DNA Nanoparticle Carriers
Project Goal.
The goal of this project is to successfully model the first-ever fully atomistic simulations of DNA Nanoparticle hybrid systems.
Timeline.
November 2019 - Present
Role.
Project Lead, First Author. I lead my team of 2 other peers to run the simulations and analyze the data together. I also track and report our progress, and set the direction for the next steps.
Skills Used.
High-Performance Computing (HPC)
LAMMPS, Molecular Dynamics
Academic Writing, Team Leading
Project Overview
DNA Nanoparticle (DNA-NP) systems are a novel technology with a myriad of potential applications, from healthcare (targeted drug delivery) to defense (SONAR protection). Although experimentalists have worked through trial and error to find appropriate configurations for various applications (DNA origami), utilizing computational software offers the ability to exponentially increase the efficiency of the DNA-NP fabrication process.
Our group is currently researching doing the first-ever fully atomistic computational modeling of the DNA-NP systems. In our case, we use silver (Ag) nanoparticles for their inherent cytotoxic effects. After having successfully modeled the systems, we are now attempting to find the most stable configuration of various parameters, including base pair length, nucleotide makeup, and system geometry.
More Information on this project can be found on my Molecular Dynamics poster in the publications section
Design Process
Modeling the DNA-NP system
The first step of the project was to create a double-strand DNA molecule in LAMMPS. We chose 11 base pairs arbitrarily, with a random nucleotide order. The DNA was then split into two single strands using Visual Molecular Dynamics (VMD), and each strand was attached to a silver nanoparticle at its 5 prime end.
The AgDNA strands were “minimized” for 5 million steps on the UCSD COMET supercomputer using Molecular Dynamics, and their binding energies recorded. Once complete, the two strands were reunited in VMD, and the double-strand complex was minimized for 5 million steps. The binding energies were again recorded.
After comparison to literature values and imaging of the minimization in VMD, we showed that our simulations had indeed accurately simulated AgDNA systems and could be used in the future. We also showed that 11 base pairs had unstable binding energies, and were not the ideal base-pair length.