Introducing fibrosis

Question

Is it possible to introduce the fibrosis (in my case, I want to apply ablation like application of scars in the tissue, so conductivity=0 in this zone) after some time from the start of the simulation and not immediately (at time t=0)?

Answer 1

You can save a statefile and then load it in a simulation in which you change to tissue conductivities in certain regions or change parameters of the ionic model. What won't work is to change the ionic model itself (e.g. from myocyte to fibroblast).

Comments

Thank you for the answer, I mean is it possible to introduce fibrosis (in this sense), after some time and not immediately after the simulation starts (t=0)?

---

Yes, fibrosis as non-conductive elements is possible by simply changing the conductivity parameters in the second simulation.

1) Tag regions in the model
2) Start simulation with normal conductivity, let run until for example t=500ms, save statefile
3) Start second simulation by loading this statefile but defining sigma_e = 0, sigma_i = 0 in your fibrosis region

---

Perfect, all clear. Is it possible to create this state file using PSD protocol?

---

openCARP +Help write_statef

write_statef:
    Defines the basename of the output file in which to write a single saved state. Each saved state will have a timestamp appended to the basename.

    type:    WFile
    default:(WFile)("state")


You can integrate this parameter to the openCARP call in any carputils script.

---

Thank you, I was able to apply your advice. Now my problem is to create a single view of the two simulations. In the sense that I carried out 2 different simulations: the first without ablation and the second with ablation. But if I wanted to hang the two simulations, how do I make the second simulation starts with the rotor tip in the position corresponding to the end of the first simulation?

---

I'm not sure if I understand your question completely.
What you want is to compare a simulation with ablation to one without? In this case:
- Start a simulation to induce AFib, store a statefile A, let's say at t=1000
- Load this statefile A and let it continue to say t=2000 for the one without ablation
- Load statefile A again in an openCARP call including your parameters for the ablation and let it continue to t=2000
Then you can compare the two output. Meshalyzer also lets you link two instances if you want to co-visualize them with the same view point, time point etc. Details are described in the mesahlyzer manual

---

Thank you for your answer. My point is that I was thinking to do in this way:  
-start a simulation to induce AFib, store the last position of the rotor tip (Phase Singularity, PS) ;
-pass the value of the rotor tip to a second simulation, in order to make it starts from the same point in which the first simulation ends and then introduce ablation.
So, my question is: Is there a way to save the coordinates of the position of the last PS of the first simulation in order to pass it as input (in the code indicated by 'center' in model.induceReentry.PSD) to the second simulation?

---

To do that you'd have to extend the carputils script.

However, this seems more complicated than necessary to me. If you store the full statefile and then load it again for your second simulation, you don't have to reinduce but can simply continue the simulation exactly from where you stopped.

---

thank you, I have tried with your strategy! Is it possible that some regions of the ablated zone remain still conductive, even if slowly? Because my ablation site is not totally black, but seems like the signal is still slowly propagating inside it. I think it is due to region tagging.

---

Yes, probably the case because you load the state before ablation with the transmembrane voltage at that time which is likely not resting membrane voltage and then reduce the conductivity drastically, so that it also cannot diffuse.
If this is a problem for your setting, I'd suggest increasing the conductivity in the ablation region a bit so that it still cannot be excited but the "remaining depolarization" can diffuse to other regions

---

Perfect, thank you so much!