Tag Archives: #BSURF

The End of an Era

And just like that, B-SURF is over. These past six weeks I’ve learned a lot about myself and the things that interest me. I came into this program not knowing what I wanted to do in science, just that I wanted to be a scientist. After spending six weeks hearing about my colleagues’ struggles in the lab moving small amounts of colorless liquid from tube to tube, I’ve decided that wet-lab isn’t for me.
At the beginning of this program the general vibe I got from people was that they felt sorry that my lab work was all virtual. Now, after going into the lab twice to make nanoparticles, I can say that I prefer coding over staring at tubes any day. I also didn’t have to deal with the frustrations of cells/organisms dying on me the day before data was ready to be collected, or the monotony of pipetting samples for hours on end. Throughout this program I was constantly engaged with my work. It was up to me to design the software pipeline for my project. I was given a task by my mentor, and it was on me to implement the features he wanted. One of the challenges that I’ve struggled with most being a self-taught programmer was finding confidence in my coding abilities. I knew that I knew how to code and problem solve, but other than stock problems I had no means to apply my skills. This program was exactly the push that I needed to give me the confidence in myself that I can accomplish problems put in front of me. As the second half of summer, and a condensed semester of organic chemistry, looms ahead of me, I am excited to say that I will continue with my project in the Reker lab. I still need to implement a machine learning model that will hopefully accurately make predictions in nanoparticle formation for me. I’m excited to see what the future holds, and I’m thankful for this experience allowing me to narrow down my search for what I want to do.

Analysis of Hydrogen Bond Formation in Molecular Dynamics Simulations Predicts Formation of Self-Aggregating Nanoparticles

Joe Laforet

Mentors: Zilu Zhang, Dr. Daniel Reker PhD

Department of Biomedical Engineering, Duke University

Co-aggregating nanoparticles can stabilize drugs with more than 90% drug loading capacity. While machine learning can be productively employed to identify nanoparticles, this approach requires large datasets. Simulations provide an opportunity to design nanoparticles without prior data generation, but this method has not yet shown sufficient accuracy. Here, I will develop a novel simulation-based approach that achieves productive accuracy of nanoparticle predictions. By pairing a predictive machine learning model and molecular dynamics simulation software, we analyzed hydrogen bond formation in simulations and used our findings to identify pairs of interest. We compared our predictions against already known data and found that the presence of hydrogen bonding indicates higher likeliness of nanoparticle formation in more than 75% of analyzed pairs. Using this analysis protocol, we plan to analyze and predict other small antiviral nanoparticle formulations aimed at targeting viral diseases such as COVID-19.

Bird Brains and Tech X

This past week we were tasked with going on stage in front of our peers and presenting an eight minute summary of our projects with nothing but a dry erase marker and a whiteboard. While I thought this experience was stressful to prepare for, I am thankful for being able to give an “old-fashioned” pitch of our work. It was interesting to see how much more challenging giving a talk is when your slides aren’t behind you. Personal reflection aside, one talk that captured my interest was George’s presentation on his work in the Mooney lab.

George is doing work with Zebra Finches and a mysterious (for proprietary reasons) biomarking drug called Technology X. Without declassifying anything important about it, Technology X is a drug that was developed with the intent of giving labels to different types of cells in the brain. If it works, it will allow researchers to better study the different parts of the brain on the cellular level. The Mooney lab isn’t responsible for developing this technology, however. They are focused on actually testing it out on live subjects. George’s job this summer is to perform careful neurosurgery on Zebra Finches and deliver Technology X to different parts of the brain.

This project is interesting to me for two reasons. First and foremost, one of my peers is performing neurosurgery on live subjects! Coming from a person who could barely dissect a pig fetus in high school biology, it blows my mind that George is able to work with that degree of precision, and keep his subjects alive after! Secondly, as someone who leans more towards the functionality of things in science, I was really interested in how Technology X works. Sadly I don’t have enough clearance to further probe its mechanisms, but it was still neat to hear about. Overall, this week was enlightening as I was able to see a wide array of the different projects going on in the B-SURF program. I find myself always being boxed into the same functional-type projects, so hearing more about applications and raw research was a welcome change of pace. I’m excited to see what my peers have to present at the poster presentation!

A Day in My Life

What does a virtual lab look like? In short, my days are whatever I make them out to be. Every Wednesday I meet with my mentor Zilu in the new Engineering building and we construct a game plan for the week. Sometimes before our meeting he’ll have me complete a short quiz to familiarize myself with the concepts I’ll use in the coming week. We then go over the quiz together while having a deeper discussion of the concepts covered. This usually takes around half an hour, so for the rest of the day we split off and get to our work for the day. We’re both doing a mix of coding and simulation analysis, so it’s challenging to have an over-the-shoulder mentor relationship. On days where I’m not in lab physically, I either work in the library on East, the library on West, or in my building’s study room. One of the perks of living in the digital age is that Zilu is just a Zoom call away if I need help debugging my code. 

I’d say that I have a love-hate relationship with coding. There’s nothing more satisfying than code working exactly how you intended it to, but that almost never happens. The bulk of what I do is trying to comb through the files I’ve made or scouring forum sites trying to make sense of the error messages I generate. I’m always learning while I work. As this program is going on I find myself running commands without even thinking of them. In the beginning I had to reference my “cheat sheet” for almost every line. Now I can generate .tsv’s and .pdb’s with my eyes closed. Everything I do follows a systematic path. It’s kind of repetitive, but since I’ve done the process hundreds of times now it’s second nature. My days are spent at my keyboard listening to jazz with my fingers dancing away at the command line. Getting in “the zone” is one of my favorite parts of this job. One of my favorite memories so far was when I had a Eureka moment at 3am. The night before I had been struggling with a bug in how to specify the parameters of the simulations. I went to bed grumpy, stewing over the red screen I had been staring at for hours before when inspiration struck. I woke up, grabbed my notebook, and then poured everything out of my head onto the page. After inspiration faded, I went back to bed and then implemented all of the features I had dreamt about in the morning. The most beautiful part? It worked like a dream.

Meet Professor Daniel Reker

Professor Reker has had a combined passion for chemistry and computer science since his high-school days. He was born in and attended school in Germany. The German school system is slightly different from the American school system. In what would be our equivalent of high school, Professor Reker focused primarily on chemistry and English while also minoring in computer science. At this stage in time, due to the lack of truly interdisciplinary, undergraduate educational programs, Dr. Reker was under the impression that he would have to choose between his two passions of computer science and chemistry. Based on the waves that computing was making in the early 2000’s and the resulting promising job market, Reker decided to pursue an undergraduate degree in computer science at the Technical University of Darmstadt, one of the top three computer science programs in Germany.

While he was accepted into a prestigious program, and was enjoying the computer science curriculum, Reker still felt like he was missing something in his education. Computer science appeared to be a powerful tool that should be applied to other domains to positively impact people’s lives. He was still passionate about biology and chemistry, so in order to stay with these fields he became involved with multiple extracurriculars in the biology department, leaning towards computational-flavored topics, and regularly attended seminars. After undergrad, Dr. Reker graduated with a degree in computer science, with added experience in computational biology. From here, he decided to further explore the overlap between computing and biology and earned a Master of Science from ETH Zurich in computational biology and bioinformatics.

As a master’s student, Professor Reker was especially drawn to the pharmaceutical science department of tETH Zurich and was interested in the application of algorithms for analysis and development of new drug candidates. After his masters, Reker stayed with the pharmaceutical science department and completed a Doctor of Science (equivalent to a PhD) with Dr. Gisbert Schneider in the “Computer-Assisted Drug Design” laboratory. After completing his PhD, Reker was yearning for more than just theoretical development of tools. He wanted to have a more translational impact, and actually use the tools he develops towards improving therapeutic options for patients. This drove him to the lab of Dr. Robert Langer at MIT, where Reker completed a post-doc in drug delivery, a later step in the drug development process with thereby higher chances of translation.

Staying true to his interdisciplinary roots, Dr. Reker’s vision for his lab is one that bridges multiple disciplines. As the lab gets more established in the new Wilkinson building, he aims to have roughly a 50/50 split between computational work and wet lab research with every student being involved in both aspects. The goal is to have a team made of people from a broad expanse of backgrounds. Having all of these different flavors of science working on the same projects greatly enriches the educational enterprise and the science, as there are multiple approaches being taken towards solving challenges in drug discovery and delivery. Professor Reker’s vision is one in which the lab is, “…an incubator space where students can learn to become multilingual in the different aspects of lab work and to come to learn what the hype around machine learning for pharmacology is about.”

Mentorship is also one of the most important aspects of science to Professor Reker. Even on the first day of lab meetings, I felt welcomed as Dr. Reker emphasized that his goal was to mentor students to hopefully surpass him as a scientist, rather than himself being a master of everything. This attitude has been something that has been with Dr. Reker for most of his academic career but was ultimately cemented as one of his core beliefs after his experience being an undergraduate TA for a very difficult computer science course. He ended up mentoring a group of students and the experience was so profound for them that they decided to become TA’s after him.

Wrapping up this interview, I learned a lot about Dr. Reker, and the journey involved with being an interdisciplinarian. Like Dr. Reker, I also find myself called to computer science, but still needing chemistry and biology in my life. Under Professor Reker’s mentorship, I hope to follow in his footsteps at the intersection between these three branches of science and become a “multilingual” student.



Dreaming of Baby Trees

What do you expect from your summer research experience?

Yep, that’s right. You understood that title correctly. You see, like many of my fellow BSURF researchers, one of the main hopes I have for my summer experience is the humble desire to just have done my experiment correctly and to see results. In my particular situation results will come in the form of sprouting seedlings of a select group of trees and shrubs. Now to see these type of results will be exciting for me for several reasons. First, as I pointed out, growth will indicate that I haven’t completely failed my experiment, which would be really great. Secondly, and this is my inner plant nerd coming out here, the idea that within my many, many petri dishes of many, many seeds, life is being brought forth to await my observation is just plain exciting to me. It’s exciting in that I am just interested in plant growth in general, and for the fact that my observation of these sprouting seedlings and any patterns I see and conclusions I draw about growth in differing salinity levels can eventually play a role in a bigger picture in which I am very passionate about, and that is conserving tree life in the actual outside world, one of the goals of my ecologically-based lab.

So, in terms of expectations I would say I expect this kind of interest and passion to grow as I (hopefully) see results. Also, I do honestly expect to see some such results eventually, partly because I feel that I have followed the procedures to my experiment carefully/with understanding and partly because at the very least, I know I will be able to ask my PI, Dr. Wright, for pointers and corrections if I end up needing to. I also believe that as time passes I will become more comfortable in my lab setting as I start becoming increasingly familiar with where things are, how to operate experiment-related machines, how to set up my experiment more and more efficiently, and as I become increasingly comfortable with those working in my lab with me. For the most part, these have been kind of short term expectations, so in the long run I expect my summer experience to impact my life by perhaps becoming a longer term project that I can alter for even more detailed and helpful results down the line. Additionally, I hope that this experience will give me insight into my academic and occupational goals. For instance, I have been weighing my interests in Duke’s Environmental Science program versus Duke’s Biology (with a focus in Ecology) program, and my new connections to other students, graduates, and biology faculty have given me more information on the program differences so that I might go where my main interests are. As another example, I wanted to walk away from this summer knowing whether research is a side of science in which I am particularly interested so that I could apply that information to my plans for my future job and/or schooling decisions.

Basically, then, to answer the question about my expectations, I am looking forward to BSURF helping me get to know my interests and goals better as well as helping fuel my ever-growing fascination with plants (especially trees!). And honestly, all along this adventurous road I’m embarking upon, I will probably be daydreaming about my little seeds bursting forth with life and becoming the most adorable baby trees ever.