E. Coli Whole Cell Model by Covert Lab Default run variant Updated 2025-07-16
The default run variant, if you don't pass any options, just has the minimal growth conditions set. What this means can be seen at condition.
Notably, this implies a growth medium that includes glucose and salt. It also includes oxygen, which is not strictly required, but greatly benefits cell growth, and is of course easier to have than not have as it is part of the atmosphere!
But the medium does not include amino acids, which the bacteria will have to produce by itself.
NIST Atomic Spectra Database Updated 2025-07-16
Searching for "H" for hydrogen leads to: physics.nist.gov/cgi-bin/ASD/lines1.pl?spectra=H&limits_type=0&low_w=&upp_w=&unit=1&submit=Retrieve+Data&de=0&format=0&line_out=0&en_unit=0&output=0&bibrefs=1&page_size=15&show_obs_wl=1&show_calc_wl=1&unc_out=1&order_out=0&max_low_enrg=&show_av=2&max_upp_enrg=&tsb_value=0&min_str=&A_out=0&intens_out=on&max_str=&allowed_out=1&forbid_out=1&min_accur=&min_intens=&conf_out=on&term_out=on&enrg_out=on&J_out=on
NIST Post-Quantum Cryptography Standardization Updated 2025-07-16
It was mind blowing when in 2022, after several years of selection, one of the 7 finalists was broken on a classical computer, not even in a quantum computer! news.ycombinator.com/item?id=30466063 | eprint.iacr.org/2022/214 Breaking Rainbow Takes a Weekend on a Laptop by Ward Beullens. Dude announced he had a break a few days before submission: twitter.com/WardBeullens/status/1492780462028300290 On Twitter. He's so young. Epic.
Edit: and then, after the third round, things were a bit unclear, so they made a fourth round with 4 choices out of the 7 from round 3, and in August 2022 one of the four was broken again on a classic CPU!!! OMG: arstechnica.com/information-technology/2022/08/sike-once-a-post-quantum-encryption-contender-is-koed-in-nist-smackdown/
NLab Updated 2025-07-16
Decent encyclopedia of mathematics. Not much motivation, mostly statements though.
Created by:
Nobel disease Updated 2025-09-11
The Eighth Day of Creation has a related quote:
In a conversation a few weeks earlier at the faculty club of the Massachusetts Institute of Technology, a couple of biologists had speculated whether Pauling, whose recent popular book on the benefits to health and sanity of massive doses of vitamin C was stacked in display near the entrance of the M.I.T. bookstore, was showing signs of what one of the men called "old scientist's disease" - which they defined as what happens to great men when they grow beyond the psychological reach of the salutary system by which scientists blow the whistle on one another's mistakes.
The Nobel Prize Winners With Crazy Theories by Qxir
. Source. E. Coli Whole Cell Model by Covert Lab Publications Updated 2025-07-16
Unfortunately, due to lack of one page to rule them all, the on-Git tree publication list is meager, some of the most relevant ones seems to be:
- 2021 open access review paper: journals.asm.org/doi/full/10.1128/ecosalplus.ESP-0001-2020 "The E. coli Whole-Cell Modeling Project". They should just past that stuff in a README :-) The article mentions that it is a follow up to the previous M. genitalium whole cell model by Covert lab. Only 43% of known genes modelled at this point however, a shame.
- 2020 under Science paywall: www.science.org/doi/10.1126/science.aav3751 "Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation"
Ciro Santilli's hardware Samsonite X-Pression Spinner Updated 2025-07-16
Looks like this:
Feels quite good.
Label markings:
Wheel hole separation:Trying to buy a replacement: www.amazon.co.uk/dp/B08KVZQSTG
E. Coli Whole Cell Model by Covert Lab Run variants Updated 2025-07-16
It would be boring if we could only simulate the same condition all the time, so let's have a look at the different boundary conditions that we can apply to the cell!
We are able to alter things like the composition of the external medium, and the genome of the bacteria, which will make the bacteria behave differently.
The variant selection is a bit cumbersome as we have to use indexes instead of names, but one you know what you are doing, it is fine.
Of course, genetic modification is limited only to experimentally known protein interactions due to the intractability of computational protein folding and computational chemistry in general, solving those would bsai.
Convert bytes to hex from Linux CLI Updated 2025-07-16
- no formatting;
- stackoverflow.com/questions/2614764/how-to-create-a-hex-dump-of-file-containing-only-the-hex-characters-without-spac
- unix.stackexchange.com/questions/10826/shell-how-to-read-the-bytes-of-a-binary-file-and-print-as-hexadecimal/758531#758531
- stackoverflow.com/questions/2003803/show-hexadecimal-numbers-of-a-file/77262369#77262369
- stackoverflow.com/questions/9515007/linux-script-to-convert-byte-data-into-a-hex-string/77262375#77262375
Human brain Updated 2025-07-16
Ciro Santilli feels it is not for his generation though, and that is one of the philosophical things that saddens him the most in this world.
On the other hand, Ciro's playing with the Linux kernel and other complex software which no single human can every fully understand cheer him up a bit. But still, the high level view, that we can have...
For now, Ciro's 2D reinforcement learning games.
Human brain connectome Updated 2025-07-16
By cranks:
- www.thehighestofthemountains.com/ has some diagrams. It is unclear how they were obtained, except that they were made over the course of 5 years by a "Space Shuttle Engineer", classic crank appeal to authority. The author belives that brain function is evidence of intelligent design.
Galaxies nearest the Milky Way Updated 2025-07-16
The first proper galaxy near the Milky Way is the Andromeda Galaxy. Everything else in the middle is a satellite of either of of those.
1987 Nobel Prize in Physics Updated 2025-07-16
This was so hot (no pun intended) and reproducible that the prize was awarded one year after discovery. Quite rare in those days already.
2007 Nobel Prize in Physics Updated 2025-07-16
2008 Nobel Prize in Chemistry Updated 2025-07-16
For the discovery of green fluorescent protein.
Quantum mechanics bibliography Updated 2025-07-16
Quantum software Updated 2025-07-16
Quantum superposition Updated 2025-07-16
Quantum superposition is really weird because it is fundamentally different than "either definite state but I don't know which", because the superposition state leads to different measurements than the non-superposition state.
Examples:
- www.youtube.com/watch?v=tt8gVXDsh7Q "Interference in quantum mechanics" by Looking Glass Universe (2015) shows how a left-right spin measurement has a defined value for a superposed half up half down state, but not for a pure up state.TODO can this be conducted? As mentioned in the video, this is closely linked to the fact that you can describe the wave function in multiple different bases (up/down or left/right), which is also at the root of the uncertainty principle.
- Video "Quantum Mechanics 9b - Photon Spin and Schrodinger's Cat II by ViaScience (2013)" gives a similar photon version
- it seems that the single particle double slit experiment can also be thought of as in terms of a superposition of "the particle goes through the right" and "the particle goes through the right", although it is a bit harder to thing about as it is not a discrete process
Quote by Ciro Santilli Updated 2025-07-16
These are "original" thoughts that Ciro had which at some point in the past amused him. Some would call them pieces of wisdom, others self delusion. All have likely been thought by others in the past, and some of them Ciro thinks to himself after a few years: "why did I like this back then??".
On the theory vs practice of computer science:
Whereas Turing completeness is enough for mathematicians, humans need "run-on-Debian-complete".
On how you make the best friends in life when dealing with hardships together.In Ciro's case, this in particular means going through high school/universities studies and work projects, though of course war would apply particularly well. Perhaps inspired by as iron sharpens iron, so one person sharpens another.
This is of course just another version of one picture is worth a thousand words.
Racing game Updated 2025-07-16
There are unlisted articles, also show them or only show them.