Molecular dynamics simulation of bio-fullerene interfaces

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Title: Molecular dynamics simulation of bio-fullerene interfaces
Author: Noon, William H.
Advisor: Ma, Jianpeng
Degree: Doctor of Philosophy thesis
Abstract: Molecular Dynamics (MD) simulations were employed to study the interaction of fullerene molecules in biological environments. Initial work considers the interaction of peptides with fullerene, where a fullerene specific antibody and a single-walled carbon nanotube (SWNT) wrapped by a peptide was simulated. Results reveal the interface between peptides and fullerene to be dominated by hydrophobic interactions. Also, pi-stacking interactions were a predominant recognition mode. Electrostatic forces primarily defined the shape of the complex around the fullerene. Another study involved the interaction of water with SWNT. Unexpectedly, water was observed to partition within the center of nanotubes. Furthermore, the water organizes into a hydrogen-bonded network that is dependent upon nanotube diameter. The phenomenon parallels the function of transmembrane proteins, and consequently, free energy calculations were completed to consider if nanotubes exhibited selective ion partitioning. Indeed, ions specifically favored certain nanotube indices and selectivity was dependent upon nanotube diameter and ion solvation structure. Much of this thesis analyzes the structure of sodium dodecyl sulfate (SDS) around SWNT. Initial results suggested that nanotubes were encased in a thick micelle that prohibited water from contacting the tube. However, later experimental data suggested a much more dynamic system and therefore new simulation techniques were developed to achieve an improved model. The new methodology was first developed by simulating the aggregation of a random mixture of SDS into micelles of experimentally expected sizes and structures. After successful testing, a random mixture was allowed to aggregate onto a nanotube. The results reveal a random monolayer exists around the tube, but the head groups and water molecules are much closer the tube, which accounts for the more dynamic fluorescence properties observed. Simple geometric modeling and recent fluorescence measurements are also considered to further support the improved model. Finally, the aggregation of polyethylene oxide (PEO) derived polymers around SWNT was completed. Results reveal a much weaker hydrophobic interaction with the tube and consequently much less of the tube is covered by polymer. The findings correlate well with fluorescence and protein adsorption experiments. The structure of the wrapping polymer is also considered, along with the effect of molecular weight.
Citation: Noon, William H.. (2004) "Molecular dynamics simulation of bio-fullerene interfaces." Doctoral Thesis, Rice University.
Date: 2004

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