Date of Graduation


Document Type


Degree Name

Master of Science in Cell & Molecular Biology (MS)

Degree Level



Biological Sciences


Jin-Woo Kim

Committee Member

Matthew Patitz

Second Committee Member

Joshua Sakon


Applied sciences, DNA, Modeling, Nanoparticles, Self-assembly


The self-assembly of nanoparticles (NPs) of varying shape, size, and composition for the purpose of constructing useful nanoassemblies with tailored properties remains challenging. Although progress has been made to design anisotropic building blocks that exhibit the required control for the precise placement of various NPs within a defined arrangement, there still exists obstacles in the technology to maximize the programmability in the self-assembly of NP building blocks. Currently, the self-assembly of nanostructures involves much experimental trial and error. Computational modeling is a possible approach that could be utilized to facilitate the purposeful design of the self-assembly of NP building blocks into a desired nanostructure. In this report, a coarse-grained model of NP building blocks based on an effective anisotropic mono-functionalization approach, which has shown the ability to construct six building block configurations, was used to simulate various nanoassemblies. The purpose of the study was to validate the model’s ability to simulate the self-assembly of the NP building blocks into nanostructures previously produced experimentally. The model can be programmed to designate up to six oligonucleotides attached to the surface of a Au NP building block, with a modifiable length and nucleotide sequence. The model successfully simulated the self-assembly of Au NP building blocks into a number of previously produced nanostructures and demonstrated the ability to produce visualizations of self-assembly as well as calculate interparticle distances and angles to be used for the comparison with the previous experimental data for validation of the model. Also, the model was used to simulate nanoassemblies which had not been produced experimentally for its further validation. The simulations showed the capability of the model to use specific NP building blocks and self-assemble. The coarse-grained NP building block model shows promise as a tool to complement the purposeful experimental design of functional nanostructures.