Don Lincoln Updated 2025-07-16
Publishes through the Fermilab YouTube channel under the playlist "Fermilab - Videos by Don Lincoln"
Some insights, but too much on the popular science side of things.
Do one thing and do it well Updated 2025-07-16
Is this exact sentence really from UNIX philosophy? en.wikipedia.org/wiki/Unix_philosophy#Do_One_Thing_and_Do_It_Well
Of course, it has precedents, e.g. jack of all trades, master of none
Do superconductors carry infinite current? Updated 2025-07-16
No, see: superconductor I-V curve.
Bibliography:
- physics.stackexchange.com/questions/62664/how-can-ohms-law-be-correct-if-superconductors-have-0-resistivity on Physics Stack Exchange
- physics.stackexchange.com/questions/69222/how-can-i-put-a-permanent-current-into-a-superconducting-loop
- www.quora.com/Do-superconductors-produce-infinite-current-I-V-R-R-0-How-do-they-fit-into-quantum-theory
- www.reddit.com/r/askscience/comments/dcgdf/does_superconductivity_imply_infinite_current/
- www.reddit.com/r/askscience/comments/7xhb46/what_would_happen_if_a_voltage_was_applied_to_a/
Double-slit experiment Updated 2025-07-16
Amazingly confirms the wave particle duality of quantum mechanics.
The effect is even more remarkable when done with individual particles such individual photons or electrons.
Richard Feynman liked to stress how this experiment can illustrate the core ideas of quantum mechanics. Notably, he night have created the infinitely many slits thought experiment which illustrates the path integral formulation.
Dr. Strangelove Updated 2025-07-16
Dual space Updated 2025-07-16
The dual space of a vector space , sometimes denoted , is the vector space of all linear forms over with the obvious addition and scalar multiplication operations defined.
Since a linear form is completely determined by how it acts on a basis, and since for each basis element it is specified by a scalar, at least in finite dimension, the dimension of the dual space is the same as the , and so they are isomorphic because all vector spaces of the same dimension on a given field are isomorphic, and so the dual is quite a boring concept in the context of finite dimension.
Infinite dimension seems more interesting however, see: en.wikipedia.org/w/index.php?title=Dual_space&oldid=1046421278#Infinite-dimensional_case
Dulong-Petit law Updated 2025-07-16
It can be seen as the limit case of an Einstein solid at high temperatures. At lower temperatures, the heat capacity depends on temperature.
Dungeon Crawl Stone Soup Updated 2025-07-16
This website is really cool! crawl.akrasiac.org:8080/#lobby You can spectate players live and chat! Also has statistics.
Devs of this game are smart, they have one good in-tree tileset, unlike some other text-based games that didn't have an in-tree option...
Build on Ubuntu 21.10:
sudo apt install build-essential libncursesw5-dev bison flex liblua5.1-0-dev \
libsqlite3-dev libz-dev pkg-config python3-yaml binutils-gold python-is-python3 \
libsdl2-image-dev libsdl2-mixer-dev libsdl2-dev libfreetype6-dev libpng-dev \
fonts-dejavu-core advancecomp pngcrush
git clone --depth 1 --branch 0.28.0 https://github.com/crawl/crawl
cd crawl/crawl-ref/source
echo 0.28-a > util/release_ver
make -j`nproc` TILES=y
./crawlThis launches the UI version already for you.
Dutch university Updated 2025-07-16
Early expansions of hominins out of Africa Updated 2025-07-16
Early human migrations Updated 2025-07-16
Eat Just Updated 2025-07-16
E. Coli K-12 MG1655 gene thrL Updated 2025-07-16
The first gene in the E. Coli K-12 MG1655 genome. Remember however that bacterial chromosome is circular, so being the first doesn't mean much, how the choice was made: Section "E. Coli genome starting point".
Part of E. Coli K-12 MG1655 operon thrLABC.
At only 65 bp, this gene is quite small and boring. For a more interesting gene, have a look at the next gene, e. Coli K-12 MG1655 gene thrA.
Does something to do with threonine.
This is the first in the sequence thrL, thrA, thrB, thrC. This type of naming convention is quite common on related adjacent proteins, all of which must be getting transcribed into a single RNA by the same promoter. As mentioned in the analysis of the KEGG entry for e. Coli K-12 MG1655 gene thrA, those A, B and C are actually directly functionally linked in a direct metabolic pathway.
We can see that thrL, A, B, and C are in the same transcription unit by browsing the list of promoter at: biocyc.org/group?id=:ALL-PROMOTERS&orgid=ECOLI. By finding the first one by position we reach; biocyc.org/ECOLI/NEW-IMAGE?object=TU0-42486.
E. Coli K-12 MG1655 operon thrLABC Updated 2025-07-16
Contains the genes: e. Coli K-12 MG1655 gene thrL, e. Coli K-12 MG1655 gene thrA, e. Coli K-12 MG1655 gene thrB and e. Coli K-12 MG1655 gene thrC, all of which have directly linked functionality.
We can find it by searching for the species in the BioCyc promoter database. This leads to: biocyc.org/group?id=:ALL-PROMOTERS&orgid=ECOLI.
That page lists several components of the promoter, which we should try to understand!
Some of the transcription factors are proteins:
After the first gene in the codon, thrL, there is a rho-independent termination. By comparing:we understand that the presence of threonine or isoleucine variants, L-threonyl and L-isoleucyl, makes the rho-independent termination become more efficient, so the control loop is quite direct! Not sure why it cares about isoleucine as well though.
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.
E. Coli Whole Cell Model by Covert Lab Other run variants Updated 2025-07-16
Besides time series run variants, conditions can also be selected directly without a time series as in:which select row indices from so
python runscripts/manual/runSim.py --variant condition 1 1reconstruction/ecoli/flat/condition/condition_defs.tsv. The above 1 1 would mean the second line of that file which starts with:"condition" "nutrients" "genotype perturbations" "doubling time (units.min)" "active TFs"
"basal" "minimal" {} 44.0 []
"no_oxygen" "minimal_minus_oxygen" {} 100.0 []
"with_aa" "minimal_plus_amino_acids" {} 25.0 ["CPLX-125", "MONOMER0-162", "CPLX0-7671", "CPLX0-228", "MONOMER0-155"]1 means no_oxygen. 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"
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.
Edge (graph) Updated 2025-07-16
Edit war Updated 2025-07-16
There are unlisted articles, also show them or only show them.