Monero Core Team by Ciro Santilli 37 Updated 2025-07-16
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Riccardo Spagni by Ciro Santilli 37 Updated 2025-07-16
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React example by Ciro Santilli 37 Updated 2025-07-16
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React class vs function component by Ciro Santilli 37 Updated 2025-07-16
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React function components do produce shorter code. But they are also impossible to understand without knowing what is their corresponding class component.
Hooks were introduced much after classes, and just require less code, so everyone is using them now instead of classes.
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React class component by Ciro Santilli 37 Updated 2025-07-16
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React function component by Ciro Santilli 37 Updated 2025-07-16
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react/ref-click-counter.html by Ciro Santilli 37 Updated 2025-07-16
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Dummy example of using a React ref This example is useless and to the end user seems functionally equivalent to react/hello.html.
It does however serve as a good example of what react does that is useful: it provides a "clear" separation between state and render code (which becomes once again much less clear in React function components.
Notably, this example is insane because at:
<button onClick={() => {
  elem.innerHTML = (parseInt(elem.innerHTML) + 1).toString()
we are extracing state from some random HTML string rather than having a clean JavaScript variable containing that value.
In this case we managed to get away with it, but this is in general not easy/possible.
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History of the electromagnetic theory of light by Ciro Santilli 37 Updated 2025-07-16
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E. Coli Whole Cell Model by Covert Lab / Condition by Ciro Santilli 37 Updated 2025-07-16
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  • reconstruction/ecoli/flat/condition/nutrient/minimal.tsv contains the nutrients in a minimal environment in which the cell survives:
    "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 NaN
    If we compare that to reconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv, we see that it adds the 20 amino acids on top of the minimal condition:
    "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 NaN
    so we guess that NaN in the upper mound likely means infinite.
    We can try to understand the less obvious ones:
    • ADP: TODO
    • PI: TODO
    • PROTON[c]: presumably a measure of pH
    • GLC[p]: glucose, this can be seen by comparing minimal.tsv with minimal_no_glucose.tsv
    • AMMONIUM: 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.tsv contains:
      "time (units.s)" "nutrients"
0 "minimal"
      which means just using reconstruction/ecoli/flat/condition/nutrient/minimal.tsv until infinity. That is the default one used by runSim.py, as can be seen from ./out/manual/wildtype_000000/000000/generation_000000/000000/simOut/Environment/attributes/nutrientTimeSeriesLabel which contains just 000000_basal.
    • reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000001_cut_glucose.tsv is more interesting and contains:
      "time (units.s)" "nutrients"
0 "minimal"
1200 "minimal_no_glucose"
      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!
    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.py
  • reconstruction/ecoli/flat/condition/condition_defs.tsv contains 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"]
    • condition refers to entries in reconstruction/ecoli/flat/condition/condition_defs.tsv
    • nutrients refers to entries under reconstruction/ecoli/flat/condition/nutrient/, e.g. reconstruction/ecoli/flat/condition/nutrient/minimal.tsv or reconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv
    • genotype perturbations: there aren't any in the file, but this suggests that genotype modifications can also be incorporated here
    • doubling 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
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E. Coli K-12 MG1655 gene by Ciro Santilli 37 Updated 2025-07-16
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Markus W. Covert by Ciro Santilli 37 Updated 2025-07-16
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Ciro Santilli really likes this dude, because Ciro really likes simulation.
Video 1.
How to build a computer model of a cell by Markus Covert (2020)
Source.
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Molecule by Ciro Santilli 37 Updated 2025-07-16
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Carl Zeiss SMT by Ciro Santilli 37 Updated 2025-07-16
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Subsidiary of Carl Zeiss AG and also part owned by ASML, sole optics vendor of ASML as of 2020.
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Focal length by Ciro Santilli 37 Updated 2025-07-16
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If you pass parallel light.
For a biconvex spherical lens, it is given by:
(1)
where:
  • n: f nidnex
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Electron configuration by Ciro Santilli 37 Updated 2025-07-16
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Term symbol by Ciro Santilli 37 Updated 2025-07-16
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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:
(1)
The can be understood directly as the degeneracy, how many configurations we have in that state.
Video 1.
Atomic Term Symbols by TMP Chem (2015)
Source.
Video 2.
Atomic Term Symbols by T. Daniel Crawford (2016)
Source.
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Radeon by Ciro Santilli 37 Updated 2025-07-16
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x86 Paging Tutorial / Basic TLB operation by Ciro Santilli 37 Updated 2025-07-16
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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   00000
The > indicates the current entry to be replaced.
And after a page linear address 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   00000
and after a second translation of 00007 to 00009 it becomes:
  valid  linear  physical
  -----  ------  --------
  1      00003   00005
  1      00007   00009
> 0      00000   00000
  0      00000   00000
Now if 00003 needs to be translated again, hardware first looks up the TLB and finds out its address with a single RAM access 00003 --> 00005.
Of course, 00000 is not on the TLB since no valid entry contains 00000 as a key.
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Average number of steps until reaching a state of a Markov chain by Ciro Santilli 37 Updated 2025-07-16
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TODO how to calculate
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Janelia Research Campus by Ciro Santilli 37 Updated 2025-07-16
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