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Ofer K

- Research Program Mentor

PhD at Harvard University

Expertise

physics of living systems; quantitative data analysis; computational projects; biological theory; applied mathematics

Bio

I am a theorist, with a background in physics, mathematics, and computer science. In my research, I aim to understand how biology manages to solve problems that have stumped us, and then leverage that understanding to further our own design capabilities. My research interests are as broad as biology is, from understanding the molecular mechanisms behind CRISPR-Cas systems, to predicting multi-molecular self-assembly of proteins/RNA, all the way to ecological questions at the level of entire communities of organisms. I'm excited to work with students on all sorts of quantitative problems, in and out of biology. In my free time, I enjoy playing tennis, going on hikes, playing piano, and hanging out with friends. Looking forward to meeting you!

Project ideas

Project ideas are meant to help inspire student thinking about their own project. Students are in the driver seat of their research and are free to use any or none of the ideas shared by their mentors.

How does the size of an ecological community affect its long-term behavior?

Mathematical models have had an enormous impact in understanding ecology. Recent work (de Pirey & Bunin, 2024) showed that a well-known model of ecological systems known as the Lotka-Volterra model (or sometimes as the resource-competition model) can give rise to surprising behavior. For very large systems with randomly chosen parameters, populations can either be stable or chaotically fluctuating, depending on the value of one parameter (the migration rate into the community). In this project, you will explore how these results depend on the size of the ecological community. As you change the number of members in a community, what are the effects on coexistence vs. extinction? And for communities that coexist, how does the nature of that coexistence change with the community size? In this project, you will write code (preferably in Python or MatLab) to simulate an ecological system as a set of differential equations. You will use this code to generate data that you will then analyze. If you'd like, there will also be opportunities to address these differential equations analytically. The preferred outcome of this project will be a scientific research paper.

Self-assembly of finite structures

Both proteins and nanoparticles often self-assemble to make multimers. (A multimer is a single object constructed from many individual monomers bound to one another). A major challenge is how to ensure these multimers don't grow too large. One option is to make the multimers curved, so that the multimer is a closed circle -- but that can often be quite limiting. In this project, you will explore another possibility: having the multimers themselves control the production of new monomers. Can this form of control be used to limit the size of self-assembled multimers? If so, how robust is this control? In this project, you will construct a model for a system of self-assembling proteins or nano-particles. You will then analyze the behavior of this model. Preferably, you will analyze this behavior numerically, with code you will write in Python or MatLab. If you'd like, there will also be opportunities for analytically addressing the system. The preferred outcome of this project will be a scientific research paper.

Coding skills

Python, Mathematica, MatLab

Languages I know

Hebrew, fluent

Credentials

Work experience

Princeton University (2021 - Current)
Lewis-Sigler Scholar

Education

Princeton University
BA Bachelor of Arts (2016)
Physics
Harvard University
MA Master of Arts (2018)
Biophysics
Harvard University
PhD Doctor of Philosophy (2021)
Biophysics

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