Week 2 - Alex

I got to Oslo on Friday, and spent the weekend touring the city with my brother. Before jumping into the science, it’s worth mentioning something about Oslo:

Oslo is beautiful. The skies are usually blue, and you can see clear water and distant hills from most of the city. The sun is out from 3am to 11pm, so you never really get sleepy. There’s plenty of outdoor seating at restaurants, cafés, and bars around the Oslo harbor. My use of the word “plenty” is deliberate, as every alcohol-friendly outdoor space in New York is shoulder-to-shoulder by 2pm. With all this praise, it’s worth mentioning Oslo is also prohibitively expensive — usually between 130-200% more expensive than New York. It makes Brooklyn feel like a college campus. 

Now for the science:

The keynote talk on Monday was from Michael Regnier. He is a University of Washington professor who researches mechanistic and translational elements of myosin activator 2-deoxy-ATP. I don’t have a strong background in myosin mechanics, but found the translational impacts of his research inspiring.

Following the keynote, we discussed introductory biophysics concepts (Gibbs, mass action, cooperativity), which I learned in a biophysics course this past semester. It was good to review, as it set a foundation for the week. The next day built upon the first, by diving into the biophysics of ion channels, and using these equations to derive systems of ODE equations to construct an action potential. In the end, the first three days built up to implementing an ODE solver in Python to construct a multi-channel action potential.

The next two days focused on heart mechanics and finite element modeling using a PDE solver called FEniCs, developed by Simula. Wednesday was taught by Andrew McCulloch and Kim McCabe, from UC San Diego and Simula, respectively. This is where I started struggling with the material. I had never seen finite elements before, and assumed I could understand the majority of the material. Not the case. I was (sort of) able to grasp the whole heart mechanics bit. I had seen a lot of pressure-volume curves in undergrad, and knew what healthy and heart failure curves looked like. Once we jumped to modeling the heart with continuum mechanics, I was… dumbfounded. My focus and facial guise turned from understanding to existing, committing the important vocabulary to my brain, and hoping no one asked me at lunch, “How do you construct the displacement gradient tensor, again?” At the very least, when the day comes that I need to model something with continuum mechanics, I’ll know some of examples of how it’s used, and what to look up.

The next day was spent on FEniCS, a finite element solver developed by Simula. My introduction to FEniCS and all of its uses may end up being the most consequential thing I learn at Simula. The tool, while difficult to understand initially, enables me to run single-cell simulations in a fraction of the time, and to scale up my research from the single cell to micro tissue, and possibly, whole heart. The day was taxing on the entire group. The programming was new for a few people, and the math was new for almost everyone. While we previously appreciated the opportunity to work on problems during the lecture time, on Friday, we struggled to even attempt the problems. 

I’m excited for Monday. We’ll implement FEniCS to solve tissue electrophysiology problems. I’m hoping that my understanding of single-cell EP problems will flatten the learning curve for FEniCS.