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Molecular Dynamics Simulations and Analysis Characterize the Structures of Supramolecular Nanomaterials
Clark, Finley Thomas
Clark, Finley Thomas
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Abstract
Nanomaterials are an important technology with emerging applications in medicine, energy, electronics, and agriculture. Bioinspired nanomaterials, such as large aggregates of peptide- or DNA-based molecules, are particularly promising for their safety and biodegradability. However, the nanoscale can be a challenging regime for chemical synthesis due a deficiency of rational design principles and ambiguities that may be presented by certain experimental characterization techniques. Seeking to address these challenges, this theoretical/computational investigation draws from molecular dynamics (MD) simulations of peptide aggregation and the experimentally observed self-assembly of novel amphiphilic DNA-containing molecules. To aid future investigations, a new framework to interpret the results of MD simulations of peptide aggregation by considering distances between peptides instead of their solvent-accessible surface area is proposed and validated. Also, a bottom-up MD simulation strategy is used to characterize at atomistic resolution the structure of a DNA amphiphile-based nanomaterial. The proposed structure is found to agree well with atomic force microscopy measurements of the thickness of the sheet-like structure.
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Date
2022-01-01