Cryogenic electron microscopy by Ciro Santilli 35 Updated +Created
This technique has managed to determine protein 3D structures for proteins that people were not able to crystallize for X-ray crystallography.
It is said however that cryoEM is even fiddlier than X-ray crystallography, so it is mostly attempted if crystallization attempts fail.
By looking at Figure 1. "A cryoEM image", you can easily understand the basics of cryoEM.
We just put a gazillion copies of our molecule of interest in a solution, and then image all of them in the frozen water.
Each one of them appears in the image in a random rotated view, so given enough of those point of view images, we can deduce the entire 3D structure of the molecule.
Ciro Santilli once watched a talk by Richard Henderson about cryoEM circa 2020, where he mentioned that he witnessed some students in the 1980's going to Germany, and coming into contact with early cryoEM. And when they came back, they just told their principal investigator: "I'm going to drop my PhD theme and focus exclusively on cryoEM". That's how hot the cryo thing was! So cool.
Figure 1.
A cryoEM image
. Source. This is the type of image that you get out of a raw CryoEM experiment.
Video 1.
The structure of our cells by Matteo Allegretti
. Source. The start is useless. But the end at this timestamp shows an interesting technique where they actually cut up cells in fine slices and image them, that's cool.
XPath by Ciro Santilli 35 Updated +Created
XPath kind of died with the rise of CSS selectors around the beginnning of the 2010's. But that is a shame. XPath is a good standard, and was generally more powerful than CSS selectors for many many years.
X-ray crystallography by Ciro Santilli 35 Updated +Created
One of its main applications is to determine the 3D structure of proteins.
Sometimes you are not able to crystallize the proteins however, and the method cannot be used.
Crystallizing is not simple because:
  • you need a considerable amount of the protein
  • sometimes it only crystallizes if you add some extra small chemical that stabilizes it
Cryogenic electron microscopy can sometimes determine the structures of proteins that failed crystallization.
X-ray diffraction by Ciro Santilli 35 Updated +Created
Often used as a synonym for X-ray crystallography, or to refer more specifically to the diffraction part of the experiment (exluding therefore sample preparation and data processing).
Microscopy bibliography by Ciro Santilli 35 Updated +Created
Pre-trained computer vision model CLI by Ciro Santilli 35 Updated +Created
Mechanical engineering company by Ciro Santilli 35 Updated +Created
Sodium channel by Ciro Santilli 35 Updated +Created
Base machinery of the nervous system.
School by Ciro Santilli 35 Updated +Created
Basically the same remarks as for university, just 10 times more useless, see also: Section "Motivation".
Fall term by Ciro Santilli 35 Updated +Created
Spring term by Ciro Santilli 35 Updated +Created
This actually happens in Winter. But they are so fucking euphemistic that winter has to be removed from the calendar.
Summer term by Ciro Santilli 35 Updated +Created
This actually happens in spring. But because they are so euphemistic winter had to be removed from the calendar, it gets shifted a left.
Boarding school by Ciro Santilli 35 Updated +Created
Mentava by Ciro Santilli 35 Updated +Created
www.mentava.com/
Mentava's software-based daily tutor gets students on track for college-level math and computer science before high school.
OpenClassrooms by Ciro Santilli 35 Updated +Created
Molecular Sciences Course of the University of São Paulo by Ciro Santilli 35 Updated +Created
A fantastic sounding full time 4-year course that any student could transfer to called that teaches various natural science topics, notably mathematics, physics, chemistry and molecular biology.
Many past students Ciro talked to however share a common frustration with the course: in the first 2 years at least, the "basic cycle", you have infinitely many courses, and no time to study, and no choice of what to study, it is only in the latter 2 years (the advanced cycle) that you get the choices.
Also, if you get low grades in a single subject, your out. And exams are useless of course.
Here's a Quora question in Portuguese about the course: pt.quora.com/Como-funciona-o-tal-do-curso-secreto-da-USP, the only decent answer so far being: pt.quora.com/Como-funciona-o-tal-do-curso-secreto-da-USP/answer/Victor-Soares-31. Very disappointing to hear.
On the advanced cycle, you have a lot of academic freedom. You are basically supposed to pick a research project with an advisor and go for it, with a small amount of mandatory course hours. Ciro was told in 2022 that you can even have advisors from other universities or industry, and that it is perfectly feasible to take courses in another university and validate the course hours later on. Fantastic!!!
Students from the entire University of São Paulo can apply to transfer to it only after joining the university, with the guarantee that they can go back to their original courses if they don't adapt to the new course, which is great!
Not doing it is one of Ciro Santilli's regrets in life, see also: don't be a pussy.
Around 2007, they were in a really shady building of the University, but when Ciro checked in 2021, they had apparently moved to a shiny new entrepreneurship-focused building. Fantastic news!!!
This place has one of the best changes of spawning the first Brazilian Nobel Prize or unicorn.
One of the Brazilians who came to École Polytechnique together with Ciro was from this course. The fact that he is one of the most intelligent people Ciro knows gave further credit to that course in his eyes.
Sitare University by Ciro Santilli 35 Updated +Created
Video 1.
Running a Charity like a Company by Sitare Foundation
. Source.
Capacitor by Ciro Santilli 35 Updated +Created
The fundamental intuition about capacitors is that they never let electrons through.
They can only absorb electrons up to a certain point, but then the pushback becomes too strong, and current stops.
Therefore, they cannot conduct direct current long term.
For alternating current however, things are different, because in alternating current, electrons are just jiggling back and forward a little bit around a center point. So you can send alternating current power across a capacitor.
The key equation that relates Voltage to electric current in the capacitor is:
So if a voltage Heavyside step function is applied what happens is:
  • the capacitor fills up instantly with an infinite current
  • the current then stops instantly
More realistically, one may consider the behavior or the series RC circuit to see what happens without infinities when a capacitor is involved as in the step response of the series RC circuit.
Video 1.
Finding capacitance with an oscilloscope by Jacob Watts (2020)
Source. Good experiment.
Server-side rendering by Ciro Santilli 35 Updated +Created
List of front-end web frameworks by Ciro Santilli 35 Updated +Created
Pinned article: ourbigbook/introduction-to-the-ourbigbook-project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Video 1.
Intro to OurBigBook
. Source.
We have two killer features:
  1. topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculus
    Articles of different users are sorted by upvote within each article page. This feature is a bit like:
    • a Wikipedia where each user can have their own version of each article
    • a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
    This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
    Figure 1.
    Screenshot of the "Derivative" topic page
    . View it live at: ourbigbook.com/go/topic/derivative
    Video 2.
    OurBigBook Web topics demo
    . Source.
  2. local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:
    • to OurBigBook.com to get awesome multi-user features like topics and likes
    • as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
    This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
    Figure 5. . You can also edit articles on the Web editor without installing anything locally.
    Video 3.
    Edit locally and publish demo
    . Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.
    Video 4.
    OurBigBook Visual Studio Code extension editing and navigation demo
    . Source.
  3. https://raw.githubusercontent.com/ourbigbook/ourbigbook-media/master/feature/x/hilbert-space-arrow.png
  4. Infinitely deep tables of contents:
    Figure 6.
    Dynamic article tree with infinitely deep table of contents
    .
    Descendant pages can also show up as toplevel e.g.: ourbigbook.com/cirosantilli/chordate-subclade
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact