Category Archives: Uncategorized

qPCR and graphene for aptamer selection

We’ve been selecting aptamers in the lab for the last year. Having a qPCR on the bench has really helped, and so we wrote up a methods paper in ACS Combinatorial Science. The company that made our qPCR instrument has put up a blurb about it, too.

The qPCR function is great for cycle course optimization, and we have been using the melt curve analysis function of the Open qPCR (thermofluorimetry) to do a binding assay. It works pretty well. We put a dye in with the aptamer and measure the temperature at which the dye dye-DNA complex melts. The bound aptamer has a different melt temperature, so it gives a specific signal. We plot that specific signal as a function of concentration and to determine the binding constant. It’s based on the Easley lab’s method paper from 2015 with low-cost equipment.

The instrument simplifies some of the more touchy parts of the aptamer selection. Undergrads have been turning rounds pretty efficiently this year with the help of the open qPCR instrument.

We have also been using graphene oxide to try some selections. I have only heard of graphene oxide SELEX recently, but it grabs unstructured DNA to separate them from aptamers bound to target. It’s looking good. I hope to report on that soon.



Thank you to Crowdfunding Supporters

Thank you to all of the kind supporters who helped raise money for undergraduate research in iron batteries here at the U of Idaho. Together we put together $5000 that will be put toward a fellowship and materials for a student to explore this and we will put together a open source plans document next year. We’re also going to document the process with a weekly video about the project, so please do stay tuned.

Crowdfunding the iron age of batteries

I’ve launched a crowdfunding campaign to try to support a student in building an iron battery. I’ve got video up that talks about where we’ve been so far this year. We have had some success in building the battery and we’re moving to a better construction method.

We would like to test different cathode salts including a better test of potassium ferricyanide. We would also like to test different solvents such as a deep eutectic solvent and ionic liquid. The big, open question is the separator. We can try some natural gels, some in-house polymers and we can see if we can find a commercial polymer that is cheap and available enough to do the job.

I think it will be a great project for an undergraduate chemist with an interest in renewable energy. If you’d like to check out or share the campaign, the link is here:

NORM 2017 Corvallis

I’m attending The Northwest Regional Meeting of the American Chemical Society in Corvallis. I just wandered around downtown. That was nice. My hope is to see some computational chemistry, commercialization, and nanoparticles tomorrow.

What tools are getting used for simulations? I’m especially interested in coarse-grained simulations of macromolecules. I see several Density Functional Theory talks and that should be interesting. Maybe folks from that world can point me in the right direction. Is anyone using tensorflow for such things?

There’s a panel on market-driven innovations. I would love to hear if people are funding academic labs through collaborations with industry. I feel like that would be a win-win, but I don’t know where to start there, either.

There’s also a bunch of analytical chemists giving MS talks and a “smart” nanoparticle talk. That’s just the morning session. I’ll have a hard time choosing.

If you’re in Corvallis and are reading this, do please shoot me a gmail (pballen). I’ll buy the first round at Tommy’s.

Negative and positive results in the quest for an all iron battery

Iron is cheap, and iron chemistry can be used to make a battery. If you want to buy a lithium-ion backup battery pack for a home solar system, it will cost as much as the solar panels. Effectively, a 24/7 solar system is about double the cost of a grid-tied system. The same is true for the grid itself. If the utilities want to move to cheap solar power, they will need to buy huge batteries. If utility companies tried this with lithium batteries, it would be such a big endeavor that it would mess with the lithium market. Iron is produced at such a huge scale that a move to grid-scale iron batteries wouldn’t completely alter the iron market.

I tried a dumb idea and it didn’t work. I tried to make an iron-oxide electrode for an iron battery. The idea was that iron oxide can be reduced to iron magnetite. That would be a cheap cathode for an all-iron battery. Plus, since iron oxide is a solid, it would stay where it was put and not diffuse over to the other electrode. So that would be nice, too.

Obviously (even to me at the time) iron oxide is an insulator, not a conductor. So if it is going to act as an oxidizing agent, it will need a path for electrons. Electrons can’t move through the iron oxide. They need to move through some other conductive material. So I embedded iron oxide particles in graphite.

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The result was nothing at all. The cell was dead on assembly. I could not detect the iron oxide reduction/oxidation with any instruments at my disposal. Other groups have reported the oxidation potential of the iron oxide nanoparticles. They put them in a suspension swirling near the electrode and that seemed to work. So maybe it’s possible, but I can’t get it to go. Iron oxide is out.

I made a better cell with Iron (III) EDTA as the oxidizing agent. It’s soluble so that makes things work better. I used a graphite felt as a current collector and it worked just great. The energy density is low (as expected) but it works.

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The next step is to optimize and stack up a bunch of cells. I think it’s getting close to being an “open source battery.”

I’ve been vlogging about this, if you want to watch progress in almost real time, have a look.