Atomic, Molecular and Optical Physics by 
Ciro Santilli 37 Updated 2025-05-21 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-05-21 +Created 1970-01-01AMO is a slightly more general area than condensed matter physics, including related phenomena with smaller numbers atoms and optics. The two terms are however sometimes used as synonyms. The term AMO has gained wide usage and acceptability, see e.g.:
If Ciro had had greater foresight, this might have been what he studied at university!
Condensed matter physics is one of the best examples of emergence. We start with a bunch of small elements which we understand fully at the required level (atoms, electrons, quantum mechanics) but then there are complex properties that show up when we put a bunch of them together.
Includes fun things like:
As of 2020, this is the other "fundamental branch of physics" besides to particle physics/nuclear physics.
Condensed matter is basically chemistry but without reactions: you study a fixed state of matter, not a reaction in which compositions change with time.
Just like in chemistry, you end up getting some very well defined substance properties due to the incredibly large number of atoms.
Just like chemistry, the ultimate goal is to do de-novo computational chemistry to predict those properties.
And just like chemistry, what we can actually is actually very limited in part due to the exponential nature of quantum mechanics.
Also since chemistry involves reactions, chemistry puts a huge focus on liquids and solutions, which is the simplest state of matter to do reactions in.
Condensed matter however can put a lot more emphasis on solids than chemistry, notably because solids are what we generally want in end products, no one likes stuff leaking right?
One thing condensed matter is particularly obsessed with is the fascinating phenomena of phase transition.
What Is Condensed matter physics? by Erica Calman
. Source. Cute. Overview of the main fields of physics research. Quick mention of his field, quantum wells, but not enough details.Quantum Field Theory lecture notes by David Tong (2007) puts it well:This is also mentioned e.g. at Video "The Quantum Experiment that ALMOST broke Locality by The Science Asylum (2019)".
In classical physics, the primary reason for introducing the concept of the field is to construct laws of Nature that are local. The old laws of Coulomb and Newton involve "action at a distance". This means that the force felt by an electron (or planet) changes immediately if a distant proton (or star) moves. This situation is philosophically unsatisfactory. More importantly, it is also experimentally wrong. The field theories of Maxwell and Einstein remedy the situation, with all interactions mediated in a local fashion by the field.
E. Coli Whole Cell Model by Covert Lab by Ciro Santilli 37 Updated 2025-05-21 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-05-21 +Created 1970-01-01github.com/CovertLab/WholeCellEcoliRelease is a whole cell simulation model created by Covert Lab and other collaborators.
The project is written in Python, hurray!
But according to te README, it seems to be the use a code drop model with on-request access to master. Ciro Santilli asked at rationale on GitHub discussion, and they confirmed as expected that it is to:
- to prevent their publication ideas from being stolen. Who would steal publication ideas with public proof in an issue tracker without crediting original authors? Academia is broken. Academia should be the most open form of knowledge sharing. But instead we get this silly competition for publication points.
- to prevent noise from non-collaborators. But they only get like 2 issues as year on such a meganiche subject... Did you know that you can ignore people, and even block them if they are particularly annoying? Much more likely is that no one will every hear about your project and that it will die with its last graduate student slave.
The project is a followup to the earlier M. genitalium whole cell model by Covert lab which modelled Mycoplasma genitalium. E. Coli has 8x more genes (500 vs 4k), but it the undisputed bacterial model organism and as such has been studied much more thoroughly. It also reproduces faster than Mycoplasma (20 minutes vs a few hours), which is a huge advantages for validation/exploratory experiments.
The project has a partial dependency on the proprietary optimization software CPLEX which is freeware, for students, not sure what it is used for exactly, from the comment in the
requirements.txt the dependency is only partial.This project makes Ciro Santilli think of the E. Coli as an optimization problem. Given such external nutrient/temperature condition, which DNA sequence makes the cell grow the fastest? Balancing metabolites feels like designing a Factorio speedrun.
There is one major thing missing thing in the current model: promoters/transcription factor interactions are not modelled due to lack/low quality of experimental data: github.com/CovertLab/WholeCellEcoliRelease/issues/21. They just have a magic direct "transcription factor to gene" relationship, encoded at reconstruction/ecoli/flat/foldChanges.tsv in terms of type "if this is present, such protein is expressed 10x more". Transcription units are not implemented at all it appears.
Everything in this section refers to version 7e4cc9e57de76752df0f4e32eca95fb653ea64e4, the code drop from November 2020, and was tested on Ubuntu 21.04 with a docker install of
docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full with image id 502c3e604265, unless otherwise noted. E. Coli Whole Cell Model by Covert Lab Install and first run by Ciro Santilli 37 Updated 2025-05-21 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-05-21 +Created 1970-01-01At 7e4cc9e57de76752df0f4e32eca95fb653ea64e4 you basically need to use the Docker image on Ubuntu 21.04 due to pip breaking changes... (not their fault). Perhaps pyenv would solve things, but who has the patience for that?!?!
The Docker setup from README does just work. The image download is a bit tedius, as it requires you to create a GitHub API key as described in the README, but there must be reasons for that.
Once the image is downloaded, you really want to run is from the root of the source tree:This mounts the host source under The meaning of each of the analysis commands is described at Section "Output overview".
sudo docker run --name=wcm -it -v "$(pwd):/wcEcoli" docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full/wcEcoli, so you can easily edit and view output images from your host. Once inside Docker we can compile, run the simulation, and analyze results with:make clean compile &&
python runscripts/manual/runFitter.py &&
python runscripts/manual/runSim.py &&
python runscripts/manual/analysisVariant.py &&
python runscripts/manual/analysisCohort.py &&
python runscripts/manual/analysisMultigen.py &&
python runscripts/manual/analysisSingle.pyAs a Docker refresher, after you stop the container, e.g. by restarting your computer or running
sudo docker stop wcm, you can get back into it with:sudo docker start wcm
sudo docker run -it wcm bashrunscripts/manual/runFitter.py takes about 15 minutes, and it generates files such as reconstruction/ecoli/dataclasses/process/two_component_system.py (related) which is required to run the simulation, it is basically a part of the build.runSim.py does the main simulation, progress output contains lines of type:Time (s) Dry mass Dry mass Protein RNA Small mol Expected
(fg) fold change fold change fold change fold change fold change
======== ======== =========== =========== =========== =========== ===========
0.00 403.09 1.000 1.000 1.000 1.000 1.000
0.20 403.18 1.000 1.000 1.000 1.000 1.000 2569.18 783.09 1.943 1.910 2.005 1.950 1.963
Simulation finished:
- Length: 0:42:49
- Runtime: 0:09:13 Quantum field theory lecture by Tobias Osborne (2017) Lecture 2 by Ciro Santilli 37 Updated 2025-05-21 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-05-21 +Created 1970-01-01- the advantage of using Lagrangian mechanics instead of directly trying to work out the equations of motion is that it is easier to guess the Lagrangian correctly, while still imposing some fundamental constraints
- youtu.be/bTcFOE5vpOA?list=PLDfPUNusx1EpRs-wku83aqYSKfR5fFmfS&t=3375
- Lagrangian mechanics is better for path integral formulation. But the mathematics of that is fuzzy, so not going in that path.
- Hamiltonian mechanics is better for non-path integral formulation
- youtu.be/bTcFOE5vpOA?list=PLDfPUNusx1EpRs-wku83aqYSKfR5fFmfS&t=3449 Hamiltonian formalism requires finding conjugate pairs, and doing a
Quantum field theory lecture by Tobias Osborne (2017) Lecture 4 by Ciro Santilli 37 Updated 2025-05-21 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-05-21 +Created 1970-01-01- quantization. Uses a more or less standard way to guess the quantized system from the classical one using Hamiltonian mechanics.
- youtu.be/fnMcaq6QqTY?t=1179 remembers how to solve the non-field quantum harmonic oscillator
- youtu.be/fnMcaq6QqTY?t=2008 puts hats on everything to make the field version of things. With the Klein-Gordon equation Hamiltonian, everything is analogous to the harmonic oscilator
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!
Intro to OurBigBook
. Source. We have two killer features:
- 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-calculusArticles 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/derivativeVideo 2. OurBigBook Web topics demo. Source. - 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: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.
- 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
Figure 2. You can publish local OurBigBook lightweight markup files to either OurBigBook.com or as a static website.
Figure 3. Visual Studio Code extension installation.
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. 
- Infinitely deep tables of contents:
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