Condensed matter physics Updated +Created
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?
But it also studies liquids, e.g. notably superfluidity.
One thing condensed matter is particularly obsessed with is the fascinating phenomena of phase transition.
Figure 1.
xkcd 2933: Elementary Physics Paths
.
Video 1.
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.
Condition Updated +Created
  • 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
On a new radioactive substance contained in pitchblende Updated +Created
This is the papaer where Marie Curie announced the discovery of Polonium.
Here's a link with OCR on the French Wikisource: fr.wikisource.org/wiki/%C5%92uvres_de_Pierre_Curie/23. It's from a 1908 collection of works, but it is the exact same paper.
First a recap of previous work:
Some minerals containing uranium and thorium (pitchblende, chalcolite, uranite) are very active from the point of view of the emission of Becquerel rays. In a previous work, one of us showed that their activity is even greater than that of uranium and thorium, and expressed the opinion that this effect was due to some other very active substance contained in small quantities in these minerals.
Note the cute terminology "Becquerel rays", which were only later understood to be electromagnetic radiation now known as gamma rays.
Then some more recapitulation of the previously discussed groundbreaking idea that only atom counts matter for radioactivity, regardless of their chemical configuration as in fluorescence:
The study of compounds of uranium and thorium had shown, in fact, that the property of emitting rays which make air conductive and which act on photographic plates is a specific property of uranium and thorium which is found in all compounds of these metals, all the more weakened as the proportion of active metal in the compound is itself lower. The physical state of the substances seems to have a completely secondary importance. Various experiments have shown that the state of mixture of the substances seems to act only by varying the proportion of active bodies and the absorption produced by the inert substances. Certain causes (such as the presence of impurities) which act so powerfully on phosphorescence or fluorescence are therefore here completely without action. It therefore becomes very probable that if certain minerals are more active than uranium and thorium, it is because they contain a substance more active than these metals.
Then the key innovation: they used radioactivity measures to guide their purification work:
We have sought to isolate this substance in pitchblende, and experience has confirmed the above predictions.
Our chemical research has been constantly guided by the control of the radiant activity of the products separated at each operation. Each product is placed on one of the plates of a condenser, and the conductivity acquired by the air is measured using an electrometer and a piezoelectric quartz, as in the work cited above. We thus have not only an indication but a number which accounts for the richness of the product in active substance.
Next they describe in high level their separation process, and I can't understand anything. But that's OK
Finally towards the end, bombs are dropped:
By carrying out these various operations, we obtain increasingly active products. Finally, we obtained a substance whose activity is about 400 times greater than that of uranium.
We have sought, among the bodies currently known, to see if there are any active ones. We have examined compounds of almost all simple bodies; thanks to the great kindness of several chemists, we have had samples of the rarest substances. Uranium and thorium are the only ones clearly active, tantalum is perhaps very weakly so.
We therefore believe that the substance that we have removed from the pitchblende contains a metal not yet reported, close to bismuth by its analytical properties. If the existence of this new metal is confirmed, we propose to call it polonium, from the name of the country of origin of one of us.
They managed to purify it enough to look at the emission spectrum and it seems novel:
Mr. Demarçay was kind enough to examine the spectrum of the body that we are studying. He was unable to distinguish any characteristic line apart from those due to impurities. This fact does not support the idea of ​​the existence of a new metal. However, Mr. Demarçay pointed out to us that uranium, thorium and tantalum offer particular spectra, formed of innumerable lines, very fine, difficult to perceive.
And once again, our radiation-based analytical chemistry technique is new:
Allow us to note that if the existence of a new element is confirmed, this discovery will be uniquely attributable to the new method of detection that Becquerel rays provide.