Biomolecule Sensing and Filtering with Tunable Semiconductor Membrane

Through recent advances in science and technology, it is now possible to fabricate artificial nanopores in solid state membranes. Understanding the translocation process of biological molecules through artificial nanopores will allow us to take full advantage of the versatile solid state membrane devices for applications in single molecule sensing and/or characterization and fast molecular filtering/separation. Theoretical modeling of the novel application becomes a desirable means in gaining fundamental understanding and optimization of the device. This thesis uses computational simulations to understand the biomolecule's motion through nanopore in solid state membrane.;To perform the computational simulations, a great part of this work is put into developing the simulation tools composed by a coupled approach of the Poisson-Nernst-Planck modeling and the Brownian Dynamics method. The Poisson-Nernst-Planck modeling calculates the electrostatic potential distribution of the entire system comprised of the membrane immersed in the electrolyte solution. The biomolecule's motion through the electrolyte membrane system is then tracked using Brownian Dynamics method. The studied molecules include single-stranded DNA, nanoparticles, and protein. A coarse grained model was used for the DNA, where a single charged bead represent a nucleotide. An full-atomic model was used for the nanoparticles where the nanoparticle is represented by a cluster of beads. Several representations were used for the protein, ranging from high resolution full-atomic, coarse grained, and single bead representation. A computational model is developed to simulate the translocation process of biomolecules through nanopore in semiconductor membrane. Due to the different characteristics and properties of biomolecules, appropriate modifications were made to the Brownian Dynamics approach to account for the different molecules.;The study of DNA translocating through a double conical nanopore shows that the type of semiconductor material used for the membrane along with the applied electrolyte and membrane biases have a prominent effect on the molecule's translocation time and gyration radius. The second study realized was using a larger cylindrical nanopore for the separation of nanoparticles. The time the particle spent in the solution before a successful translocation becomes an important indicator for separation/filtering. The results show that dielectrophoresis has negligible effect on the particle's dynamic due to the specific nanopore geometry. The electroosmotic fluid flow had a surprisingly strong influence on the particle's dynamics. For the protein study, results show that the coarse grained protein representation strikes the best balance between the accuracy of the results and the computational effort required. The effect of the protein's net charge on the protein's motion is evident when no electrolyte bias was applied and become negligible in the presence of electroosmotic fluid flow.;An optimal combination for the parameters of the electrolyte membrane system can be used to achieve an order of magnitude increase in the translocation time of DNA. For nanoparticles, the optimal combination of applied electrolyte and membrane biases of the same membrane can effectively separate same-sized particles based on charge. In the case of protein, depending on the applied electrolyte bias, the time spent by proteins before translocation can be up to 80 times different for different applied membrane biases.