MD Simulations of Bio-Nano-System: Controllable Translocation and Selective Separation of Single-Stranded Dnas Through a Polarized Cnt Membrane

This dissertation, "MD Simulations of Bio-nano-system: Controllable Translocation and Selective Separation of Single-stranded DNAs Through a Polarized CNT Membrane" by 謝迎洪, Yinghong, Xie, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Abstract of thesis entitled MD SIMULATIONS OF BIO-NANO-SYSTEM: CONTROLLABLE TRANSLOCATION AND SELECTIVE SEPARATION OF SINGLE-STRANDED DNAS THROUGH A POLARIZED CNT MEMBRANE Submitted by Yinghong Xie for the Degree of Doctor of Philosophy at the University of Hong Kong August 2007 Carbon nanotubes (CNTs) have attracted considerable scientific interest due to their striking structural, mechanical and electrical properties. In recent years, the fabrication of nanoscale devices using carbon nanotubes as the constructing blocks has led to the rapid growth of nanotechnology. Before bioapplications associated with carbon nanotubes can be established, it is of considerable importance to improve their solubility in an aqueous environment and thereby realize the dispersion and separation of as-produced nanotube bundles. For this purpose, functionalization of carbon nanotubes with the assistance of a wide range of biological species, such as carbohydrates, proteins, nucleic acids and enzymes, is categorized as a new branch of biology and material science. In the present work, molecular dynamics (MD) simulations are carried out to study the conjugation mode of the initially separated CNT and amylose molecules. Typical association fashions include wrapping of amylose around the outer surface of single-walled carbon nanotube, and encapsulation of amylose inside a hollow cavity of nanotube, which is mostly governed by the relative size (e.g. diameter) of the simulated nanotube and amylose fragments. These two different conjugations are primarily driven by the intermolecular van der Waals interactions. To achieve a better understanding of the intrinsic mechanisms governing the combination of nanotubes and biological polymers, the present study focuses on the investigations of the electric field-induced translocation of single-stranded DNA molecule through a polarized carbon nanotube membrane. As a matter of fact, the applied electric field would result in rearrangement of the dipole moment within the nanotube, indicating that the consideration of nanotube polarization is a prerequisite for an accurate MD description of a CNT-based system. Hence, a modified force field for MD simulations of polarizable carbon nanotubes is developed based on the concept of a shell model, in which the motion of a network of negatively charged shell particles approximately represents the charge redistribution in the nanotube, as well as the electrical polarization and the associated electronic degree of freedom in response to an external electric field. This shell CNT model offers a much more realistic platform for the studies of the translocation kinetics of DNA oligonucleotide through a polarized CNT membrane. A nonlinear dependence of translocation velocity and an inversed quadratic dependence of translocation time on the electric field strength are observed, and the threshold field is estimated, below which no translocation process can be accomplished within the simulation timescale of several nanoseconds. The translocation process is found to be nanopore-size and DNA length and composition dependent. In particular, the different translocation velocities of a series of ssDNA fragments offer the opportunity to use a polarized CNT membrane to selectively separate the ssDNA chains of different sizes or compositio