Most of the helium in the Earth's atmosphere comes from alpha decay, since helium is lighter than air and naturally escapes out out of the atmosphere.
Wiki mentions that alpha decay is well modelled as a quantum tunnelling event, see also Geiger-Nuttall law.
As a result of that law, alpha particles have relatively little energy variation around 5 MeV or a speed of about 5% of the speed of light for any element, because the energy is inversely exponentially proportional to half-life. This is because:
- if the energy is much larger, decay is very fast and we don't have time to study the isotope
- if the energy is much smaller, decay is very rare and we don't have enough events to observe at all
Highly radioactive isotope of caesium with half-life of 30.17 y. Produced from the nuclear fission of uranium, TODO exact reaction, not found in nature.
The fucked thing about this byproduct is that it is in the same chemical family as sodium, and therefore forms a salt that looks like regular table salt, and dissolves in water and therefore easily enters your body and sticks to things.
Another problem is that its half-life is long enough that it doesn't lose radioactivity very quickly compared to the life of a human person, although it is short enough to make it highly toxic, making it a terrible pollutant when released.
This is why for example in the goiânia accident a girl ended up ingesting Caesium-137 after eating an egg after touching the Caesium with her hands.
The key model database is located in the source code at
reconstruction/ecoli/flat
.Let's try to understand some interesting looking, with a special focus on our understanding of the tiny E. Coli K-12 MG1655 operon thrLABC part of the metabolism, which we have well understood at Section "E. Coli K-12 MG1655 operon thrLABC".
We'll realize that a lot of data and IDs come from/match BioCyc quite closely.
reconstruction/ecoli/flat/compartments.tsv
contains cellular compartment information:"abbrev" "id" "n" "CCO-BAC-NUCLEOID" "j" "CCO-CELL-PROJECTION" "w" "CCO-CW-BAC-NEG" "c" "CCO-CYTOSOL" "e" "CCO-EXTRACELLULAR" "m" "CCO-MEMBRANE" "o" "CCO-OUTER-MEM" "p" "CCO-PERI-BAC" "l" "CCO-PILUS" "i" "CCO-PM-BAC-NEG"
CCO
: "Celular COmpartment"BAC-NUCLEOID
: nucleoidCELL-PROJECTION
: cell projectionCW-BAC-NEG
: TODO confirm: cell wall (of a Gram-negative bacteria)CYTOSOL
: cytosolEXTRACELLULAR
: outside the cellMEMBRANE
: cell membraneOUTER-MEM
: bacterial outer membranePERI-BAC
: periplasmPILUS
: pilusPM-BAC-NEG
: TODO: plasma membrane, but that is the same as cell membrane no?
reconstruction/ecoli/flat/promoters.tsv
contains promoter information. Simple file, sample lines:corresponds to E. Coli K-12 MG1655 promoter thrLp, which starts as position 148."position" "direction" "id" "name" 148 "+" "PM00249" "thrLp"
reconstruction/ecoli/flat/proteins.tsv
contains protein information. Sample line corresponding to e. Coli K-12 MG1655 gene thrA:so we understand that:"aaCount" "name" "seq" "comments" "codingRnaSeq" "mw" "location" "rnaId" "id" "geneId" [91, 46, 38, 44, 12, 53, 30, 63, 14, 46, 89, 34, 23, 30, 29, 51, 34, 4, 20, 0, 69] "ThrA" "MRVL..." "Location information from Ecocyc dump." "AUGCGAGUGUUG..." [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 89103.51099999998, 0.0, 0.0, 0.0, 0.0] ["c"] "EG10998_RNA" "ASPKINIHOMOSERDEHYDROGI-MONOMER" "EG10998"
aaCount
: amino acid count, how many of each of the 20 proteinogenic amino acid are thereseq
: full sequence, using the single letter abbreviation of the proteinogenic amino acidsmw
; molecular weight? The 11 components appear to be given atreconstruction/ecoli/flat/scripts/unifyBulkFiles.py
:so they simply classify the weight? Presumably this exists for complexes that have multiple classes?molecular_weight_keys = [ '23srRNA', '16srRNA', '5srRNA', 'tRNA', 'mRNA', 'miscRNA', 'protein', 'metabolite', 'water', 'DNA', 'RNA' # nonspecific RNA ]
23srRNA
,16srRNA
,5srRNA
are the three structural RNAs present in the ribosome: 23S ribosomal RNA, 16S ribosomal RNA, 5S ribosomal RNA, all others are obvious:- tRNA
- mRNA
- protein. This is the seventh class, and this enzyme only contains mass in this class as expected.
- metabolite
- water
- DNA
- RNA: TODO
rna
vsmiscRNA
location
: cell compartment where the protein is present,c
defined atreconstruction/ecoli/flat/compartments.tsv
as cytoplasm, as expected for something that will make an amino acid
reconstruction/ecoli/flat/rnas.tsv
: TODO vstranscriptionUnits.tsv
. Sample lines:"halfLife" "name" "seq" "type" "modifiedForms" "monomerId" "comments" "mw" "location" "ntCount" "id" "geneId" "microarray expression" 174.0 "ThrA [RNA]" "AUGCGAGUGUUG..." "mRNA" [] "ASPKINIHOMOSERDEHYDROGI-MONOMER" "" [0.0, 0.0, 0.0, 0.0, 790935.00399999996, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] ["c"] [553, 615, 692, 603] "EG10998_RNA" "EG10998" 0.0005264904
halfLife
: half-lifemw
: molecular weight, same as inreconstruction/ecoli/flat/proteins.tsv
. This molecule only have weight in themRNA
class, as expected, as it just codes for a proteinlocation
: same as inreconstruction/ecoli/flat/proteins.tsv
ntCount
: nucleotide count for each of the ATGCmicroarray expression
: presumably refers to DNA microarray for gene expression profiling, but what measure exactly?
reconstruction/ecoli/flat/sequence.fasta
: FASTA DNA sequence, first two lines:>E. coli K-12 MG1655 U00096.2 (1 to 4639675 = 4639675 bp) AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTG
reconstruction/ecoli/flat/transcriptionUnits.tsv
: transcription units. We can observe for example the two different transcription units of the E. Coli K-12 MG1655 operon thrLABC in the lines:"expression_rate" "direction" "right" "terminator_id" "name" "promoter_id" "degradation_rate" "id" "gene_id" "left" 0.0 "f" 310 ["TERM0-1059"] "thrL" "PM00249" 0.198905992329492 "TU0-42486" ["EG11277"] 148 657.057317358791 "f" 5022 ["TERM_WC-2174"] "thrLABC" "PM00249" 0.231049060186648 "TU00178" ["EG10998", "EG10999", "EG11000", "EG11277"] 148
promoter_id
: matches promoter id inreconstruction/ecoli/flat/promoters.tsv
gene_id
: matches id inreconstruction/ecoli/flat/genes.tsv
id
: matches exactly those used in BioCyc, which is quite nice, might be more or less standardized:
reconstruction/ecoli/flat/genes.tsv
"length" "name" "seq" "rnaId" "coordinate" "direction" "symbol" "type" "id" "monomerId" 66 "thr operon leader peptide" "ATGAAACGCATT..." "EG11277_RNA" 189 "+" "thrL" "mRNA" "EG11277" "EG11277-MONOMER" 2463 "ThrA" "ATGCGAGTGTTG" "EG10998_RNA" 336 "+" "thrA" "mRNA" "EG10998" "ASPKINIHOMOSERDEHYDROGI-MONOMER"
reconstruction/ecoli/flat/metabolites.tsv
contains metabolite information. Sample lines:In the case of the enzyme thrA, one of the two reactions it catalyzes is "L-aspartate 4-semialdehyde" into "Homoserine"."id" "mw7.2" "location" "HOMO-SER" 119.12 ["n", "j", "w", "c", "e", "m", "o", "p", "l", "i"] "L-ASPARTATE-SEMIALDEHYDE" 117.104 ["n", "j", "w", "c", "e", "m", "o", "p", "l", "i"]
Starting from the enzyme page: biocyc.org/gene?orgid=ECOLI&id=EG10998 we reach the reaction page: biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=HOMOSERDEHYDROG-RXN which has reaction IDHOMOSERDEHYDROG-RXN
, and that page which clarifies the IDs:so these are the compounds that we care about.- biocyc.org/compound?orgid=ECOLI&id=L-ASPARTATE-SEMIALDEHYDE: "L-aspartate 4-semialdehyde" has ID
L-ASPARTATE-SEMIALDEHYDE
- biocyc.org/compound?orgid=ECOLI&id=HOMO-SER: "Homoserine" has ID
HOMO-SER
- biocyc.org/compound?orgid=ECOLI&id=L-ASPARTATE-SEMIALDEHYDE: "L-aspartate 4-semialdehyde" has ID
reconstruction/ecoli/flat/reactions.tsv
contains chemical reaction information. Sample lines:"reaction id" "stoichiometry" "is reversible" "catalyzed by" "HOMOSERDEHYDROG-RXN-HOMO-SER/NAD//L-ASPARTATE-SEMIALDEHYDE/NADH/PROTON.51." {"NADH[c]": -1, "PROTON[c]": -1, "HOMO-SER[c]": 1, "L-ASPARTATE-SEMIALDEHYDE[c]": -1, "NAD[c]": 1} false ["ASPKINIIHOMOSERDEHYDROGII-CPLX", "ASPKINIHOMOSERDEHYDROGI-CPLX"] "HOMOSERDEHYDROG-RXN-HOMO-SER/NADP//L-ASPARTATE-SEMIALDEHYDE/NADPH/PROTON.53." {"NADPH[c]": -1, "NADP[c]": 1, "PROTON[c]": -1, "L-ASPARTATE-SEMIALDEHYDE[c]": -1, "HOMO-SER[c]": 1 false ["ASPKINIIHOMOSERDEHYDROGII-CPLX", "ASPKINIHOMOSERDEHYDROGI-CPLX"]
catalized by
: here we seeASPKINIHOMOSERDEHYDROGI-CPLX
, which we can guess is a protein complex made out ofASPKINIHOMOSERDEHYDROGI-MONOMER
, which is the ID for thethrA
we care about! This is confirmed incomplexationReactions.tsv
.
reconstruction/ecoli/flat/complexationReactions.tsv
contains information about chemical reactions that produce protein complexes:The"process" "stoichiometry" "id" "dir" "complexation" [ { "molecule": "ASPKINIHOMOSERDEHYDROGI-CPLX", "coeff": 1, "type": "proteincomplex", "location": "c", "form": "mature" }, { "molecule": "ASPKINIHOMOSERDEHYDROGI-MONOMER", "coeff": -4, "type": "proteinmonomer", "location": "c", "form": "mature" } ] "ASPKINIHOMOSERDEHYDROGI-CPLX_RXN" 1
coeff
is how many monomers need to get together for form the final complex. This can be seen from the Summary section of ecocyc.org/gene?orgid=ECOLI&id=ASPKINIHOMOSERDEHYDROGI-MONOMER:Fantastic literature summary! Can't find that in database form there however.Aspartate kinase I / homoserine dehydrogenase I comprises a dimer of ThrA dimers. Although the dimeric form is catalytically active, the binding equilibrium dramatically favors the tetrameric form. The aspartate kinase and homoserine dehydrogenase activities of each ThrA monomer are catalyzed by independent domains connected by a linker region.
reconstruction/ecoli/flat/proteinComplexes.tsv
contains protein complex information:"name" "comments" "mw" "location" "reactionId" "id" "aspartate kinase / homoserine dehydrogenase" "" [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 356414.04399999994, 0.0, 0.0, 0.0, 0.0] ["c"] "ASPKINIHOMOSERDEHYDROGI-CPLX_RXN" "ASPKINIHOMOSERDEHYDROGI-CPLX"
reconstruction/ecoli/flat/protein_half_lives.tsv
contains the half-life of proteins. Very few proteins are listed however for some reason.reconstruction/ecoli/flat/tfIds.csv
: transcription factors information:"TF" "geneId" "oneComponentId" "twoComponentId" "nonMetaboliteBindingId" "activeId" "notes" "arcA" "EG10061" "PHOSPHO-ARCA" "PHOSPHO-ARCA" "fnr" "EG10325" "FNR-4FE-4S-CPLX" "FNR-4FE-4S-CPLX" "dksA" "EG10230"
The half-life of radioactive decay, which as discovered a few years before quantum mechanics was discovered and matured, was a major mystery. Why do some nuclei fission in apparently random fashion, while others don't? How is the state of different nuclei different from one another? This is mentioned in Inward Bound by Abraham Pais (1988) Chapter 6.e Why a half-life?
The term also sees use in other areas, notably biology, where e.g. RNAs spontaneously decay as part of the cell's control system, see e.g. mentions in E. Coli Whole Cell Model by Covert Lab.
Ciro Santilli finds it interesting that radioactive decay basically kickstarted the domain of nuclear physics by essentially providing a natural particle accelerator from a chunk of radioactive element.
The discovery process was particularly interesting, including Henri Becquerel's luck while observing phosphorescence, and Marie Curie's observation that the uranium ore were more radioactive than pure uranium, and must therefore contain other even more radioactive substances, which lead to the discovery of polonium (half-life 138 days) and radium (half-life 1600 years).