History of the electromagnetic theory of light by 
Ciro Santilli 35 Updated 2025-04-18 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-04-18 +Created 1970-01-01reconstruction/ecoli/flat/condition/nutrient/minimal.tsvcontains the nutrients in a minimal environment in which the cell survives:If we compare that to"molecule id" "lower bound (units.mmol / units.g / units.h)" "upper bound (units.mmol / units.g / units.h)" "ADP[c]" 3.15 3.15 "PI[c]" 3.15 3.15 "PROTON[c]" 3.15 3.15 "GLC[p]" NaN 20 "OXYGEN-MOLECULE[p]" NaN NaN "AMMONIUM[c]" NaN NaN "PI[p]" NaN NaN "K+[p]" NaN NaN "SULFATE[p]" NaN NaN "FE+2[p]" NaN NaN "CA+2[p]" NaN NaN "CL-[p]" NaN NaN "CO+2[p]" NaN NaN "MG+2[p]" NaN NaN "MN+2[p]" NaN NaN "NI+2[p]" NaN NaN "ZN+2[p]" NaN NaN "WATER[p]" NaN NaN "CARBON-DIOXIDE[p]" NaN NaN "CPD0-1958[p]" NaN NaN "L-SELENOCYSTEINE[c]" NaN NaN "GLC-D-LACTONE[c]" NaN NaN "CYTOSINE[c]" NaN NaNreconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv, we see that it adds the 20 amino acids on top of the minimal condition:so we guess that"L-ALPHA-ALANINE[p]" NaN NaN "ARG[p]" NaN NaN "ASN[p]" NaN NaN "L-ASPARTATE[p]" NaN NaN "CYS[p]" NaN NaN "GLT[p]" NaN NaN "GLN[p]" NaN NaN "GLY[p]" NaN NaN "HIS[p]" NaN NaN "ILE[p]" NaN NaN "LEU[p]" NaN NaN "LYS[p]" NaN NaN "MET[p]" NaN NaN "PHE[p]" NaN NaN "PRO[p]" NaN NaN "SER[p]" NaN NaN "THR[p]" NaN NaN "TRP[p]" NaN NaN "TYR[p]" NaN NaN "L-SELENOCYSTEINE[c]" NaN NaN "VAL[p]" NaN NaNNaNin theupper moundlikely means infinite.We can try to understand the less obvious ones:ADP: TODOPI: TODOPROTON[c]: presumably a measure of pHGLC[p]: glucose, this can be seen by comparingminimal.tsvwithminimal_no_glucose.tsvAMMONIUM: ammonium. This appears to be the primary source of nitrogen atoms for producing amino acids.CYTOSINE[c]: hmmm, why is external cytosine needed? Weird.
reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/contains sequences of conditions for each time. For example:reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000000_basal.tsvcontains:which means just using"time (units.s)" "nutrients" 0 "minimal"reconstruction/ecoli/flat/condition/nutrient/minimal.tsvuntil infinity. That is the default one used byrunSim.py, as can be seen from./out/manual/wildtype_000000/000000/generation_000000/000000/simOut/Environment/attributes/nutrientTimeSeriesLabelwhich contains just000000_basal.reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000001_cut_glucose.tsvis more interesting and contains:so we see that this will shift the conditions half-way to a condition that will eventually kill the bacteria because it will run out of glucose and thus energy!"time (units.s)" "nutrients" 0 "minimal" 1200 "minimal_no_glucose"
Timeseries can be selected with--variant nutrientTimeSeries X Y, see also: run variants.We can use that variant with:VARIANT="condition" FIRST_VARIANT_INDEX=1 LAST_VARIANT_INDEX=1 python runscripts/manual/runSim.pyreconstruction/ecoli/flat/condition/condition_defs.tsvcontains lines of form:"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"]conditionrefers to entries inreconstruction/ecoli/flat/condition/condition_defs.tsvnutrientsrefers to entries underreconstruction/ecoli/flat/condition/nutrient/, e.g.reconstruction/ecoli/flat/condition/nutrient/minimal.tsvorreconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsvgenotype perturbations: there aren't any in the file, but this suggests that genotype modifications can also be incorporated heredoubling time: TODO experimental data? Because this should be a simulation output, right? Or do they cheat and fix doubling by time?active TFs: this suggests that they are cheating transcription factors here, as those would ideally be functions of other more basic inputs
Ciro Santilli really likes this dude, because Ciro really likes simulation.
If you pass parallel light.
This notation is so confusing! People often don't manage to explain the intuition behind it, why this is an useful notation. When you see Indian university entry exam level memorization classes about this, it makes you want to cry.
The key reason why term symbols matter are Hund's rules, which allow us to predict with some accuracy which electron configurations of those states has more energy than the other.
web.chem.ucsb.edu/~devries/chem218/Term%20symbols.pdf puts it well: electron configuration notation is not specific enough, as each such notation e.g. 1s2 2s2 2p2 contains several options of spins and z angular momentum. And those affect energy.
This is why those symbols are often used when talking about energy differences: they specify more precisely which levels you are talking about.
Basically, each term symbol appears to represent a group of possible electron configurations with a given quantum angular momentum.
We first fix the energy level by saying at which orbital each electron can be (hyperfine structure is ignored). It doesn't even have to be the ground state: we can make some electrons excited at will.
The best thing to learn this is likely to draw out all the possible configurations explicitly, and then understand what is the term symbol for each possible configuration, see e.g. term symbols for carbon ground state.
It also confusing how uppercase letters S, P and D are used, when they do not refer to orbitals s, p and d, but rather to states which have the same angular momentum as individual electrons in those states.
It is also very confusing how extremelly close it looks to spectroscopic notation!
The form of the term symbol is:
Atomic Term Symbols by TMP Chem (2015)
Source. Atomic Term Symbols by T. Daniel Crawford (2016)
Source. Bibliography:
- chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/Spectroscopy/Electronic_Spectroscopy/Spin-orbit_Coupling/Atomic_Term_Symbols
- chem.libretexts.org/Courses/Pacific_Union_College/Quantum_Chemistry/08%3A_Multielectron_Atoms/8.08%3A_Term_Symbols_Gives_a_Detailed_Description_of_an_Electron_Configuration The PDF origin: web.chem.ucsb.edu/~devries/chem218/Term%20symbols.pdf
- chem.libretexts.org/Bookshelves/Inorganic_Chemistry/Inorganic_Coordination_Chemistry_(Landskron)/08%3A_Coordination_Chemistry_III_-_Electronic_Spectra/8.01%3A_Quantum_Numbers_of_Multielectron_Atoms
- physics.stackexchange.com/questions/8567/how-do-electron-configuration-microstates-map-to-term-symbols How do electron configuration microstates map to term symbols?
After a translation between linear and physical address happens, it is stored on the TLB. For example, a 4 entry TLB starts in the following state:
valid linear physical
----- ------ --------
> 0 00000 00000
0 00000 00000
0 00000 00000
0 00000 00000The
> indicates the current entry to be replaced.And after a page linear address and after a second translation of
00003 is translated to a physical address 00005, the TLB becomes: valid linear physical
----- ------ --------
1 00003 00005
> 0 00000 00000
0 00000 00000
0 00000 0000000007 to 00009 it becomes: valid linear physical
----- ------ --------
1 00003 00005
1 00007 00009
> 0 00000 00000
0 00000 00000 Average number of steps until reaching a state of a Markov chain by Ciro Santilli 35 Updated 2025-04-18 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-04-18 +Created 1970-01-01TODO how to calculate
Big goals:
- the pursuit of AGI
- physics simulations, including scientific visualization software
- formalization of mathematics
For some reason, this is one of the things that makes Ciro Santilli want to puke the most. More than surgery or blood.
Sequence and organization of the human mitochondrial genome by Sanger et al. (1981) by Ciro Santilli 35 Updated 2025-04-18 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-04-18 +Created 1970-01-01 There are unlisted articles, also show them or only show them.