Arya Biological and Soft Materials Modeling Lab 

Principal Investigator: Dr. Gaurav Arya

Project #1: Modeling Bottlebrush Surface Adsorption

May 2020 – Aug 2021

Hours: 250

Designed coarse-grain molecular dynamics (MD) model to imitate the adsorption of bottlebrush polymers onto a surface to optimize grafting-to polymer brush density for better lubricative and antifouling properties

Fig. 1: Biotin-headed bottlebrush polymers adsorbing onto fixed streptavidin beads.

Functionalizing a surface with polymers can endow it with many unique properties such as lubrication, protein resistance, and biocompatibility. Currently, grafting-from techniques can yield high polymer density but often use harsh chemicals which are not suitable for use in situ. The alternative is the grafting-to approach, which uses preformed polymers and allows them to adsorb onto a surface. This allows for a less harsh approach to adding polymers onto a surface such as a knee joint to provide lubrication relief for patients with osteoarthritis. However, this approach is limited in that the kinetics of the adsorption process are not well understood. This project aimed to replicate a previously experimentally tested grafting-to, biotin-streptavidin-based system to study how these bottlebrush polymers adsorbed onto a surface and what conformations they adapted. Using an MD model, I was able to simulate bottlebrushes at a variety of densities, lengths, and widths during different conditions. The information from this project could help scientists optimize and tailor polymer-based therapeutics to be as effective as possible.

Unfortunately, this project was discontinued after little progress was being made and the experimental lead was no longer interested in pursuing it. However, it did serve as a valuable learning experience and gave me headway into my next simulation project.


Project #2: Organization of DNA origami tiles

Aug 2021-Current

Hours: 50

Designing a molecular dynamics (MD) simulation to study the self-assembly of DNA origami tiles on a surface in collaboration with the Ke Lab at Georgia Tech.

Fig. 2: Preliminary data on cluster size formation as a function of spacing

DNA origami offers a precise, sensitive, and controllable way of functionalizing a surface. This project aims to understand the self assembly behavior of these


Segura Biomaterials Lab

Principal Investigator: Dr. Tatiana Segura

Mentor: Dr. Shangjing Xin

Project #3: Microporous Annealed Particles for Stroke Recovery

Feb 2021-Current

Hours: 350

I am studying the effect of adding various proteins and cell components to microporous annealed particles and their effect on improving brain regeneration through both angiogenesis and synaptogenesis.

Stroke is the leading cause of death in America. After stroke, the brain can be damaged, leaving dead cell and tissue at the stroke location. To help the stroke site or other wound sites regenerate, porous biomaterials are a promising candidate that offers a scaffold upon which the cells can grow. However, ways to integrate porous scaffolds are often invasive and caustic. Microporous annealed particles (MAP) are an emerging class of biomaterials where the gel can be injected into the wound site alongside the crosslinker allowing it to form a porous network in situ, adapting to the wound cavity in a less invasive manner. The aim of this project is to use these MAP gels to improve the regeneration of stroke sites in mice. This work can help inform development of future therapies to help patients heal better and faster.