graph bandits lab

2024 november - phd, money

11 min read

overview

  • I started this month in Beijing with PhD applications to complete and these questions to attempt to act on the preparation:
    • What perspective in my background could most likely help with other applied materials science topics? How to verify the rigor? Which concepts do I need to study more? From a physics perspective, how else should I describe this phase diagram? Ecologically, what observational data does Albert need to provide? What’s the most counterintuitive but meaningful plot in the story? What actionable points are in the PhysRevLett writing advice videos? Channel-wise, is arXiv or a visual blog more suitable for cell physics audiences?
    • and I said, in a braver honesty and as a hypothesis, that I want to do/learn/play with theoretical biophysics.
  • i ended the month having actually submitted most applications, wow. and back in chapel hill, after transit for 3 days in paris, and with the anticipation of freedom from phd applications and welcoming the winter to go to new york, to start living with yutaro, to be freeeee.

biophysics, paper, phd application

this section is the ‘well’ for depth in my top focus endeavor. in november it was phd application.

  • i was writing a fellowship application essay to get several years of phd funding and network with other researchers.
  • in the phd application process we are encouraged to reach out to and talk to researchers we would want to work with or at least share a topic with.
    • i was happy to get to talk to or read about interesting researchers. that was a reward of its own. playlist - interesting research labs and what they do
    • i also learned more things about me and the biophysics world in the conversations Biophysics (the field)
      • “US physics education doesn’t prepare you for mechanics in morphogenesis either, they focus on field theory too much”
      • “Enthusiasm > background. We learn in class and journal club later”
      • from profs’ descriptions and curiosities of me i realized that I like mathematical analysis and biological beings, want to learn physics intuition but not dogma, have intention to work hard but struggle with focus. and i am “crossing scales and disciplines with personal interest in Hawaii/other field not (yet) translated to academia”
  • for the application i wanted to wrap up the animal paper, the project that i used to explore the interest in sensory ecology / collective intelligence how do fish follow anonymous guides, as seen also in playlist - sensory network and information transfer in animal groups
    • i was frustrated that it’s taking so long and the story isn’t clear, after 2 years on and off working on it! the key insights from this experience of how to write a paper are:
      • “2-3 years is bit too long of a cycle - where you get interested in the next thing already, just wrap it up”
      • “Having a MVP makes me safe because I will definitely not die”
      • “When you get strange results, first check the intermediate expectations; don’t think rerunning the computer is more time-efficient, it’s just a bomb thrown to your future self”
      • “Last night it was actually pretty fun to check what went wrong… but also, yeah this still has a long way to go”
  • i was also planning a research collaboration between theorist and experimentalist as a followup to a conference chat how to facilitate a research collaboration chat
  • reading about biophysics labs and papers Biophysics (the field)
    • ex vivo is pretty interesting because you make a simulation physically (in maik’s case)
    • karen alim’s physarum is a giant single cell damn (while searching the max planck matter to life network of labs)
    • the perspective vs traditional physics
    • the modeling/theroy in biophysics
      • good example of a modeling section NatureSubcellular localization of type IV pili regulates bacterial…](https://www.nature.com/articles/s41467-022-33564-7): “Having established the molecular connection between the Pil-Chp system and subcellular T4P localization, we next sought to determine the biological consequences for dispersed vs. linear long-axis T4P. A. baylyi lacks genes encoding a flagellum and can grow as either individual cells or in a multicellular biofilm-like community18. T4P are known to regulate biofilm formation in other bacteria so we considered the possibility that T4P might affect A. baylyi multicellular biofilm formation19,20. In some species, including P. aeruginosa, twitching motility is thought to play a critical role in biofilm development1. However, A. baylyi does not exhibit classical twitching motility under laboratory growth conditions (Supplementary Fig. 7). To explore general principles of how the geometric distribution of T4P might affect multicellular interactions in nonmotile cells, we first used a computational approach. Specifically, we performed molecular dynamics simulations comparing interactions between “cellular objects” possessing self-adhesive structures (“adhesins”) that were either localized to one side of the object or dispersed around each object (similar to T4P in wildtype or fimV mutants, respectively (Supplementary Fig. 8)). Simulation data show that asymmetric localization of adhesins results in small groups of cells, whereas dispersed adhesin localization results in larger multicellular aggregates (Fig. 4a, b, Supplementary Fig. 9). This finding suggests that localizing adhesins together sterically reduces the ability of any one cell to interact with multiple cells, thereby limiting multicellular connectivity and large-scale aggregation.”

art, community, self, emotion

this section is supposed to be about anything that was not my main task or work. organically, in november, it was about alternative therapy, paris surrealism too. i felt more social / genuine directed than interesting / intellectual directed this month overall. i had more feelings of social relationships. i think the chats with researchers and family / friends count. also got some resonance in the chinese ling school community on my writing parts that were about “i can do whatever i want” and “to recall the genuine” and “to have a slow start of morning”. like i said, quick chats help me reduce anxiety about getting back on track with work and problems to solve. and the application process is better when you know from the other side, eg what is a smarter strategy that accounts for risk. socializing helps.

  • i was in china for a family wedding and in my family time, i got to try some alternative therapies that my dad is using.
    • cranial sacral therapy: right shoulder left knee rotation along the axis + sacrum / Muladhara has irregular rhythm → insecure, unsafe from the world.
    • accupuncture: abdomen repressing energy that should be released as emotions in words
  • i talked to my dad who tends to be astute about life strategies. how to decide what to do with life
    • “Calculate the bottom line of how much money you need to allow you to do what you want”
    • “Do what you like well (in your own standard)”
    • “Don’t try to get respect from others, they may have misaligned motivation. You give yourself respect”
    • “Don’t assess based on how good the outcome will be, that’s not predictable. Decide only when you have choices”
  • i spent 3 days in transit in paris with friend nana. we walkd, talked, visited pompidou’s surrealist exhibit. i was writing the application essays and she was reading Ipson so we ideated around how i could do more art. this is a thread as nana and i continue to talk, in the note Nana, Ipson women and surrealist trees. the notes are more like diary snippets, but i think these parts i like to keep how i framed things instead of let AI make them sound more proper.
  • tying all the conversations together (emotional truths) from fragments of diaries
    • skepticism to self and field: how to decide what to do with life && Biophysics (the field)
      • I’m still uncertain about what it truly means to challenge assumptions in my field. I need to learn more about what these assumptions actually are before I can propose alternatives. Groups like Swarma have been helpful, as they repost valuable articles from sources like Quanta and academic journals. Perhaps if I suspend judgment, I might experience less resistance and allow ideas to emerge more naturally.
      • if i suspend judgment i might feel less resistance and natural birth faster?
    • project ideas for connecting science with community, art and other things i love
      • felt a bit of holy-ness when i re-read notes about malama aina, and a bit of spicy-ness when I re-read notes about soft living matter meeting. to be honest, i do know what i want. i want the place-based rightness of malama. i want the question pattern chain rightness of biophys institution. i wish they can talk to each other - the latter have so much money. can they poor some into community technologies (cent centrifuge, bacteria remedy) instead of nuclear powered AI. do they know that the drugs don’t work in the body because they forgot to consider what the body actually contains, or the GMO golden rice. and do they realize it requires more than physics to study the physics of living systems — the kupuna who know 2000 signs of nature of the living, the birds route, the dolphin nest location, the wave cycle, they are facts as well as a way of knowing that the one sided hypothesis wouldn’t include. i do know this is the conflict in my body. maybe it’s the source of all the sleeplessness or sleepiness the dread the hope. science with local community
      • wish i could take the madness of surrealism and ipson and harbin and acupuncture and cranial sacral and grandma history back into biophysics. is that too crazy or far? was encouraged to do that anyways, by sohit, because i mean even if research requires basic capital production, they internally worship the idea of interest-guided exploration and genuine (truth) curiosity. curiosity that is then followed through on by hard studying, that part is required to ground the feet. science through art
    • sensing what i want
      • "I'm allowed to be interested in anything my heart really wants?!" “oh but i have to know what my heart wants. and i have to follow through to learn to walk.” how to decide what to do with life
    • dreams
    • descatter to action
      • I must be cautious about my tendency to generate too many ideas. While watching a movie about a startup CEO with numerous ideas that weren’t particularly good, I recognized that ideas themselves might have more entertainment value than practical value. Ideas implemented in reality have significant worth, but we must consider the time required to bring them to fruition. how to live as a scatterhead
    • talk to learn
      • Fortunately, I’ve found coping mechanisms to navigate challenges by talking to people and giving time. Quick conversations help reduce my anxiety about getting back on track with work and problems that need solving. Starting the day with a walk, coffee, and breakfast, followed by organizing my to-do list in the morning, helps me begin work without feeling behind. I’ve also learned that application processes become more manageable when you understand the perspective from the other side, allowing for smarter strategies that account for risk. how to socialize as a human
    • other actual feelings
      • “genuine”. im trying to recall!
      • what i see around me, the pointy leaf, that is real. what i hear in words, they might not be, only if i clip twos together, it’s up to me.
      • alabama shakes speak my deep sea emotion that i look forward to cherishing after i send this all.

questions to friends

  • what more can i learn from the emotional truths section?
  • how to know what the heart wants to do?!
  • ideas / interest in
    • take the madness of surrealism and ipson and harbin and acupuncture and cranial sacral and grandma history back into biophysics?
    • host an animation festival calling for short entries on the reverse entropy of life?

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