Introduction

Before we start simulating, I want you to understand the system and Rivanna. Our system is inspired by a PhD student: James Tang. His paper is this. Professor Letteri and her experimental team have also created this amazing paper which is the experimental side of our project.

TLDR. We are simulating stereochemical mixtures of peptides. As shown in the papers, different mixtures of L and D amino acids show different behaviors in their ability to self assemble into hydrogels. For example, pure ratios of L and D form a stiffer fibrous gel while a mixture form a weaker plate like gel.

By creating simulations, we also are able to gather more information on the micro level of peptides by lowering the cost and time. We are able to quantify the microscale peptide peptide interactions (hydrogen bonds, pi pi stacking, etc) that are hard to see experimentally. That's why I personally enjoy computational work due to the power of how much data we can extract.

My personal advice throughout research is to try something new! If you are interested in a topic, go full speed ahead and research on those topics. Papers, tutorials, and youtube videos are great resources to research about your chosen topic. After that, go ask google, stack overflow, chatgbt, and basically the internet to understand how to code something. If something isn’t on the internet, just trial and error until something makes sense (and you can back it up to something/experimental work).

For example, our D amino acids have been a big hassle throughout the past 2 years. I’ve tried to research topics about it but due to the complexity of our simulations and the lack of github repositories, I decided to just go face first and brute force learn and simulate experiments based on one change at a time. Once I got something I liked, I compared it back to other papers and double checked with our amazing professor! That shows you the power of computational work. It's easy, it’s fast, it’s frustrating, but rewarding in the end with the infinite amount of possibilities you can do.

So that's part of my motivation to continue computational work! I hope you find your passion to continue and investigate more on this topic (some ideas include changing NAMD parameters, pH conditions, other solvents other than water, etc).

See Tutorials here