Elsa was struggling. She had a lot of fun that first night and it was tough to get out of bed the next morning. Somehow, the next day they had excavated a lab space and set her up. She was staring at hundreds of small dishes with microchips in the bottom. The robot arm Matt had built was great - it switched out the chips and sterilized the dishes. Lata had even helped her set up the program to interface with the chips.
Depressing was that they had so many tests to run. There were about 20 variations of chips they were testing. Each one had thousands of possible configurations to try and bind with an amino acid, and in an orientation that it could bind. On top of this, the chips had a high frequency of defects, so she had to run multiple sections of the chip in isolation to verify any results. All this had to be done for 20 different amino acids.
For each test she had to add the correct amount of amino acid, ATP solution, and protein enzymes. Then it needed to sit for 10 minutes before she would run an analysis, then sterilize and try a different test or tell the machine to switch the chip out.
After about 4 hours she was exhausted and worried she would make mistakes. She knew objectively this was important science, but it was so boring!
Barry came into the lab.
“Hey, you look like you could use a break. Want to go get some dinner? You can tell me about your day,” Barry said. He seemed excited. Clearly, he wanted to tell her about his awesome day and was trying to be polite. Big jerk!
“Sure, that sounds great. I’d love to hear about your day too,” Elsa lied. Well, she was hungry. That part sounded good.
The house wasn’t fancy, but it was amazing having a chef to cook you a meal when you wanted it. They also had people to bring drinks and clean up. Barry was looking cleaned up and dressed nicely. Of course, she looked like a mess. This would be an amazing vacation if it wasn’t for her stupid work.
The chef recommended some options he could cook. Elsa chose filet and lobster, because it was kind of awesome to just have that for lunch. Barry ordered some red snapper dish that also sounded pretty good.
“Fine, tell me about how great your day was,” Elsa laughed. She couldn’t really stay mad. Barry was great and this trip was quite an adventure.
“I thought you’d never ask!” Barry laughed. “Nah, it’s no big deal but I got a fusion cell working that only weighs 10 kg. We had to use some really expensive materials, but it proves the concept. Professor Springer was dancing around on our video conference. It was kind of hilarious.”
“I hope you recorded that. It would be fun to play that at his Nobel Prize acceptance.” Elsa said.
“Hah I wish!” Barry said. “So, it sounds like you are pretty frustrated. Want to tell me about it?”
“Ugh! I’m going to tell you and then you are going to solve my problem and I’ll feel stupid.” Elsa grumbled.
“Hey, I can’t help it if I’m amazing!” Barry said. “Well, how about I listen, and you figure it out on your own? Or if I figure it out, we can just tell everyone it was all you.”
“You’re kind of a brat. Fine, so I have to do all this tedious lab work. We’re trying to figure out what chip parameters and binding settings will work for all the amino acids. Assuming there even is a correct combination. I kind of got Glycine to bind a little, but we couldn’t make chains of it. Anyway, there isn’t even a guarantee that it will work with anything we try. There are about half a million variations to test and each one takes about 20 minutes between setup, letting it react and then cleanup. I run them in batches of 200, but still it’s going to take forever and if it doesn’t work, we will need to change the chip designs and do more tests!”
“That sounds hard. I thought Matt built you a robot arm to help with the tests.” Barry said.
“Um yeah. It’s actually pretty great. It swaps out the chips which used to take a lot of effort when we first started. Hard to get those things placed without damaging them.” Elsa admitted.
“Oh, I should ask Matt to help me automate some of the other steps,” Elsa concluded.
“See, I knew you’d figure it out if you took a break.” Barry laughed.
Elsa’s phone rang. It was Melinda.
“Hey, I was spying on your conversation.” Melinda admitted. “We need to have a meeting about what you are working on. I’m inviting Lata and Scott too.”
“Do you have cameras everywhere in this house?” Elsa asked with suspicion.
“Entrances, living room, dining area and kitchen. I asked Sergio to install them in the bedrooms, but he said they weren’t needed for security. I told him it was for entertainment purposes, and he gave me a dirty look and wouldn’t install them.” Melinda admitted.
“Our boss is harassing us,” Barry complained. “Too bad our HR department is only Scott.”
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Shortly after dinner, the group met up.
“Elsa, I explained the difficulties you were having.” Melinda started.
“I’d be happy to help you with some robotics to automate your lab testing. Rafael will help program the robots and I will work with Philip to assemble them. We should be able to get something set up tomorrow. Tests and adjustments might take a couple days after that.” Matt said.
“Will this interfere with your mining plan?” Scott asked.
“Not really,” Rafael admitted. “We have a design that uses Barry’s new fusion cell, but we only have one of them. We don’t really need them while we are close to the surface. We can test it after we help Elsa.”
“Matt and Rafeal have time. They were screwing around with a rail gun design yesterday.” Phillip tattled.
“Oh?” Barry said with interest. “I totally want to try that out when you build a prototype.”
“Boys and their guns.” Elsa sighed.
“Invite Sergio and his boys when you try that out.” Melinda ordered.
“Our geriatric security forces?” Matt asked rudely.
This tale has been pilfered from Royal Road. If found on Amazon, kindly file a report.
“Oh, I forgot to tell you boys.” Melinda said with a smirk “Our old timers just helped the police take out a group of about 20 cartel mercenaries that were causing problems in the area. You might want to be careful about insulting them.”
“Ugh, I should have known Glitch_HR would find a bunch of retired action heroes.” Matt sighed. “Well, maybe they’ll forgive me when they see some of the toys Rafael and I want to build.”
“Enough about this, this meeting has gotten off track. Let’s get back to Elsa’s work.” Melinda declared.
“Right,” Elsa started. She explained the difficulties with chip types, electrical configuration, and effort to run the tests. “So, I think with some robotics we can speed up setting up the tests and it will be less tedious. But I still don’t know if it will even work. Also, by my math, even if it could work round the clock the tests could take over a year. Given how expensive the reagents are we would run out of money long before then and there is no guarantee it will even work.”
“So, it sounds like a brute force approach. In coding there is usually a way to improve your odds with a bit of extra work,” Scott said. “We could prioritize configurations to test. My training lately has had a fair number of articles on 3D modeling and simulation of molecular interaction. It doesn’t directly apply but I think I could code something that could reduce the number of tests you would need to run.”
“That would be helpful.”
“So, I know a fair bit of chemistry.” Barry said. “Catalyzing a reaction with a fixed electrical configuration sounds like you are depending on molecules to hit in the right place at the right angle. You can speed it up with higher concentrations and temperatures, but there might be a better way.”
“Well, we were trying to optimize concentration and temperature, but there were already so many variables we were going to tune that after we succeeded on the basic conditions that would bind.” Elsa said defensively.
“Might want to look at it sooner if you are looking at a year of testing. Saving one minute per test would add up. That wasn’t really my point.” Barry continued. “Anyway, traditional catalyst reactions work like what you described but we are setting up a digital catalyst. Instead of a static pattern, you could animate a sequence that would match the molecule colliding at different orientations and rotate it to the correct position.”
Scott looked excited. “Yeah, if we had a proper 3D model, we could try that. The problem is we don’t get any feedback from the chip. If it was just running a loop, I think it wouldn’t be any more likely to bind and might even mess the reaction up.”
“What if we had something built on the chip to sense if the molecule had bound?” Lata asked.
“That would help a lot!” Scott agreed. “But is that possible?”
“We could add some layers on the original etching that could detect changes in resistance at the site where the molecules are supposed to bind. It wouldn’t give you any detail on what was there or which way it was facing.”
“That could work.” Scott said. “We could train the computer to match the resistance state of a sensor and its neighbors. If something stayed in place for a certain time at a certain temperature you could assume it was bound. So we go through patterns that match various orientations. When something sticks, we rotate to the correct orientation and position it for binding.”
“See why we needed this meeting?” Melinda asked with a smile. “Lata will get her people to run some new chip configurations that use this idea. Scott will work on the coding, and Matt’s guys will work with Elsa getting the lab automated.”
Elsa left the meeting in a bit of a daze. If she understood correctly, they would only need to test a few configurations per amino acid. Robots would run the experiments, and the reactions should run at least 100 times faster. Instead of a year of mind-numbing work with low prospects of success, they might get this working in a week. She pitied the scientists toiling away in labs that didn’t have the right people around to make their jobs easy.
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Adrianna had also been very busy. She had initially asked Scott to help her while she designed a submarine that could transport ore from their mining operation to a cargo ship. He had been interested in her work, but he was kind of useless. So, she continued her work the next day without asking for his input.
She had learned to use a CAD tool that was optimized for ship design, based on training recommendations from Glitch_HR. Melinda had approved spending money on this, and it was helpful even though not intended for submarines.
Her current design was a cargo freighter which could detach an underwater portion that would act as an unmanned submarine container. It was guided by wire and much easier to design without worrying about an onboard crew. The underwater part would fill with water and could be loaded by the robots. When it docked back up with the container ship, they would pump out the water and unload.
She had started work on other designs that had crewed submarines that could dock with an underwater habitat. These were much more complex and expensive, so she set these aside until they had a lot more money to spend.
The cargo freighter design was on the small side, technically a mini-bulk carrier that was about 120m in length and could hold about 10,000 tons of material in 3 cargo holds. Typically, something this size would probably cost more than 20 million to build given the high level of customization. Not to mention it could be years before they could get approval and find a shipyard who could handle it.
After seeing what was going on here, Adrianna was pretty confident they could build the ship themselves with some of the robots Matt’s team could create. They would need about $2 million in materials. After setting up this facility, she was pretty sure they didn’t have much left from the initial funding. She called Melinda.
“I finished a design for a small freighter to haul ore from our mine. It includes a remote submarine that can pull stuff up from underwater down to about half a mile depth. That will be more than enough for our current location. Problem is, just the materials to build will be about $2 mil.”
“I see. I’m assuming that it doesn't include electronics, hvac, cabin fittings, engines etc.” Melinda said.
“Yes, I assumed we could use one of Barry’s generators for power and the rest of the equipment and fittings is about 300k, not counting labor to install. That’s assuming the boys can program the sub controls and we get low end gear.”
“Thanks,” Melinda replied. “This is excellent work. The boys are busy the next couple days, but go ahead and finalize the design and we will start building it. Send me a list of materials and parts we need to order or fabricate. Our purchasing guys are good, but they will need time for such a large order.”
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The next few days were a whirlwind of activity. The boys helped refit Elsa’s lab and Lata’s new chip design was sent by air freight to their location. Scott spent half his time pulling code and articles from skill training that were relevant to the project. The rest of his time was spent trying to put something usable together and test it. He noted that his ranking was now in the top million junior programmers. He knew he had built some great stuff, but he was still mostly pulling together pieces of code from other programmers who had done the hard work. Most of the articles he read now were labeled advanced, although he did get “3D Modeling of Molecules for Beginners” when he started this project. This seemed way more advanced than a hello world app, but the article was helpful, if a bit condescending.
The work crew had finished the concrete wall around their property and crews were starting to load large piles of steel plates inside the wall in the front yard. Most of these were covered with tarps and starting to rust a bit. Barry was experimenting with a process to embed graphite fibers into the surface of the plates to make them resistant to corrosion. As a bonus they would have less drag in water.
With two days to go before they all had to return to school, Elsa had started to test the new process using Scott’s code, Lata’s chip and Matt’s robots. The first few experiments did not produce anything. Scott checked his code and found a few bugs. The next few runs produced some short strands. This was comparable to her best result when she had done everything manually for a whole day. They took a break for a few hours as Scott added code to give feedback to the machine learning based on the chromatography results. He seemed embarrassed he hadn’t thought of it before.
Then they left the lab running. It was amazing watching the robots set up tests, then clean the equipment and do it all again. They all took a break to get lunch, leaving the machines to run.
The so-called essential amino acids were cheap because they were sold in bulk as nutritional supplements. They had used Valine for testing because it was relatively cheap. When they returned from lunch, the computer indicated it was no longer improving. The results were impressive. They could make chains of Valine of various lengths at a very high reaction rate. The error rate on longer chains was a bit high, but hopefully they could improve that with some changes to the chip fabrication and lab procedure.
In short, the grand experiment might actually work. Her thoughts racing to the next steps, Elsa felt deep down that this was something that would change the world.