This page contains links to the documentation for some of my projects that do not classify into the typical academic categories. Almost all of these are work-in-progress and are updated intermittently.

Evolvability in 2-dimensions

In our paper on the evolution of evolvability in digital organisms, we found that populations localize on areas of the genotype space that lie on the boundary between phenotypes in a changing environment. The simulations here model a similar phenomena under a simpler Wright-Fisher population genetic model.

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Building the ZE3 macroscope

This project documents the construction of a macroscope, a fluorescence imaging platform that can take timelapse pictures of growing microbial cultures. This hardware is heavily inspired by previous work on imaging spatial dynamics in microbial communities. I am currently using this device to address questions on the evolution of evolvability in phage populations.

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Embedded spatial simulations

Tiny, powerful, and cheap microcontrollers have become extremely abundant in the last few years. In order to learn how to program these devices, I am trying to create a small computer that can be used to simulate spatial biological processes (including spatial SIR models, population genetics, and models of speciation). I started out with a STM32 MCU but have recently switched to the RP2040 chip for this project.

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Theoretical Evolutionary Biology I: Mathematical Population Genetics

This is the website for a course designed to introduce theoretical ideas in population genetics to students from theoretical biology and physics backgrounds. Covered areas (tentative) include: Deterministic models of evolution, Wright-Fisher and Moran models with two alleles, infinitely many alleles, two and many loci, diffusion theory, the coalescent, and spatially structures populations.

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Theoretical Evolutionary Biology II: Modern Evolutionary Theory

This is the website for a course designed to introduce modern theories in the field of evolutionary biology to an audience adept to classical population genetics. Covered areas (tentative) include: Quasispecies and the error threshold, evolution on the genotype-phenotype map, clonal interference, robustness and evolvability.

Go to the project page