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Simulation studies of the mechanisms of interaction between carbon nanotubes and amino acids Abadir, George Bassem Botros


In this thesis, molecular dynamics and ab initio density functional theory/nonequilibrium Green’s function simulations are used to study the interaction between carbon nanotubes and amino acids. Firstly, rules for the proper choice of the parameters used in these simulations are established. It is demonstrated how the improper choice of these parameters (particularly the basis set used in ab initio simulations) can lead to quantitatively and qualitatively erroneous conclusions regarding the bandgap of the nanotubes. It is then shown that the major forces responsible for amino-acid adsorption on carbon nanotubes are van der Waals forces, and that hydrophobic interactions may accelerate the adsorption process, but are not necessary for it to occur. The mechanisms of interaction between carbon nanotubes and amino acids are elucidated. It is found that geometrical deformations do not play a major role in the sensing process, and that electrostatic interactions represent the major interaction mechanism between the tubes and amino acids. Fully metallic armchair tubes are found to be insensitive to various amino acids, while small-radius nanotubes are shown to be inadequate for sensing in aqueous media, as their response to the motion of the atoms resulting from the immersion in water is comparable to that of analyte adsorption. Short semi-metallic tubes are revealed to be sensitive to charged amino acids, and it is demonstrated that the conductance changes induced by the adsorption of the analyte in such tubes in a two-terminal configuration are bias-dependent. The effects of the length of the tube and adsorption-site position on the conductance of the tube are discussed. In addition, the adsorption near metallic electrodes is shown to have a negligible effect on the conductance of the tube due to the metal-induced gap states injected from the metal electrodes into the tube. Finally, the results are used to provide general guidelines for the design of carbon-nanotube-based biosensors, as well as to help explaining previously published experimental results.

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