2022 was a year of transition. I received a post-doc fellowship at the University of Wageningen in the Netherlands to study cuttlefish biomechanics and develop new soft robots. We moved in July and are still working to settle in here in NL. The research has been altogether new and fascinating. I’ve been mentoring undergraduate students while they work on theses […]
How to swap the bearings in a Leybold Turbovac 150 turbo pump
The bearings went out on our reactor turbo pump. It started making a loud whine. A rebuilt Leybold 150 costs like $4000, so swapping them out myself seemed like the only real option. Here’s how it went: Step 1: Remove the heatsink and housing. Use a metric allen wrench to remove the housing. It’s got a rubber o-ring holding it […]
How to align a 4F optical system for digital inline holographic microscopy.
The goal of a 4F system in holography is to generate a collimated beam of single-wavelength light, shine it through a sample, and then magnify and refocus this light onto a camera sensor. When the collimated light hits the sample, it creates concentric rings around the objects known as diffraction patterns or Airy discs, like this: These diffraction patterns provide […]
How to use Zotero (and keep your papers on Dropbox).
Zotero is a simple, open-source solution for organizing your papers, books, websites, and other sources. It works great with Sci-Hub and even has a Firefox/Chrome add-ons so that you can quickly add papers straight from your browser. Additionally, it works flawlessly with Word to quickly add in-text citations and produce a bibliography of your cited sources. What you’ll need: Zotero […]
IEC Reactor Update
After a bit of a hiatus, we’re making good progress on the reactor! We recently replaced the cathode and feedthrough with a titanium surgical rod and a titanium bicycle stem spacer. Alumina tubing at this size is extraordinarily expensive, so we repurposed TIG welding nozzles for the shielding. I’m quite impressed with the results, but the new materials have added […]
How to install Ubuntu Linux and run Jupyter Notebook on Windows 11 (with CUDA!)
Dual-booting Windows 10/11 and Ubuntu is still the preferred method for power users, but for regular folk like me I think using the new WSL (Windows Subsystem for Linux) is totally serviceable. It makes it so much easier to multi-task since you can operate within both ecosystems at the same time. I tried a number of different methods to get […]
How to do scientific research like a scientist.
When a scientist makes a discovery or completes an experiment, they communicate their results by publishing a paper in a peer-reviewed scientific journal. This peer-review process can be quite challenging, involving months of back-and-forth editing, new analyses, and potentially rejection. These peer reviewers are usually experts in the same field as the author, and provide critical feedback to improve the […]
Building an IEC Fusion Reactor
This may sound crazy, but it’s been my dream to build a nuclear reactor since I was a kid. I started college as a physics major, but switched when I discovered biology. Now that I’m working in the UPS Physics Department, the stars have aligned and I finally have an opportunity build a fusor! What’s a fusor, you ask? It’s […]
Designing a 3D-printed flow chamber
I’m working on a small, water-tight chamber to measure how flow affects feeding kinematics in Vorticella, a single-celled protist that adheres to surfaces. There are some real design constraints, namely that it must be small enough to accommodate the relatively short (10mm) working distance of the objective lens we’re using. I designed a prototype in Solidworks. The clear interrogation area […]
How to create an ultrametric dichotomous phylogeny in R
If you’re doing comparisons between species, you might be interested in plotting those species on a phylogenetic tree. Once you’ve created the tree, you might want to do some statistics. Generally, you’ll need a phylogeny that is both ultrametric and dichtomous to do these stats. Here’s one way to create this kind of tree in R. Start by downloading a […]