trying to make a diagram to capture the difference between biophysics vs traditional physics
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 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.”
about what are the core skills in biophysics
i was chatting with granular matter physicist zia. she said: “you expressed suspicion when I said you are a great candidate and I would be happy to take you. why?” I said, “i didn’t show you my projects. how do you know if i just talk idea or can implement the idea? how do you know if i know what thermodynamics is about if i just took the class?” she replied “because i assess from the interaction. your questions and your explanation about why you are interested in that paper. enthusiasm > background. we learn in class and journal club later” but i think in my head, “(do you know i have this self-demolishing insecurity and distractedness that make me not really a good labor)”. so she asks more explicitly:
do you like math? the real analysis yes. i like the feeling of oh i know how to go step by step. the hard parts sometimes impatient if pressed for time.
do you like cell biology? the beings yes. the task management I’m learning. the job too long.
do you want to learn physics? the intuition yes. the dogma no.
do you work hard? the intention yes. the focused output not enough. because i scatter.
and she said that’s all i needed to know.
i talked to a cell modeling engineer Neda Bagheri
got a better handle on what the engineers do — model, data analysis, technical vs empirical fitting. I guess I am familiar with 2/3! (familiar as in i witnessed it). And it feels nice to know that the projects they have are exactly exactly fitting what I can provide. Though I personally want to learn more physics, a bit more, than the more library-building they can provide. I also appreciated that she gave me feedback on basically my statement that I managed to (with self agreement) verbalize in simple words and concrete cases in 5 minutes. maybe that’s what I need — I wish this is all interviews instead of an essay hahahahaha. well sohit said the essay is a squint eye bubble for the interview that levels the playing field afterwords. ok fine.
talked to geometrician and biophysicist noah mitchell. really good conversation with Mitchell. we talk the science and there’s endless followup. would be happy to work with him and learn more geometry on the way. he also went from metamaterial to biological metamaterial (morphogenesis) which is arguably more interesting in both what it can do with energy and what it becomes. the chiral bias in molecules become the chiral coil in the organ (fly midgut, fish gut, sex organs). What are the mechanical modes you need for that? probably one is truer than the other. both are just awesome that we get to see it through in deep, live imaging.
“what was it like to go to this revolutionary education thing?” i said i got to blow my world view by various brave people. at the cost of a hardcore STEM training?
apparently US physics education doesn’t prepare you for mechanics in morphogenesis either, they focus on field theory too much. but mechanical engineering or french system is great for prep. result is everyone still need to learn mechanics on their own.
“in the essays thread the needle. what made you interested from one project to the next? why are you in biology now?”
talked to organism biophysics and cheap tools engineering Saad Bhamla. Finding my field site
before: excited about frugal technologies. field work. flocking finally, in tangle worms and sheep dogs.
after: he’s really good at turning personal/familial interests into money and rigor traction. like he enables the student to have money to go to their personal fieldwork, and he supports them on the rigorous modeling/paper writing part. i would only need the second part if it comes to a choice. need to follow his advice — email to get more touch points, information and traction / tailoring, while staying true. he describe me as crossing scales and disciplines and have personal interest in hawaii / other field not translated to academia.
