chemistry, Coding, Electricity, JavaScript, Notes on everyday life, Simon makes gamez, Simon's Own Code

Test Tube Games

Simon has had hours of fun with Test Tube Games, a science games portal featuring interactive explanations and dynamic puzzles on Chemistry and Physics. He has created two simulations based on the games he played. The first one is an electromagnetic field simulator:

This project was inspired by the game/explanation “The Electric Shocktopus” on TestTubeGames.com

Code: https://editor.p5js.org/simontiger/sketches/nIwYhXLdj

Press “1” for positive charge, “2” for negative charge, “R” to run. Press “3” and “4” to create magnetic fields/ press “0” to erase them. Press Shift+1 and Shift+2 for “lazy particles”.

Simon’s other TestTubeGames-inspired project is called “Floating Astronaut”:

This project was inspired by the game/explanation “Why Do Astronauts Float?

Code: https://editor.p5js.org/simontiger/sketches/obGZyfVze

Haven’t figured out a way to put the astronaut inside the rocket yet though.

One more science game is definitely a hit at our home, “Bond Breaker” (on chemical bonds). At a certain point, it gets so hard you start feeling like a secret agent on a mission.

Simon playing “Bond Breaker”
Biology, chemistry, Engineering, Milestones, Murderous Maths, Thoughts about the world

What do we know: COVID-19 and Protein Folding

On April 9, Simon finished his World Science Scholars course “From Chemistry to Living materials” and had his final live session with MIT’s Professor Markus Buehler who works on COVID-19. Professor Buehler, who leads the Laboratory for Atomistic and Molecular Mechanics (LAMM), shared some cutting edge stuff, some of it not even published yet. Here’re the important takes:

COVID-19 can travel much further than 6 feet/ 1.8 meters, namely at least 20 feet/ 6 meters. Human coughing produces gas clouds that initially rise up (due to their warm temperature) and then hang/ float in the air/ follow the air currents for a prolonged period of time.

screenshot from Professor Buehler’s live session

We still know very little about the COVID-19 virus. Its RNA contains 30,000 letters, but we only recongnize 29 proteins. We’re studying the structure of those proteins as we speak.

Looks like its mortality rate is quite high.

We don’t have the luxury of spending two years in the lab, growing the virus and applying the trial and error method. So our main hope is computation (computational material science), trying to understand the virus mechanistically.

Proteins are like folded spaghetti, unfolding them will destroy their structure and neutralize the virus. You can help look for ways to unfold the proteins via this app: https://fold.it/ (The most promising solutions will be tested at the University of Washington Institute for Protein Design in Seattle.)

What is mainly being studied are the ways to destroy the protein structure of the virus’s spikes. That can be done in several ways:

1. What is the virus’s thermostability? This is what is primarily being looked at, as it is still unclear how each protein reacts to temperature fluctuations.
2. What makes COVID-19 so infectious is the flexibility of its spike protein. Is there a way to make the spike protein more rigid (less flexible)? Maybe another protein or maybe a totally different engineering solution.
3. Destroying the protein with sound, with acoustic waves. Analyzing the protein’s vibrations and trying to find a frequency that can “shatter” the protein when excited (similar to how high pitched sound can shatter a glass).

Targeting the entire structure of the virus can damage human cells, so scientists want to target specific proteins/ frequencies.

This Science Magazine story with a video clip featuring Professor Buehler’s lab and COVID-19 proteins encoded as sound, “Corona music”.

screenshot from Professor Buehler’s live session (on the left you can see the protein’s spaghetti-like structure)
Simon and Neva observing diffusion, something professor Buehler also covered in the course.
chemistry, Crafty, motor skills, Notes on everyday life, Simon teaching

Messing with the Periodic table

I want to mess with the Periodic Table to see what arrangements I can put it in.

This is called the Wide Arrangement. There are aso a few other arrangements, like the Left Step Wide (or Loop) arrangement, various 3D arrangements (like the ones where you make sure any consecutive numbers are next to each other and it looks like a layered cake).

Although it would be even nicer if we moved H and He over there where they obviously belong.

Spiral periodic table with no gaps between consecutive elements.
You can put it on the top of the Christmas Tree!
Mendeleev’s Flower

Simon learned this from a Minute Physics video.

chemistry, Experiments, Together with sis

MEL Chemistry Experiments: Foil Etching, Magnetizing Magnesium, Metal Contest

In the Foil Etching experiment we had copper burn a whole in the aluminium foil.

This is the reactivity chart from the MEL science website, as you see aluminium is a lot more reactive than copper

As you can see, aluminum Al is much more reactive than copper Cu, but nothing happens when aluminum foil comes into contact with the copper sulfate CuSO4 solution! How come? Unfortunately, it’s all a bit more complicated than it first looks. Being quite an active metal, aluminum Al  reacts with oxygen O2 in the air, forming a very strong film of aluminum oxide Al2O3 on its surface . This film protects the metal from reacting any further.

When you add some sodium chloride NaCl, a vigorous reaction starts as Cl ions are able to compromise the otherwise-strong Al2O3 shield. Once Cu2+ is face-to-face with the aluminum Al itself and not its Al2O3 shield, the reaction can proceed, and quite spectacularly!

the hole in aluminium foil as active aluminium atoms have fled

In the next experiment, we obtained a magnetic substance from two non-magnetic ones, magnesium Mg and iron sulfate FeSO4, via a simple chemical reaction! The Fe2+ from the FeSO4 solution turned into metallic iron Fe on the surface of the magnesium particles, so we ended up with magnesium shavings covered with a thin layer of iron! The picture below shows how the magnesium shavings actually hold a heavy neodymium magnet in the air!

a heavy magnet hanging on the bottom of a glass beaker thanks to electromagnetism

And lastly, we did what MEL Chemistry calls a “Metal Contest”, because here too, three metals (zink, copper and tin) were competing in reactivity. “If you arrange metals from more active to less active, you’ll see that zinc Zn is a more adventurous fellow than tin Sn and copper Cu. That’s why, when you put a zinc rod into a solution containing, say, copper ions Cu2+, the latter are happy to settle inside the comfortable cloud of electrons, forming metallic copper Cu on the surface of the rod. Zn ions Zn2+, in turn, go swimming in the solution. The reaction with the tin chloride SnCl2 solution is essentially the same”, MEL Science website explains.

copper and tin on the surface of the zink rods


chemistry, Experiments, Physics, Simon teaching, Simon's sketch book, Together with sis

Chemistry Experiments: Polarized light iridizes crystals

Today we have made beautiful rainbow chrystals! Polarized light iridizes sodium thiosulfate crystals, so we made the crystals in between two polarizing films and then observed them through the microscope. In the video, Simon also explains how polarizing film works.

From the scientific description at the MEL Science website: Sodium thiosulfate crystals contain five molecules of water per one unit of sodium thiosulfate Na2S2O3. Interestingly, when heated, the crystals release the water, while sodium thiosulfate dissolves in this water. This solution solidifies rapidly when cooling, forming beautiful crystals. If these crystals are put between polarizing films, they take on an iridescent sheen. This is because the polarizing films only let light with certain characteristics through, and this light in turn “iridizes” the otherwise-colorless sodium thiosulfate crystals.

chemistry, Crafty, Experiments, Together with sis

MEL Chemistry Experiments: Making Batteries

We did two more experiments a couple days ago: Liquid Wires (creating a simple circuit using graphite and liquid glass, a sodium silicate solution) and making our own Zinc-Carbon Battery, a chemical source of electric current that relies on an oxidation-reduction (redox) reaction between manganese dioxide (MnO2) and zinc (Zn). 

A redox reaction involves the transfer of electrons from one element (the reducer) to another element (the oxidizer).

Our battery is divided into two sections, separated by wadding: one section holds the oxidizer MnO2 and the other contains the reductant Zn. When the crocodile clips are connected to a diode, the circuit is closed and the reaction can begin: electrons start migrating from the zinc section to the manganese section (manganese dioxide mixed with graphite o make it a better conductor). We used ammonium chloride NH4Cl as the electrolyte.

chemistry, Experiments, Together with sis

MEL Chemistry Experiments: Flames and Minerals

Monday was a chemistry day as we went to the post office to fetch our brand new delivery from the MEL Science subscription! We set a record of 6 chemistry experiments in one day! We just couldn’t stop, maybe because all of the experiments involved fire.

We started with the Minerals box. The first experiment was about heating up some semiprecious stones, amethysts (a species of quartz widely used in jewellery). The nature of amethyst’s color is still a mystery: some theories suggest that the color is of organic origin because it changes when amethyst is heated. Our purple amethyst became completely white after we heated it!

Simon watching the solid fuel burn (C6H12N4 – hexamethylenetetramine)
solid fuel C6H12N4 – hexamethylenetetramine – burning with the amethyst wrapped in aluminium foil on top of the flame diffuser
Amethysts in their original color
Amethyst has become white

We also repeated the same experiment with a piece of red coral.

Chemically, coral consists almost entirely of calcium carbonate CaCO3—the same compound chalk is made of (plus the red pigments known as carotenoids). When coral is heated, a strong smell should arise, because of the organic remains left in the skeletal structure. We didn’t really smell much, the coral seemed unchanged after heating:

What we did next was dissolve some malachites! We used NaHSO4 (sodium hydrogen sulfate) as an acid that the mineral would react with and heated the solution up to speed up the process. The big question was: will the malachites dissolve? And will a certain metal come free as a result?

Pieces of malachite in a beaker
The solution turned blue when heated
We added K4[Fe(CN)6], or potassium ferrocyanide, to the solution to detect metal ions. The indicator substance turned brown, which indicates copper ions!

Malachite is a mineral that contains copper Cu! In fact, malachite consists of (CuOH)2CO3 – basic copper carbonate. This compound has been used as a source of pure copper since antiquity, the MEL Science website explains. 

What was left of the malachites

Now it was high time for some fireworks!

This one was our favourite! We performed it many times, just to see the mesmerising green sparkles. All one has to do is dip a stick in paraffine, then in CuSO4 (copper(II) sulfate) for 30 seconds, then in paraffine and (very briefly) in water. This creates a kind of homemade sparklers, like the ones popular on New Year’s Eve, spitting spectacular flashes of green.

What made the flame green is its copper Cu2+ component. Metal ions such as copper ions Cu2+ can emit light of a certain color when heated to high temperatures. Copper emits green, while rubidium Rb creates red and sodium Na creates yellow, and so on. You can create colorful fireworks, but you can also detect which metal is present in a sample by examining the color of the flame.

What else should we burn? Magnesium! Because it lights up so pretty:

From a chemistry perspective, burning is the process of giving electrons to oxygen O in the air, releasing a lot of heat and light. One of the most obvious trends in the periodic table is that the elements on the left side of the table are generally more willing to give electrons away than the ones on the right. But, as we learned from our last experiment called Rocket Fuel, not only oxygen can take electrons from the fuel, in other words, there are other substances that can act as the oxidant (the substance that wants to take electrons from the fuel). If you want your fuel to burn without air, you have to include your own oxidant too. This is how space rockets work.

In our experiment, we mixed the oxidant, calcium nitrate Ca(NO3)2 and the fuel, potassium ferrocyanide K4[Fe(CN)6] that doesn’t burn very well in air (used as fuel for small model rockets and fireworks), and heated them up. When we later set the mix on fire, it didn’t quite produce the effect we had hoped for, the flame went out too quickly to take a good picture.

The oxidant and the fuel
A porridge of oxidant and fuel, calcium nitrate Ca(NO3)2 and potassium ferrocyanide K4[Fe(CN)6]
The very end of the rocket fuel flame burning
Biology, chemistry, Math Riddles, Milestones, Murderous Maths, Physics

Bayes’ Theorem

Bayes’s Theorem calculates the probability of an event based upon the conditions that might be relevant to the event and is widely used to test the precision of medical tests and drugs efficacy.

Simon explains Bayes’ Theorem to Dad. To illustrate the theorem, he loves using the math riddle he first saw on the Veritasium channel, about someone getting positive results on a rare disease test: The test has a precision rate of 99% and it is also known that the disease occurrence rate is 1/1000. What is the probability that the person tested positively really has the disease? (Answer: 11/1000 or 9%).