Samuel B
- Research Program Mentor
PhD candidate at Harvard University
Expertise
Biophysics, biochemistry, computational biology, protein evolution
Bio
I am a Biophysics graduate student at Harvard University. As an undergraduate at Yale, I studied biochemistry, and grew increasingly fascinated in how the simple, one-dimensional amino acid sequences of proteins allow them to take on their complex structures and functions. This led me to an interest how we can design new proteins from scratch, and how naturally evolved proteins may be different from a protein that you try to design to have a stably folded structure alone. At Harvard, I am investigating the relationship between protein structures' and how they evolve, both in order to gain a deeper understanding of life's history and to be able to better design new proteins for applications throughout biotechnology and medicine. To do so, I am interested in combining computational and experimental methods. Outside of the laboratory, I like to cook, write, hike in the mountains, and hang out with my orange tabby cat, Linus Pawling.Project ideas
Literature review on a topic related to protein structure, evolution, dynamics or design
Proteins are extraordinary molecular machines that carry out the vast majority of essential biological functions in your body - from breaking down sugar into energy to firing neurons in your brain - and here you will be able to explore in depth a topic related to the chemical and physical foundations about how these incredible nanoscale machines perform their functions; how they originated through evolution and continue to evolve today; or how we might be able to leverage this knowledge to design new proteins. We would begin with a series of more broad sessions before narrowing down on a specific subtopic, learn to engage with primary literature, and summarize your findings through a blog post or news article.
A computer-based project looking at the structure and evolutionary history of a particular protein family
After learning the basics of biochemistry and molecular evolution, you would choose an interesting and exciting family of proteins and collect a large number of protein sequences from many different families. After aligning the positions in this family, you could build a phylogenetic tree and compare your tree to experimentally solved structures of the protein and its known functional properties. This would culminate in a research report hypothesizing about how the different functions of proteins in this family may have diverged and proposing possible future experiments. Does not require programming experience, but for an interested student, we could incorporate some coding!
Introduction to scientific computing with applications to biochemistry or medicine
Ideal for a student with some programming background, although I am also happy to work with a student without experience who is interested in getting started learning scientific programming. We would begin by going through the basics of the Python programming language and its scientific computing libraries numpy and scipy, and then applying it to a simple coding project where you would write up your own code to analyze a set of real biological data and make predictions. The project would then culminate in a research report or blog post.
Final Notes
I am open to mentoring projects that are structured primarily as a literature review, culminating in a paper or blog post, or ones in which a somewhat more computationally-minded student could work with real scientific data and write up a final report.
Coding skills
Proficient in Python.Languages I know
Conversational knowledge of FrenchTeaching experience
I have taught a series of one- to three-lecture classes to interested high schoolers for Splash at Yale, ranging from "Protein Structure, and Design" to "Genome Editing with CRISPR/Cas9" and "Atoms and Molecules." In these classes, I tried to inspire high schoolers to take the topics that they had learned about in their high school science courses and apply them to the cutting edge of scientific research, so that they could understand how the principles of chemistry and physics help explain the extraordinary complexity of the biological world.Credentials
Education
Reviews
"My experience with Sam was exceptional! He helped me so much in the implementation of my project - I would not have been able to get as far as I did if he hadn't showed me the resources, tools, and code that I needed to . His advice and guidance was absolutely invaluable, and he was an amazing person to work with as well! Sam was very easy to communicate with, always urging me to ask questions or reach out whenever I ran into a problem, and I really appreciate how he took the time to introduce me to all of the new concepts I used in my project."