze fluid-structure interaction problems encountered in human cardiovascular systems. Fluctuating hydrodynamic equations coupled with the particle equation of motion were introduced and were verified with the analytic solution. The simulation of many interacting nanoparticles demonstrated the importance of stochastic behavior and showed that thermal fluctuations influence the motion and self-assembly of nanoparticles at room temperatures. The framework was further extended to incorporate electrokinetics, now coined the IMEFEM framework, that is based on the previously developed and validated immersed electrokinetic finite element method.;The newly developed IMEFEM framework was then utilized to study the electric field strength around the nanotip, the thermal motion forces and the dielectrophoretic force exerted on an oligomer molecule immersed in a suspending medium. The effects of these forces were examined numerically in order to understand the preconcentration and the capturing mechanism at the terminal end of a nanotip. This computational tool set was successfully used for a low cost pathogen screening nanotip sensor device design and was able to efficiently capture the optimum parameters required to enhance its performance. The IMEFEM approach demonstrated possible predictive capabilities that may be exploited during the design and characterization of complex biological nanoscale devices.