Date of Completion
2022
Document Type
Honors College Thesis
Department
Chemistry
Thesis Type
Honors College, College of Arts and Science Honors
First Advisor
Jianing Li
Second Advisor
Chris Danforth
Third Advisor
Dave Punihaole
Keywords
computational/theoretical chemistry, supramolecular chemistry, multiscale modeling, nanomaterials, peptides, DNA amphiphiles
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.
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License.
Recommended Citation
Clark, Finley Thomas, "Molecular Dynamics Simulations and Analysis Characterize the Structures of Supramolecular Nanomaterials" (2022). UVM Honors College Senior Theses. 519.
https://scholarworks.uvm.edu/hcoltheses/519