Tag Archives: RF2021-Week1

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Diving into the Realm of Quantum Simulation

     Nanoparticles, quantum mechanics, molecular dynamics, supercomputers, and machine learning. All five of these topics sound like things that Tony Stark and Bruce Banner work on in their free time. However, with modern advances in computing technology these fields are actually able to exist and coexist in a beautiful way giving rise to the real-life field of nanomedicine. 

   I’m coming into the Reker lab as a rising sophomore BME student still trying to figure out what I actually want to study. My interests are spread over multiple disciplines, and it’s hard to pin down exactly one thing that I like. Growing up I loved playing with computers. Not building them like Jimmy Neutron, but simply playing video games like Minecraft. I loved how the computer was able to generate an environment that had similar rules to reality. You have objects in the world, collision rules, like when you jump on slime blocks, gravity, and a day-night cycle. Each of these parts of the simulation combine in a unique way to create the “world” and give a fun experience while playing the game. The combining of multiple processes to generate a real-life simulation is basically what Dr. Reker and other computational chemists are doing with Molecular Dynamics.        

 Before the B-SURF program I had no idea that computational chemistry even existed. After reading through some papers and meeting with Dr. Reker and my mentor Zilu, I’ve learned that computational chemistry could revolutionize the field of drug development. Through simulating interactions of molecules with the Molecular Dynamics software, we’re able to predict what the resulting body would be if we combined the reactants in real life. Specifically, I’m going to spend my Summer researching the potential formation of nanoparticle complexes between different drug and excipient molecules. While most of the chemistry is flying a bit over my head, I hope that as the Summer goes on, and as I finally get around to taking Organic Chemistry, I will understand more about the chemical details of why and how our simulations of molecules form. I’m also excited to learn more about optimizing the parameters of the simulation to perform more accurate predictions. For now though, I’m happy with this past week’s work and my little knowledge in how to generate simple simulations. I might just be a big nerd, but I find it magical that we’re able to take a simple string of letters and pass through a coding pipeline and out comes a visual model of molecules interacting with each other.


     While I don’t get to go to an in-person lab like my fellow B-SURFer’s, I wouldn’t want to change anything about my experience so far. I’m a learn-by-doing kind of guy, and the flexibility of working in a computational lab fits that perfectly. I also know that as time goes on, and as Dr. Reker’s lab gets established in the new engineering building, we’ll eventually get to translate our simulations into real-life. Overall, I’m very excited for what the future holds, and am extremely grateful for Dr. Reker and Zilu for giving me the chance to study underneath them. Here’s to the start of a great summer!

Here is one of my first simulations. In this example, I simulated the interactions between the anti-cancer drug Sorafenib and Cholic Acid. I’m still working on finding the best way to make a movie to upload, so stay tuned for more cool gifs.

 

Tipsy Tails In Lab

As a recently declared neuroscience major, my experience with the neuro department is pretty limited. While I’ve known for some time that all things concerning the brain are my primary interest, it’s always been over a pretty broad scope. Throughout this week, it’s been completely the opposite. I’m working in the Bilbo lab and it focuses on all things microglia. For those that don’t know microglia are the resident immune cells of the brain, but they do so much more. A lot of the research in the lab, in very simplistic terms, involves messing with microglia in some way and seeing the outcomes. That brings me to the experiment I’ve been helping with this week.

I’m working with mice and as someone who did not even grow up with pets, it was a bit of a shock the first day. But over two days, I’ve learned quite a few interesting things about them. Fun fact: mice can’t see red light, so whenever we work with them in the dark, we wear headlamps that shine red light. Speaking of the dark, a big part of the experiment is giving mice alcohol when the lights are off. I don’t exactly understand all of the scientific reasoning, but there is a really interesting relationship between alcohol (causes an inflammatory response) and microglia, so I’m excited to keep working on this project throughout the summer and to hopefully analyze some data.

Lastly, I wanted to talk about how working in research feels for the first time. As someone who was usually stressed during chemistry lab, I thought I would have a similar feeling when engaging in research. But I am happy to say that this has been an incredibly positive experience so far. Everyone I have interacted with in the lab has been super encouraging and responsive to the questions I have. I already feel like I’ve learned a lot, not only about microglia but how to be a better scientist so I’m looking forward to how much I know by the end of this program.

My Field Frog

This week, I virtually met everyone I’m working with at the Bernhardt Lab, AKA Duke’s Aquaterrestrial Biogeochemistry Lab! It’s quite a mouthful. and a bit overwhelming to hear at first, but so far I’m enjoying the lab. At the lab’s weekly zoom meetings, everyone is encouraged to state their “weekly frog.” This frog is a weekly goal that we set for ourselves in front of everyone so we can be held accountable for these goals for at the next meeting. I enjoyed hearing the impressive goals that people set for themselves–I’m bad at remembering names however one wonderful person is collecting data to see how the United States’ rivers have changed temperature since the 1950s. I have the opportunity of taking thermal images of rivers! I’m very excited to learn about all the different field methods and techniques that environmental science has to offer 🙂

My weekly frog is to be in the field as much as possible and learn everything I can about my work. So far I’ve been in the field twice and I loved it! My project involves sampling aquatic and terrestrial bugs at three different river sites in Durham to see what the differences in biodiversity are between each site. We are currently focusing on fly larvae. We will use our knowledge of which Orders of flies are sensitive to pollution and our data to show the quality of each site. Then, we will grind the bugs up to see if there is any bioaccumulation of contaminants in their food webs. I’m excited to go into the field and learn more about the work I’m doing.

I’m specifically excited about working with the Bernhardt lab this summer because I will also be working with them in the following fall and spring through Bass Connections. Coming into this project early will allow me to get the hang of the work quickly so I can have more time to explore my interests. All in all, I’m grateful for the for the opportunity of working in the Bernhardt Lab and I look forward to what this summer has to offer.