Decent Week
Sunday, October 5
158.2 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (6/6)
Today was a very productive day. I wrote two blog posts, did meal prep (much easier now thanks to the new oven), cleaned, and did a quick indoor run (new 5K PB)! I wish there were another day in the weekend (though it would be awkward to call it a “weekend”😅). A good setup for a productive week ahead.
Monday, October 6
157.9 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (1/6)
Fresh workout this morning. These days the sunrise is later than in summer, so when I headed to the gym a beautiful orange sky greeted me. Today I did a lot of computational work. Finally the oligos we designed arrived, so starting sometime this week things will be much busier than usual. I also need to synthesize a molecule before the yeast surface display is ready, and I felt a little overwhelmed. I really do not like being the rate-determining step in a team project, so I went back to the lab after dinner and set up an overnight reaction. I had failed twice with the conventional method, so this time I followed the exact SI protocol from the paper that reports this molecule’s synthesis, even though it felt weird from the principle of basic organic chemistry. I hope I can finish it safely within a week.
Tuesday, October 7
156.0 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (2/6)
The reaction I ran yesterday didn’t go well (It looked pretty because it’s a dye🌈). Even though I tried to reproduce every step in the procedure, the major product wasn’t the target; it was a predictable side product under those conditions (That’s the reason I thought it’s weird). I may need a different coupling reagent, but first I’ll try to purify the desired product again by reversed-phase chromatography tomorrow, even though the amount is small.
I spent the rest of the time working on protein design. It seems to be going well, but there are so many possible ways to approach the same problem that it’s hard to choose a path. I hope a reasonable direction becomes clear with time.
Wednesday, October 8
156.2 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (3/6)
I purified the sample by reversed-phase chromatography (with manual selection of a wavelength); the LC–MS looked great. I’ll lyophilize it and then check the NMR again.
For computational design I realized that per-user storage on the HPC cluster really matters for the pipeline, especially when you want to run thousands of backbone-generation, sequence-design, and structure-prediction jobs. To manage this, I’m investigating which outputs can be regenerated from small retained artifacts and which must be kept; when files are deletable, removing them in parallel is also an important part. I learned this during scale-up, a reminder that even dry-lab work has resource limits😕 I think keeping the workflow within a manageable footprint by choosing more efficient strategies could be itself a meaningful scientific decision.
After work I did a quick run on my favorite route (home to the Bay Bridge along the waterfront). The weather was wonderful, and I slept well.
Thursday, October 9
155.7 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (4/6)
Today I focused on computational protein design and kept going. I ran into a statistical problem where I had to simultaneously optimize two variables (I learned a lot!). I am not sure my approach was the best, but at least I now have a clear, logical way to explain it.
In the afternoon, for an upcoming QBC retreat, I filmed a short skit. All second-year students have to participate😇 It was definitely my first time doing anything like that, also acting in English felt a bit awkward. My cohort kindly accommodated me by giving me a very simple role (a mostly silent professor), so I managed fine. It was fun, and I am actually looking forward to seeing the edited video at the retreat in November.
Also, for the first time, I went to the student grocery market where UCSF students and employees can get free fruit and vegetables (and even some snacks) that would otherwise go unsold at local grocery stores. It’s held every Thursday, but I’ve never tried it before. Since I was already there, I went with a friend after we filmed the skit and picked some up. It was great and I’ll probably go back often.
Friday, October 10
156.7 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (5/6)
Today I finally started working on yeast surface display (YSD). It has been a while since I did PCR and ran a gel, so it feels completely new. Doing chemistry, biology, and computation (literally everything except in vivo🤓) feels great; on the flip side, it is hard to stay familiar with all of it. Practice makes perfect, right?
Since we are moving forward, I feel more eager to finish the molecule I am working on. Unfortunately, the lyophilized product (after two purifications) still had some impurities and the amount was small. I set up another reaction; this time I hope to purify on a larger scale and dry-load to get better resolution and remove the impurities.
It is Friday, so running an overnight reaction means I will be in over the weekend. To be honest, if this is what I want to do, it does not matter whether I am in the lab on the weekend or not. The lab is also much closer than when I was a master’s student in Korea, so it is not a big hassle. But to be honest, it would still be nice to spend my leisure time on the weekend😅
Saturday, October 11
157.1 lbs (from 165.4 lbs on Aug 24) | 🏃🏻 Done (6/6)
I went to the lab, quenched, and purified the overnight reaction. It showed the same pattern as last time😱 After carefully investigating the undesired LC–MS peak, I identified it, so I decided to return to the conventional route; unlike the SI method, mechanistically it should avoid the formation of that side product. This time I’ll document every detail as carefully as possible. To be honest, I wasn’t as cautious during the first two attempts because HATU has been such a reliable reagent for amide couplings. We’ll see!
After wrapping up the morning lab routine, I went to the gym, then headed to my cozy library and managed to get some work done even though I was exhausted. As a reward for fighting off the sleepiness, I had an amazing pork-belly kimchi stew, honestly better than the one I had at a Korean fine-dining spot in SF. Productive day!
