Ciro Santilli started taking some notes at: github.com/cirosantilli/awesome-whole-cell-simulation. but they are going to be all migrated here.
It is interesting to note how one talks about single cell analysis, in contrast to whole cell simulation: experimentally it is hard to analyse a single cell. But theoretically, it is hard to simulate a single cell. This mismatch is perhaps the ultimate frontier of molecular biology.
A Computational Whole-Cell Model Predicts Genotype From Phenotype by Markus Covert (2013)
Source. Theory that describes electrons and photons really well, and as Feynman puts it "accounts very precisely for all physical phenomena we have ever observed, except for gravity and nuclear physics" ("including the laughter of the crowd" ;-)).
Learning it is one of Ciro Santilli's main intellectual fetishes.
While Ciro acknowledges that QED is intrinsically challenging due to the wide range or requirements (quantum mechanics, special relativity and electromagnetism), Ciro feels that there is a glaring gap in this moneyless market for a learning material that follows the Middle Way as mentioned at: the missing link between basic and advanced. Richard Feynman Quantum Electrodynamics Lecture at University of Auckland (1979) is one of the best attempts so far, but it falls a bit too close to the superficial side of things, if only Feynman hadn't assumed that the audience doesn't know any mathematics...
The funny thing is that when Ciro Santilli's mother retired, learning it (or as she put it: "how photons and electrons interact") was also one of her retirement plans. She is a pharmacist by training, and doesn't know much mathematics, and her English was somewhat limited. Oh, she also wanted to learn how photosynthesis works (possibly not fully understood by science as that time, 2020). Ambitious old lady!!!
Experiments: quantum electrodynamics experiments.
Combines special relativity with more classical quantum mechanics, but further generalizing the Dirac equation, which also does that: Dirac equation vs quantum electrodynamics. The name "relativistic" likely doesn't need to appear on the title of QED because Maxwell's equations require special relativity, so just having "electro-" in the title is enough.
Before QED, the most advanced theory was that of the Dirac equation, which was already relativistic but TODO what was missing there exactly?
As summarized at: youtube.com/watch?v=_AZdvtf6hPU?t=305 Quantum Field Theory lecture at the African Summer Theory Institute 1 of 4 by Anthony Zee (2004):
- classical mechanics describes large and slow objects
- special relativity describes large and fast objects (they are getting close to the speed of light, so we have to consider relativity)
- classical quantum mechanics describes small and slow objects.
- QED describes objects that are both small and fast
That video also mentions the interesting idea that:Therefore, for small timescales, energy can vary a lot. But mass is equivalent to energy. Therefore, for small time scale, particles can appear and disappear wildly.
- in special relativity, we have the mass-energy equivalence
- in quantum mechanics, thinking along the time-energy uncertainty principle,
QED is the first quantum field theory fully developed. That framework was later extended to also include the weak interaction and strong interaction. As a result, it is perhaps easier to just Google for "Quantum Field Theory" if you want to learn QED, since QFT is more general and has more resources available generally.
Like in more general quantum field theory, there is on field for each particle type. In quantum field theory, there are only two fields to worry about:
- photon field
- electromagnetism field
Lecture 01 | Overview of Quantum Field Theory by Markus Luty (2013)
Source. This takes quite a direct approach, one cool thing he says is how we have to be careful with adding special relativity to the Schrödinger equation to avoid faster-than-light information.Gospel of Matthew 4 King James Version:
18 And Jesus, walking by the sea of Galilee, saw two brethren, Simon called Peter, and andrew the Apostle his brother, casting a net into the sea: for they were fishers.19 And he saith unto them, Follow me, and I will make you fishers of men.
Page size extension.
Allows for pages to be 4M ( or 2M if PAE is on ) in length instead of 4K.
PSE is turned on and off via the
PSE bit of cr4.- superuser.com/questions/133082/what-is-the-difference-between-hyper-threading-and-multiple-cores/995858#995858
- stackoverflow.com/questions/680684/what-are-the-differences-between-multi-cpu-multi-core-and-hyper-thread/73405312#73405312
- unix.stackexchange.com/questions/88283/so-what-are-logical-cpu-cores-as-opposed-to-physical-cpu-cores/739296#739296
Hyperthreding is the Intel brand-name, TODO generic name.
Basically the Royal Society's scientific vulgarization cousin.
The Principles of Quantum Mechanics by Paul Dirac (1930) Updated 2025-01-10 +Created 1970-01-01
This channel contains several 2D continuous simulations and explains AI techniques used.
The engine appears to be open source: github.com/Primer-Learning/PrimerTools (previously at: github.com/Helpsypoo/primer). Models are closed source however.
They have several interesting multiagent game ideas.
Ciro became mildly jealous of this channel when he found out about it, because at 800k subscribers at the time, the creator is likely able to make a living off of it, something which Ciro thought impossible.
As of 2022 he was at 1.6M followers with only 17 videos! Of course, much of those videos is about the software and they require infinite development hours to video time ratios.
Much of this success hinges a large part on the amazing 3D game presentation.
Well done!
Created by Justin Helps. Awesome name.
To make things better, the generically named channel is also the title of one of the best films of al time: Primer (2004).
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