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A protein that is a catalyst for some chemical reaction.

For an initial concrete example, consider e. Coli K-12 MG1655 gene thrA.

Video 1.

How Enzymes Work by RCSBProteinDataBank (2017)

Source. Shows in detail how aconitase catalyses the citrate to isocitrate reaction in the citric acid cycle.

New International Version by

Ciro Santilli 40 Updated 2025-07-16

Direct translation from oldest documents deemed reliable, originally in a mixture of Hebrew, Aramaic, and Greek. Interesting project.

This is notably opposed to the approach taken by many versions which were based on the Septuagint, which was a much earlier full-Greek translation.

E. Coli Whole Cell Model by Covert Lab / Condition by

Ciro Santilli 40 Updated 2025-07-16

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

Bird-and-flower painting by

Ciro Santilli 40 Updated 2025-07-16

Figure 1.
Early Autumn by Qian Xuan (13th century)
. Source.

Chinese government by

Ciro Santilli 40 Updated 2025-07-16

The enemy: github.com/cirosantilli/china-dictatorship.

Suspension (film) by

"Suspension" is a film that was released in 2015. It is a psychological horror film directed by Dave R. Sheppard, featuring a storyline that revolves around a group of friends who find themselves trapped in a series of bizarre and suspenseful situations. The narrative often intertwines elements of fear and the supernatural, typical of the horror genre. The film delves into themes of isolation and psychological strain, often keeping viewers on edge through its suspenseful atmosphere and twists in the storyline.

Suvini Zerboni by

As of my last update in October 2023, there is no widely recognized entity or subject known as "Suvini Zerboni." It’s possible that it could refer to a person, a brand, or a concept that emerged after that date, or it might be a relatively niche or obscure reference.

Syntagmatic analysis by

Syntagmatic analysis is a concept derived from linguistics and semiotics, primarily associated with the structuralist approach to language and meaning. It refers to the relationships and associations that words or signs have with one another within a sequential context—essentially, how elements operate in conjunction with one another in a sequence (or "syntagm"). In syntagmatic analysis, the focus is on the horizontal relationships of elements that are combined to create meaning.

Tarski–Kuratowski algorithm by

The Tarski-Kuratowski algorithm is a method used in topology and related fields to determine the connectivity and separation properties of sets in a topological space. Specifically, it addresses the problem of determining whether two sets are separated or not by exploring their topological relationships. The algorithm operates on pairs of closed sets in a topological space and can be used to find whether one set is contained within another, whether they are disjoint, or whether they intersect.

Telephone Preference Service by

The Telephone Preference Service (TPS) is a service in the UK that allows individuals to register their preference not to receive unsolicited telemarketing calls. When someone registers their phone number with TPS, it signals telemarketers that the person does not wish to be contacted for marketing purposes. Here are some key points about the Telephone Preference Service: 1. **Registration**: Individuals can register their home or mobile phone numbers for free. Registration can usually be done online, via phone, or by mail.

Terrace ledge kink model by

The term "terrace ledge kink model" pertains to a concept in the field of materials science, particularly in the study of crystal growth and surface morphology. This model is used to describe the dynamics of crystal surfaces during growth processes, where the arrangement of atoms or molecules leads to the formation of specific surface features. Here's a brief overview of the key components: 1. **Terraces**: These are flat regions on the crystal surface where atoms are arranged in an orderly, two-dimensional array.

The Simulacra by

"The Simulacra" is a philosophical and theoretical work by the French sociologist and philosopher Jean Baudrillard, published in 1981. In this book, Baudrillard explores the concepts of simulation, hyperreality, and the nature of signs and symbols in contemporary society. He discusses how, in modern culture, representations of reality have become more significant than reality itself, leading to a situation where the distinction between the real and the simulated blurs.

Peter Debye by

Peter Debye (1884-1966) was a Dutch-American physicist and chemist renowned for his contributions to the fields of physical chemistry and electrodynamics. He is best known for his work on the Debye model, which describes how dielectric materials respond to electric fields. He also investigated the behavior of polar molecules, leading to the introduction of the concept of the dipole moment and Debye temperature, which relates to specific heat capacities in solids.

Wildfire by

A wildfire, also known as a bushfire, forest fire, or grassfire, is an uncontrolled fire that burns in wildland areas, including forests, grasslands, and other ecosystems. Wildfires can occur naturally due to events such as lightning strikes, but they are often exacerbated or ignited by human activities, such as campfires, discarded cigarettes, or arson.

Weather rock by

A "weather rock" is a humorous and simple tool often used to indicate weather conditions. It is essentially a rock that is accompanied by a set of guidelines or a legend that explains how to interpret the weather based on the condition of the rock. For example: - If the rock is wet, it's raining. - If the rock is white, it's snowing. - If the rock is moving, it's windy. - If the rock is hard to see, it's foggy.

Prelog strain by

Prelog strain refers to a type of strain observed in certain polymers that exhibit a characteristic behavior under stress. Particularly, it is defined in the context of the mechanical properties of polymers, where it is related to their ability to deform elastically or plastically. The term is often used in relation to the study of polymer mechanics and the response of materials to external forces.

Ursula Gather by

Ursula Gather is a prominent figure in the field of mathematics, particularly known for her work in algebraic geometry and commutative algebra. She has made significant contributions to the understanding of various mathematical concepts and has been involved in academic research and education.

Undercompressive shock wave by

An undercompressive shock wave is a type of wave phenomenon that occurs in certain fluid dynamics and gas dynamics contexts. In contrast to traditional shock waves, which are characterized by an increase in pressure, density, and temperature across a discontinuity, undercompressive shock waves exhibit a decrease in pressure and density.

Units of electrical potential by

The unit of electrical potential is the volt (symbol: V). The volt is defined as the potential difference between two points in an electric circuit when one joule of energy is used to move one coulomb of electric charge between those two points.

Kathekon by

"Kathekon" is a term derived from the Greek word "καθέκον," which can be translated as "that which restrains" or "that which holds back." In various philosophical and theological contexts, particularly in the works of St. Augustine and later in discussions of the Christian eschatological framework, the term refers to an entity or principle that restrains evil or chaos in the world.