Tag Archives: chemistry

Sad Gap and Coffee Comic

I made a vlog today about how I address the Sad Gap. If you’re not a part of the nerdfighteria youtube sphere, I will explain. The Vlogbrothers have both talked about it recently (see Hank’s video or John’s video). The sad gap is the place between finding out about a problem and being in a position to do something – anything – about it. It’s possible to fall right into the sad gap and end up not actually doing anything at all.

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My phone is eating my brain, also new video is up!

I posted a video about chromatography, but first I want to talk about focus and cell phones. The comic is almost a verbatim conversation I had with my wife. It’s hard to escape my phone even for the time it takes to use the restroom. That can’t be good for my psyche.

I was thinking about doing a deeper dive on that, but it just doesn’t fit the theme of the blog/vlog any more. It fits better over at my other site, Student Pro Tips, but I have not updated that for a long time. Then I thought, maybe I SHOULD update that site and maybe add a video, too! Because I need more projects. I have not done that yet… we will see. [EDIT: I posted the video and blog post about this whole thing]

Research summary on the subject:

  1. There have been several meta-analyses and reviews on smartphone addiction and smartphone effects on cognition and learning.
  2. There’s a thing called Nomophobia now: “The term NOMOPHOBIA or NO MObile PHone PhoBIA is used to describe a psychological condition when people have a fear of being detached from mobile phone connectivity.”

All that from a comic.

Ok, about chromatography. Here’s the video.

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Killifish, aging, and carbon-silicon composite batteries

Genetic study uncovers clues to explain how killifish stop aging during diapause

Killifish are really interesting organisms for scientific experiments. They are vertebrates, so they are closer to us genetically than insects or worms. But they are a lot easier to grow and care for then mice or rats. Some killifish have life spans of only three months. This makes them very attractive as aging model animals. If treatment extends their lifespan, you only have to wait 3 months to find out. With mice, you have to wait for several years.  This paper discusses another cool feature of the killifish model animal. Some kinds of killifish can go into a kind of suspended animation. I did not know that and it is fascinating.


Nano/Microstructured Silicon–Carbon Hybrid Composite Particles Fabricated with Corn Starch Biowaste as Anode Materials for Li-Ion Batteries | Nano Letters

Researchers develop high-capacity EV battery materials that double driving range

This article discusses a new composite silicon/carbon material for hosting lithium ions. Cramming lithium ions into a silicon matrix makes for an even higher energy battery than a standard lithium-ion battery. unfortunately, silicon expands under these conditions and can destroy the battery. By incorporating the silicon into a carbon matrix, these researchers increase the conductivity and the resilience of the battery to multiple charger Cycles. The result was a very nice paper. I love that they tried to make their composite material from readily available substances.


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crystals of potasium phoaphate incorporating the chemical amaranth dye

Amaranth Potassium Phosphate Crystals

Potassium phosphate crystal chemistry

This weekend I grew some potassium phosphate crystals with amaranth dye. I did this back in 2001 in Bart Kahr’s O-Chem class and remembered it recently. It’s a fun demonstration of the chemistry of crystal growth, the different chemistry of the crystal faces, and it’s pretty. I found Prof. Kahr’s paper[1] that gives a “foolproof recipe” and it did not disappoint. Even this fool could make it work.

As the crystals grow, each face of the crystal has a unique topology. The corners are growing with a different spacing of atoms than the faces, and the faces can be different from each other. Sometimes, the faces have the right spacing to allow a dye molecule to stick. In this case, there is a big difference between how well amaranth dye sticks to each face. So as the crystal rows, it only gets dyed in two quadrants.

We can learn about chemistry from crystals

Crystals are super useful to chemists. A good crystal of a chemical can be used to get x-ray diffraction data on the structure of the chemical. The most detailed structures are derived from x-ray diffraction data.

Knowing how molecules assemble into crystals is also really important to materials scientists. If you want to design a material from its atoms, you need to know how they are going to come together. I’ve been working on making an iron battery and reading up on battery chemistry. One of the interesting papers I read talked about designing a cathode material to hold sodium atoms. The chemists designed the “holes” in the structure to hold sodium atoms – and they needed to know how the other atoms would come together to make that shape.

Why chemically dyed crystals are cool

Of course, dyed crystals just look cool. Maybe that’s silly, but if you’re trying to teach organic chemistry, it’s good to have something visual and striking to hold on to. A lot of O-chem is solvents and white powder, so anything that sticks in the memory is a help.

The other reason I think that dyed crystals are so cool is that they dyes can be held still very precisely. One of prof. Kahr’s later papers used a crystal to hold a fluorescent dye in place at a specific orientation. Then they used a fluorescence microscope to look at single dye molecules[2]. I think that’s just really cool. I gather that they are more stable in the crystal than they are in solution.

I also made a time-lapse movie of the crystallization

Instructions (following [1])

  • Dissolve 17 g potassium dihydrogen phosphate (KDP) in 50 ml water with heating. Using a teflon stir bar helps.
  • Dissolve 4 mg amaranth dye in ~1ml of water and add to the mix.
  • Pour into a wide dish and allow to cool and evaporate slowly over ~4-24 hours.


1.Kahr, B. & Vasquez, L. Painting crystals. CrystEngComm 4, 514–516 (2002). http://dx.doi.org/10.1039/B204845K

2.Wustholz, K. L., Kahr, B. & Reid, P. J. Single-Molecule Orientations in Dyed Salt Crystals. J. Phys. Chem. B 109, 16357–16362 (2005).http://dx.doi.org/10.1021/jp053051x

Raspberry Pi Computer: standalone “safe” machine

I want a computer that does not rely on a software service agreement to function. Cell phones obviously have to operate as a service since they need a network to operate. The phone is a gateway to the cell service. My kindle is similar for Amazon services. Laptops feel different to me. Computers feel like products. I own my laptop and I want to think of it as a standalone device, not a gateway to a cloud service.

Windows 10 is now a service. The future is clearly going in the direction of software as a service (SaaS as the kids put it). That’s fine, but I like to have at least some device that can’t be remotely bricked by a company.

Raspberry Pi Computer in a Box parts list:

Quick catch-up for other topics this week: I made a video I about sodium-ion batteries and people seemed interested. I think a sodium ion battery would be really cool. But I think the expectations of the youtube viewers may be a little inflated. Sodium is heavier than lithium. It yields less energy per atom, too. So it’s not going to be great for mobile. I made another video talking about that. So why bother with sodium? Lithium is relatively rare and expensive… so sodium might be better for stationary applications. It’s hard to say at this point, but I’m investing my time in an iron battery.