Decoding equations that encode the atrial cells

I dived into the world of ionic modeling of the atrial cells and managed to unravel a little bit this vast field

After some weeks with many changes and new things to learn and see in Maastricht, it was time to get my hands dirty again and dive into my project in PersonalizeAF. As I mentioned before, most of my initial work is focused on improving the current modeling of atrial fibrillation done by our group. But this is a complex task and, in order to make it clearer to me and everyone else in the group, I was asked to do a seemingly simple task: document the ionic model of the cell that we want to implement.

What seems like a relatively straightforward task has many layers within, as anyone who did a literature review on any topic must know. Luckily, I had been prepared by our Information Search course during the Summer School! One important point is that relatively few papers are focused specifically on the models, but rather on what has been investigated using that model. This makes a lot of sense and highlights the science in it, but it also means that most of the content I was looking for was hidden in supplementary data and referenced from previous works. The image below gives an idea of the web I got myself into.

A cloud of papers related to the ionic model we are implementing; I started with the highlighted one. Source:

But eventually I started untangling this web and found my way through it, understanding better which contributions were made by each author, eventually getting to the model on which the following were based (it is not even in this picture, since it is from 1998).

As a real cell, the models evolve to include ever more realistic simulations of the electrical behavior of the atrial myocites, which is related to the dynamics of ionic currents. A long way has been traveled from the first models, which simulated the dynamics of three ionic channels, to the model proposed by Skibsbye et al. in 2016, which models 17 ionic channels and the intracellular dynamics of the ions in a very detailed way.

This very, very brief overview of the road to get to the current cellular models of the atrial myocyte gives an idea of the evolution in the field and the increase in complexity. The version used in Skibsbye et al., 2016 is very similar to the rightmost one.

I have myself travelled a long way while digging in into these models, from barely understanding the equations to getting a more detailed idea of what I am dealing with. With the help of this review, I managed to run some simulations with the improved ionic model and we are a step closer to reproducing more realistically the dynamics of atrial fibrillation.

It has been a very theoretical month, but it felt great to finally get a grip of what is going on with the models, so I can then start building upon the massive work that was conducted so far. I hope I can come with exciting results on this side in the next months.

By the way, this is possibly my last post before Christmas (are we not in March anymore?), so I hope you can all enjoy the holidays in a safe manner to recover the energies from this very unusual year. In the meantime, follow the progress of the PersonalizeAF project and of the other ESRs in our social media channels and blog!

See you soon!