The Simulated Heart

For the past few months, I’ve been playing around in a program called NetLogo that allows you to simulate agent-based emergent systems with pretty much no effort whatsoever. Being something of a cardiology nerd, I had the idea a while ago to build a vastly simplified model of the electrical conduction in the heart. With the Belousov-Zhabotinski reaction in mind — which appears in James Gleick’s excellent book Chaos, which also has a chapter on the electrical waves of the heart, which is probably what sparked my inspiration in the first place — I set out to build a simple electrical-wave model. What I got was competent enough. At the beginning of the simulation, a single “spark” in the center of the simulation grid would produce a radiating wave. Sometimes, a defect on the front of that wave would cause the wave to dimple, and then to curl in on itself, producing a self-sustaining oscillation.

Some time later, when I began to get interested in cardiology — especially cardiac arrhythmias — I began to realize that my simple little model produced some behavior that was actually strangely comparable to that of a real heart. So, I modified it to be even more heart-like. I programmed the simulator to generate an initial spark at the center of the grid every fifty time steps or so. As I watched the waves propagate across the screen, I was, frankly, mesmerized. For a while, the waves would march along. Then, one of them would go wobbly, curl in on itself, and start oscillating rapidly. It bore a great deal of similarity to some of the real computer simulations of electrical activity in the heart that I’d seen, specifically to those that generated ventricular tachycardia.

With this as an impetus, I spent many hours revising and playing with my system. I recently downloaded the newest version of NetLogo, and decided that it was time to re-write the heart simulator, which had been mangled and cluttered beyond recognition by the process of incremental revision — something that happens to most of my programs.

This newest version — Version 3, by my count — is my most complete yet. A simulated beat travels through the simulated atrium (in the simulation, the atrial activity is represented by yellow waves), then hits the simulated AV node — the part of the heart’s conduction system that connects the atria (the upper chambers) and the ventricles (the lower chambers) — hangs around for a moment, then starts to propagate as a new wave (this one red) through the simulated ventricles. I’ve observed quite a lot of fascinating and remarkably heart-like behavior in my simple model. I’ll run through some of it here.

This is the main screen. All those buttons and sliders set up the simulated heart’s various parameters. If you can see it in this image, the “refract-length” slider controls how quickly the cells become able to fire again after each firing. The quicker that interval, the more easily the heart will go into fibrillation. That’s why I built in the handy little “defibrillate” button you can see to the right of the display.

As I did a run of the simulation to produce an image for this post, I was lucky enough for the simulation to do something interesting almost immediately. Note the oddly distorted third beat. That’s actually the result of an extra breakaway wave in the simulated ventricles. In real life, we call things like that “palpitations” or “premature ventricular contractions.” When the model’s heart rate is faster, you can actually observe the compensatory pause that comes after most premature ventricular contractions.

A final note on this image: in order to make the pretty EKG-like display, I had to cheat a little. In reality, the small waves represent just as much activity as the large ones (since the two grids are exactly the same size) but since the atria are a lot smaller than the ventricles in a real heart, I thought it would be a good idea to de-emphasize their activity a bit. This also has the benefit of making my fake EKG look a lot more like a real one. I’m currently working on a way to make the conduction in the simulated atria more realistic.

Here, the simulated heart degenerates into the deadly arrhythmia known as ventricular fibrillation. In this often-fatal arrhythmia — which is the primary cause of sudden cardiac arrest syndromes — the ventricles, which represent the majority of the heart’s mechanical pumping power, simply begin to wiggle and wobble randomly, rather than beating in an organized fashion. The result is that no blood gets to the body and the brain, and death results in about ten minutes.

I observed quite a lot of fibrillation of one kind or another in my simulated heart. Since I intentionally set the refractory time short — that is, the cells recovered their firing ability quickly — the waves had a strong tendency to curl in on themselves and break up into spirals. These spiral waves quickly degenerated into clusters of randomly-oscillating cells. About two-thirds of the way through the run, you can see that the fibrillation suddenly stops. That was the result of me pressing the “defibrillate” button, which sends ninety percent of the cells into the refractory phase, unable to fire until they recover. Towards the end, you can see that the “normal sinus rhythm” returns.

I’m actually quite pleased with this little simulation. It wasn’t terribly hard to build — then again, nothing in NetLogo is — and it produces interesting results. Here are my current goals for it:

  • Change some of the parameters so that they better reflect the physical disparities between the atria and the ventricles.
  • Improve my model of the AV node so that it discharges more realistically. Currently, it simply causes the electrical particles to pause for a moment, after which they are released. This means that, unlike the real AV node, my simulated one has a “memory,” and rather than discharging all at once like the real version, it simply discharges in the same order as the pulses that strike it.
  • Incorporate some kind of system to simulate damage to the heart.
  • Refine the electrical model so that the simulation is capable of producing ventricular tachycardia — a dangerous but more organized cousin of ventricular fibrillation in which a single self-sustaining oscillating spiral causes the ventricles to contract too fast to pump effectively. At the moment, the simulated ventricular tachycardia tends to degenerate into ventricular fibrillation almost immediately, making it difficult to study.
  • Make the translation between the simulated heart and the simulated EKG more realistic, so that it produce something more like a real EKG.
  • Make the model more analog. I’m hoping that this will solve a lot of my problems, but it’s probably going to be one of the hardest features to implement, with the possible exception of the better AV node simulation.

I’ll post updates as they come, and I soon hope to have a Java version of the simulator uploaded so that other people can play with it.


4 Responses to “The Simulated Heart”

  1. SimHeart 2.0 « The Life of a Math Major Says:

    […] sit down to work on my heart-simulation project, I get a lot more done than I was expecting. In my last post on the subject, I talked about how I wanted to integrate a more realistic model of the […]

  2. Nicanor I. Moldovan Says:

    Hi! Congrats on this nice modeling! Although I am a newbie in NetLogo, my little cardiology background allows me to appreciate the importance of this work. Do you plan to publish it (recommended)?
    Somewhere you said “This means that, unlike the real AV node, my simulated one has a “memory…” . It might not be the same thing, but heart does have memory (in its electrical activity), and it would be interesting to see what is that, and how it arises ,using this model. More tempting, therapy with stem cells could both help and jeopardize a sick heart’s electrical activity. Do you want to model that too? If so, I could help with what I know. Personally, I want to learn more netLogo with someone advanced, like you. Do you want to make a deal?

    Best regards,


    Nicanor I. Moldovan, Ph.D.
    Assistant Professor
    Departments of Internal Medicine/Cardiology
    Ophthalmology and Biomedical Engineering
    Davis Heart and Lung Research Institute
    473 W. 12 Ave, Room 305A
    Columbus, OH 43210
    tel. 614-247-7801
    fax 614-293-5614

  3. asymptote Says:

    Thank you very much! I’ve replied to your comment more fully via e-mail, since it was too long to write as a comment.

  4. SimHeart 3.0 « The Life of a Math Major Says:

    […] months ago, I wrote a series of posts about the behavior of my NetLogo heart simulation (namely, this one and this other one). SimHeart has been on the backburner since then, partly because I was making […]

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