From REU to Population Biology Workshop Participant: A Conversation with Mete Yuksel
- NITMB
- Jul 17, 2025
- 6 min read
More than a research institution, the NSF-Simons National Institute for Theory and Mathematics in Biology (NITMB) is a community collaborating to expand our understanding of biological systems. The NSF-Simons NITMB community is composed of researchers at all career levels, from distinguished faculty to undergraduates beginning to determine their research interests. Preparing the next generation of interdisciplinary experts will be crucial to expanding the potential of mathematical biology research. NITMB is committed to training tomorrow’s leaders in this space through programs like the Summer Undergraduate Research Program, which is currently running until August 15th. This program provides undergraduates with access to interdisciplinary research opportunities, skill preparation workshops, and integration into NITMB’s expansive network of researchers through attendance at NITMB’s Scientific Programs. Ultimately, the Summer Undergraduate Research Program equips undergraduates for a thriving career with continued support and inspiration from the NITMB community. One researcher who began their journey at an NITMB-adjacent program and has grown along with NITMB is Mete Yuksel.
Mete Yuksel’s connection to NITMB began before the Institute was formed. Prior to the launch of NITMB, Northwestern University developed the NSF-Simons Center for Quantitative Biology (CQuB). This Center would serve as a framework for developing NITMB, which replaced the Center. Yuksel first encountered the NSF-Simons Center for Quantitative Biology while looking for summer research opportunities as an undergraduate and discovered the Center’s Research Experiences for Undergraduates (REU). After participating in the REU, Yuksel continued to engage with the evolutionary biology community, and more recently attended the Modeling and Theory in Population Biology workshop at NITMB. With his return to the CQuB and NITMB community, we spoke with Mete Yuksel to discover the trajectory of his research after the REU and his hopes for the future of NITMB.
How did you first discover the NSF-Simons Center for Quantitative Biology REU? Why did you choose to participate in the REU?
“I came across the CQuB REU program website when I was looking for research opportunities during the Spring of 2021. I was excited to see that there was a program that combined math, computing, and biology. I liked the idea of working on something applied, and I was excited to see so many faculty members with interdisciplinary interests (ecology, development, physics, math) were participating in the program.”
During the REU, what research did you support?
"I worked with Drs. Alvin Baylis, Vladimir Volpert, and Thomas Stiadle (who was, at the time, their graduate student). We analyzed the behavior of a spatially-explicit formulation of the two-species Lotka-Volterra competition model. This is a classic model in ecology, which has been studied for over a hundred years and is often taught in introductory differential equations and ecology courses. In the absence of spatial structure, the model predicts that differences in competitive ability between the interacting species give rise to competitive exclusion of one species (i.e., extinction of that species in the long-run) when competition between species is stronger than competition between them. When interactions occur in one continuous spatial dimension (e.g., along a coastline or river) and movement is diffusive, differences in movement can also give rise to exclusion. We showed that there is another mechanism of competitive exclusion in two spatial dimensions (i.e., the plane): curvature in the boundary of regions occupied by the two species under consideration. It turns out that, even if species are equally ‘fit' and mobile, the spatial configuration of individuals can still lead the system to a state dominated by only one species. This is because there is, in some sense, more space outside of a region of positive mean curvature than on the outside. In the special case one species is in a circular patch and surrounded by the other species, the species on the outside becomes concentrated as it moves inward and the species on the inside becomes less and less concentrated. This leads to exclusion of the species on the inside and, using asymptotic analysis, one can calculate the approximate speed at which the circular patch shrinks.
This was a super fun project to work on! My favorite aspect was applying various tools in numerical analysis to solve the system of PDEs describing the densities of the two species. (I had just taken a numerical methods course, which I had really enjoyed, and this was the perfect way to put that knowledge to use! A bunch of interesting mathematical objects popped up.) I used the FORTRAN programming language to numerically solve the system. Although it was frustrating at times — I remember others in my cohort were shocked when I told them I was learning this language — it was a really valuable experience. After completing the project, I also became interested in the connections between stochastic microscopic models (namely, interacting particle systems) and deterministic macroscopic models (including the reaction-diffusion system we were studying), which are obtained by taking certain limits. There are very rich connections between these types of models, which I have come to appreciate more and more as I’ve continued to work in theoretical population biology.”
In your current work, what is a central problem or question you’ve been asking in your research?
“A central problem I am working on is how evolutionary processes such as mutation and recombination — which are usually thought of as inputs to the evolutionary process but are also outputs — vary and evolve. I combine mathematical models and comparative genomics to do this, and like using RNA viruses as a model system.
I am developing mathematical models to describe how the recombination landscape, i.e., the probability distribution crossing over to the left of any location on a focal chromosome, evolves. In the last 20 or so years, we’ve learned a lot about where recombination events occur. In some species, recombination occurs in small stretches of the genome called “hotspots” while, in others, no hotspots exist. (In fact, the gene that underlies the localization of recombination in humans, PRDM9, is among the most rapidly evolving in mammals!) In some species, recombination tends to occur near the end of chromosomes while, in others, landscapes are more uniform. It’s variation all the way down! And, excitingly, there is a large (growing) amount of data that can be used to get a better handle on the causes and consequences of this variation. With collaborators, I have recently developed a mathematical model to understand how recombination landscapes vary and evolve under neutrality and am currently using data from flowering plants (among other taxa) to parameterize the model and test hypothesis about landscape evolution over macroevolutionary timescales (e.g., if some chromosomes’ landscapes evolve faster than others).”
How did your experiences in the REU influence your current research interests?
“The REU was influential in a couple of ways. First, it was a great way to cement my interest in theoretical population biology! The REU project showed me that there are a bunch of interesting mathematical objects that crop up when describing ecology and evolution, and that there is a lot about biology one can learn by modeling the core features of a system. Second, I think it has shaped how I approach the interpersonal aspects of science. I was fortunate to have great mentors throughout my time in science, including during the REU, and I think that’s a big thing that has kept me going. I remember that after I presented on the work I did during the summer — at a “student showcase” at the end of the REU — Alvin sent me an email with a subject line that amounted to ‘That was excellent! I’m proud of you.’ Having people support you and your growth as a scientist is one of the best parts of the job, and something I’ve tried to recapitulate in teaching as a graduate student. Similarly, I think the collaborative aspects of the work I did in the REU have inspired me to be more open to collaborations in other projects.”
What excites you about NITMB?
“Attending the Society for Modeling and Theory in Biology (SMTPB) meeting was the first way I engaged with the NITMB since the REU, but I’d be very eager to return and make use of the incredible research support provided by the Institute. When I did the REU, the NITMB was not yet called the NITMB and was definitely not operating from the 35th floor of a very nice building in downtown Chicago! It was really exciting to see how much it’s grown and how many people have been touched by the infrastructure (physical and otherwise) to support mathematics and theory in biology.”
What are you hoping to work on in the future?
“One of the things I like about theory is that I can work on a lot of different problems! That said, I see myself continuing to work on recombination (it is so interesting!) and modeling the evolution of function-valued traits in the near future. The SMTPB meeting at NITMB helped foster connections with others who are interested in these problems, and I’d love NITMB to work with them and the amazing community of mathematical/theoretical biologists in Chicago.”
Mete Yuksel’s ongoing enthusiasm for mathematical biology research and his active involvement in NITMB programs and community exemplify the impact of NITMB’s approach to education and training. We are proud to have Yuksel as a part of the NITMB community, and we look forward to the innovative discoveries his work in evolutionary biology will bring. More information on Mete Yuksel’s research is available on Yuksel’s website. Yuksel is also available to discuss his work over email.
