Sun, milk and forests. Making the party go on

0 Setup

Picture this.
It’s 7 a.m. in the morning. Nobody speaks.
You just woke up.
You unpleasantly turn the lights on.
You do your personal hygiene and other morning routines.
You sit in kitchen, prepare breakfast, make coffee and pour milk in.
You scroll on your phone.
You tap on a not very user friendly website.
You have hard time navigating in it.
You get bored, so you stand up and leave home to go to work.

During this relatable (?) situation, there are 3 moments that are somehow related to what I do here in the University of Ljubljana.

Stick with me.

1 Lights

1a Lights out

A cat turning on the lights.

The moment you turned on the lights, you pressed a button, you allowed electric current to a bulb, which was received from a cable, and if you follow its lead, you end in a power plant. A place that generates power.

But, with a cost. Either to the environment, the environment or to the environment. Despite that the second is more sustainable than the first and the third more sustainable than the second, all energy generation methods have drawbacks.

You might think that drawbacks are inevitable. We always have to sacrifice something.

1b spotLight

A spotlight stock image.

What if there is a way to generate power from something trivial like water? A way to generate power

  • like the magician pulls a rabbit from an empty hat
  • like the sun generates heat
  • like Zeus’ lightning bolt generates infinite lightnings
  • like internet creates memes out of nothing.

There is a way that allow us to generate very very large amounts of energy from water molecules (Hydrogen, we don’t need oxygen), and some other atoms (Deuterium).

One of the examples in the list is the actual way, and no, memes are not the answer.

1c sunLight

Sun doesn’t have a cable connected to a power plant. However is always shining and providing energy for poor planets like ours. The cheat sun uses, is called plasma fusion.

In short, if small atoms became very hot (more than 10K K or 9727℃), electrons and nuclear separate, and ions and electrons float all over the place like having a party (this is plasma).
If plasma gets very very hot (more than 100M K or 99999727℃), ions are partying so hard, that after one point they can’t stand partying anymore and are coupling into forming larger atoms in a process called plasma fusion. During this coupling, they are having a fest and they celebrate by releasing energy. Big amounts of energy.

For decades, scientists try to construct a hat from which they are able to pull rabbits. They try to create a new small “sun on Earth” to generate power. They tried and designed a Токамáк machine. By using magnets it makes plasma run in circles very very fast and therefore plasma becomes very very hot, and release very very much energy.

A Токамáк machine stock image.

But it didn’t work as effectively as planned. And one of the problems is what happened when you added milk to your coffee.

2 Pour

2a Pour milk in my coffee

When you add milk to your coffee, you will see a mesmerizing image of milk’s random movement in a damn good coffee.

A damn good coffee cup.

A scientist will call this movement turbulent flow, but why you should care?

2b Pour very very very hot plasma
in my very hot plasma

When plasma is running circles inside Токамáк, the core of plasma is the hottest, while plasma on the outer part is colder. It would be ideal if this hot plasma remained steady on its route and didn’t steer right and left (difficult thing to do when partying hard).
Of course, this is not the case.

The so-called plasma microturbulence, is when the central part, the core of plasma, the heart of the party, possibly the hottest thing on Earth,
moves towards the colder part, the peripheral, the party pooper, possibly the second hottest thing on Earth.
When this happens, the heat is dispensed to the colder parts, no fusion is achieved, the party is over, the dream of limitless energy supply gets distant.

2c Pour some computers in my science

Scientists tried to find out how to control microturbulence. But they couldn’t figure things out in small scale experiments. The sun ought to be bigger. However, it is not an easy task to create a machine that makes a large “sun on Earth” just to perform some experiments with it.

Here comes the computers to save the day. Scientists with some help from some computer people, managed to create simulation tools that by solving known equations, allowed the computer to calculate the level of microturbulence in the plasma of the Токамáк machine given specific plasma and machine parameters. Since the scale should be big enough, enormous computational power is needed, and computers have to work day and night.

Here comes HPCs to save the night. Computers in parallel can perform much better than the conventional computers. Hence, most simulation tools have integrated the ability to run in parallel. With these simulations, scientists might understand how to avoid the microturbulence that causes the party to stop, and then we may not be far from day when we could say…

Here comes the sun

The Beatles, Abbey Road

3 Navigate

3a Navigate among trees

Navigation is very important. If you navigate in a tropical forest, you may need a guide to help you.

Me navigating in a forest in Vienna, without a guide.

However if you navigate in a web browser, needing a guide to help you is devastating enough to make you stand up and leave home to go to work.

3b Navigate among numbers

Scientists also have to navigate. In our story, they have to navigate in the results of the simulation. Thousand calculated numbers have to be translated in plots and schemes, in a humanly interpretative way. However, needing a guide to help you navigate and create these plots can be devastating. And if there is no such guide available it can be devastating enough to make you stand up and leave work to go home.

A free to reuse lots-of-numbers image by re_birf

This is the case for a plasma microturbulance simulation, known as Gyrokinetic Electromagnetic Numerical Experiment or GENE. GENE has a proprietary plugin program for visualizing the results. This program was originally created some decades ago, and the GUI (graphic user interface) is very old-school, buggy and not easy to interpret. In fact, if you search “bad UI”, the top results seem very close to the GUI of this program.

3c Navigate among widgets

This is finally where I come. The reason I am here in Ljubljana, Slovenia for this summer, is using some GENE output files that I ‘ll create, and based on the aforementioned GUI, I will create a modern, customizable, interactive, open-source, well-documented GUI to visualize the results of this simulations.

We are on the middle of this summer project, and I have already managed to read and manipulate all the output files, to create the base for the new GUI using PyQt5, to make some first plots, and travel around Slovenia.

So, what I am trying to do here is that I am trying to help scientists do magic, I try shine on the hat so scientists can easily make rabbits appear from it.

I am a Greek master's degree student of biomedical data science. I am going to spend the summer doing a visualization project in Ljubljana, Slovenia.

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