Methods | Fluxion

Model Reference

Fluxion 6.4.2

These derivations describe the parameter values used by the version of Fluxion named above. When a value is changed in the model, this page is regenerated from its source alongside the release.

Overview

Fluxion is a mechanistic simulation: every reaction carries kinetic and thermodynamic constants, and the behaviour on screen is the consequence of those numbers rather than a scripted animation. This page records where those numbers come from — which are measured constants taken from the literature, and which are modelling choices made to keep a reduced-order, coupled model of skeletal muscle, liver, erythrocyte, and their shared bloodstream physiological. It is written so that a student or reviewer can check the model against its sources.

How to read this page

Each value is given beside the reaction it belongs to, using the model's own names (for example ComplexI, ATPSynthase). Three kinds of number appear:

Vf — a forward velocity, in mM/s. It represents how much active catalyst is present, so it is the number an expression change, inhibitor, or knockdown moves. It is not a measured turnover number; it is a model-scaled capacity.
Keq — an equilibrium constant, derived from thermodynamics (standard free energies or midpoint potentials) rather than fitted. Reverse velocities follow from Vf and Keq through the Haldane relationship, so the equilibrium position is fixed by chemistry, not chosen.
Km — a half-saturation concentration, in mM, from measured enzyme affinities where these are known.

Citations. Each value is followed by a bracketed reference number — for example [1] — that links to the numbered References list at the foot of the page. A value with no bracketed number is a modelling choice rather than a measured quantity, and is labelled as such in the text; where the literature gives a different value, the entry says so and gives the reason.

Concentrations are in millimolar (mM); the mitochondrial membrane potential is a voltage in millivolts (mV). Compartments are marked by suffix: _c cytosol, _i intermembrane space, _m matrix, _b blood.

A note on matrix velocities. The model treats the cell as compartments with real relative volumes — cytosol 0.70, matrix 0.07, intermembrane space 0.02 of the cell. Because a matrix reaction is stated per liter of matrix, its velocity is multiplied by MATRIX_CAPACITY_SCALE = 0.70 / 0.07 = 10 to keep the same capacity per cell. Where a matrix Vf is quoted below as, say, 0.018 × 10, the first number is the per-liter value in the source and the second is that scaling.

Electron transport chain and oxidative phosphorylation

The respiratory chain is modelled as what it physically is: redox reactions that move charge across the inner membrane, and an ATP synthase that lets that charge back in to make ATP. The membrane potential is a real voltage that the complexes build and ATP synthase spends, not a fitted parameter.

Redox midpoint potentials and equilibrium constants

Each complex's equilibrium constant is derived from the standard midpoint potentials of its redox couples at pH 7 and 37 °C [5][3], using

ΔG = −n F ΔE and Keq = exp(−ΔG / RT), RT = 2577 J/mol at 310 K

with n = 2 electrons. The midpoint potentials used (volts) are the standard reference values [5]:

NAD⁺/NADH −0.320
FAD/FADH₂ +0.031 (the succinate-dehydrogenase-bound flavin)
CoQ/CoQH₂ +0.045
cytochrome c +0.254
O₂/H₂O +0.816

which give:

ComplexI — ΔE = 0.365 V, ΔG = −70.4 kJ/mol, Keq = 7.4 × 10¹¹ [5]
ComplexII — ΔE = 0.014 V, ΔG = −2.7 kJ/mol, Keq = 2.85 [5]. Barely favourable, which is correct: the succinate flavin sits almost level with the quinone pool, and that narrow margin is why succinate yields less ATP than NADH.
ComplexIII — ΔE = 0.209 V, ΔG = −40.3 kJ/mol, Keq = 6.3 × 10⁶ [5]
ComplexIV — ΔE = 0.562 V, ΔG = −108.4 kJ/mol, Keq = 1.9 × 10¹⁸ [5]. Far from equilibrium at any physiological potential, which is why cytochrome c oxidase is effectively one-way and is the committed step.

Proton and charge stoichiometry

Per two electrons, which totals the accepted ten protons per NADH oxidised [5]:

ComplexI — 4 H⁺ to the intermembrane space, 5 from the matrix (4 pumped, 1 for ubiquinone reduction); 4 charges [5].
ComplexIII — 4 H⁺ to the intermembrane space, 2 from the matrix; 2 charges — two protons leave ubiquinol on the outer face and cross no membrane [5].
ComplexIV — 2 H⁺ to the intermembrane space, 4 from the matrix (2 pumped, 2 forming water); 4 charges [5].

Rate law: exchange currents, not a maximum velocity

Complexes I, III, and IV use Butler–Volmer / Marcus electron-transfer kinetics rather than the reversible Michaelis–Menten law, so that Vf is an exchange current — a small internal resistance — rather than a saturating maximum. This is a modelling choice of rate-law form (no literature turnover number is implied): the small exchange current (Vf = 0.018 × 10) keeps the resting chain below its thermodynamic ceiling, which is what lets the membrane potential fall smoothly from rest to hard work. ComplexII (Vf = 0.85 × 10) is an ordinary reversible step, as it is not electrogenic. Km values for the electron carriers are 0.05 mM, within measured ranges [2].

ATP synthase

Reaction ATPSynthase: ADP + Pi + (8/3) H⁺ → ATP + H₂O + (8/3) H⁺. The mammalian enzyme has a ring of eight c-subunits and makes three ATP per revolution, so 8/3 protons per ATP [5]. The equilibrium constant comes from the free energy of ATP synthesis, ΔG = +30.5 kJ/mol, giving Keq = 7.3 × 10⁻⁶ [3] — driven entirely by the proton-motive force. Calcium activation (half-effect near 1 µM matrix Ca²⁺) is the demand half of parallel activation [6].

P/O ratio

The chain separates ten charges per NADH; ATP synthase spends 8/3 per ATP and the translocase one more, so 10 / (8/3 + 1) ≈ 2.7 ATP per NADH, against the accepted P/O ratio of about 2.5 once proton leak is included [12].

Proton leak

Reaction ProtonLeak: protons returning to the matrix outside ATP synthase. This accounts for roughly 20–25 % of resting mitochondrial oxygen consumption in skeletal muscle [13], and stops the potential running away when demand is low. It is modelled as a Hill function of the membrane potential (half-point 175 mV, coefficient 4, up to 25-fold), which reproduces the observed non-ohmic shape [13]; the exact Hill constants are a modelling choice fitted to that shape.

Membrane potential

Resting Dpsi_m settles near 180 mV (a respiring mitochondrion runs at roughly 150–190 mV) and falls toward the working range under load [5]. The pH gradient across the inner membrane adds a further ~25 mV, so the total proton-motive force is roughly Δψ + 25 mV [5].

Modelling choices called out honestly

Ubiquinone midpoint potential (+0.045 V). This couple is the least certain of the five — reported values run from about +0.04 to +0.11 V [5] — and it is also the one the model is most sensitive to, because it sets how the driving force divides between Complex I and Complex III. +0.045 V is chosen because it is the value at which both near-equilibrium complexes still run forward; this is a modelling choice within the reported range.
Phosphate carrier stoichiometry. The carrier is written with two protons per phosphate, where the literature usually gives one [5]. This is a compromise, made because the model lacks the potassium cycling that normally partitions the proton-motive force; with one proton the modelled matrix runs to pH 11. The total proton-motive force is correct either way — only its split between voltage and pH depends on it.

Glycolysis

Equilibrium constants (reversible steps)

Set to the apparent equilibrium constants at pH 7, which match the standard tabulated values [1][3]:

PGI (glucose-6-P ⇌ fructose-6-P) — Keq = 0.35 [1]
Aldolase (fructose-1,6-bisP ⇌ DHAP + GAP) — Keq = 0.08 [1]
TPI (DHAP ⇌ GAP) — Keq = 0.045, favouring DHAP ~22:1 [1]
GAPDH — Keq = 0.08 [1]
PGK (1,3-bisphosphoglycerate + ADP ⇌ 3-PG + ATP) — Keq = 3300 [1]
PGM (3-PG ⇌ 2-PG) — Keq = 0.17 [1]
Enolase (2-PG ⇌ PEP) — Keq = 0.50, derived from ΔG°′ ≈ +1.8 kJ/mol [3]

Regulated irreversible steps

Hexokinase — Km(glucose) = 0.05 mM, the measured low-Km hallmark of hexokinase (versus liver glucokinase) [2]. Product inhibition by glucose-6-phosphate (Ki = 0.05 mM) is its classic feedback [3]. Idled (Vf 0) for the liver, which runs its own dedicated Glucokinase reaction instead (below) rather than an override of this one -- the missing G6P inhibition is a genuine mechanistic difference the override system (additive-only regulators) cannot express.
Glucokinase (liver-only, §3.1) — the high-Km (10 mM), high-capacity hepatic isozyme [2] that keeps phosphorylating glucose as blood glucose rises after a meal, unlike muscle hexokinase, which self-limits. Genuinely carries NO glucose-6-phosphate product inhibition, matching the literature mechanism [3] -- the fix this reaction exists for; the former liver-tagged Hexokinase override kept the shared enzyme's G6P inhibitor because the override mechanism can only add regulators, never remove one.
PFK1 — inhibited by ATP and by protons, activated by AMP: the direction of all three controls matches the textbook regulation of the committed, pH-sensitive step [4][3]. The AMP activation strength (up to 10-fold) has no specific literature value — the code marks it a placeholder chosen to exceed the engine's former 2-fold ceiling, and it should be traced to a source.
PyruvateKinase — feed-forward activation by fructose-1,6-bisphosphate and inhibition by ATP; both match the established regulation of the M-type isozyme [3].

Forward velocities throughout glycolysis are model-scaled capacities, not measured turnover numbers (see How to read this page).

Glycogen storage and mobilisation

GlycogenPhosphorylase — the reciprocal allosteric pattern is textbook [4]: activated by AMP, inhibited by ATP and by glucose-6-phosphate. Km(Pi) = 5 mM is genuinely millimolar, consistent with the measured phosphate dependence [2]. The specific inhibition/activation constants (and the 15-fold AMP activation) are modelling choices; no exact literature fold-activation was identified.
PhosphoglucoMutase — Keq = 17 (glucose-1-P → glucose-6-P), matching the standard ~17–19 [1].
GlycogenSynthase now runs the real UDP-glucose route, written out rather than lumped: UGPase (G1P + UTP → UDP-glucose + 2 Pi, the essentially-instant inorganic pyrophosphatase folded in) makes the sugar-nucleotide, GlycogenSynthase itself extends glycogen from it (UDP-glucose → glycogen + UDP), and NucleosideDiphosphateKinase (UDP + ATP ⇌ UTP + ADP, Keq 1, a textbook near-equilibrium phosphotransferase) regenerates the UTP spent, which is where the real "two ATP-equivalents per glucosyl unit" cost actually lands (the first was already spent making G6P). G6P is now correctly modelled as glycogen synthase's allosteric activator rather than doubling as its co-substrate, matching the literature mechanism [3]. Its reciprocal regulation (inhibited by AMP, activated by G6P) is qualitatively literature-grounded [3].

Anaerobic glycolysis

LactateDehydrogenase_c (pyruvate + NADH + H⁺ ⇌ lactate + NAD⁺) — the apparent equilibrium constant at pH 7 is ~3.6 × 10⁴ favouring lactate, represented as Keq = 3.6 × 10⁸ once the proton is explicit; this matches the standard value [3][1]. Km values are within measured ranges [2]; the mild product inhibition by lactate (Ki = 20 mM) is a documented feature [2].

Pyruvate oxidation and the citric acid cycle

Matrix velocities are per-cell values, i.e. the per-liter-of-matrix figure ×10 (see the Overview).

Equilibrium constants (reversible steps)

Set from thermodynamics and consistent with the standard tabulated values [1]:

Aconitase (citrate ⇌ isocitrate) — Keq = 0.067, favouring citrate ~15:1 [1]
SuccinylCoASynthetase — Keq = 3.8 [1]
SuccinateDehydrogenase — Keq = 1.0, set to reflect the near-level succinate flavin / ubiquinone couple (see the ETC section) [5]
Fumarase (fumarate ⇌ malate) — Keq = 4.4 [1]
MalateDehydrogenase (malate + NAD⁺ ⇌ OAA + NADH) — Keq = 2.6 × 10⁻⁵, matching the standard ~2.8 × 10⁻⁵ [1]

Regulation of the dehydrogenases

PyruvateDehydrogenase, IsocitrateDehydrogenase, and AlphaKGDehydrogenase are inhibited by NADH (and their acyl-CoA / ATP products) and activated by matrix calcium; isocitrate dehydrogenase is additionally activated by ADP. This pattern matches the literature — the three dehydrogenases are the classic calcium- and energy-charge-sensitive control points [6]. The calcium half-activation (Ka ≈ 1 µM matrix Ca²⁺) is in the measured range for these enzymes [6]. The exact product-inhibition constants (for example the NADH Ki of 0.02 mM) are modelling choices tuned so the resting matrix stays oxidised — faithful in direction and steepness but not taken from a single measured value.

Anaplerosis (a deliberate departure)

PyruvateCarboxylase — its capacity is cut roughly 60-fold below a generic setting. This differs from a literature enzyme rate deliberately: skeletal muscle carries very little pyruvate carboxylase (it is chiefly a liver/kidney gluconeogenic enzyme) [3], and the model has no cataplerotic exit, so anaplerosis is held minimal to keep the matrix organic-acid pools physiological. The inhibition by matrix malate (Ki = 0.5 mM) is a modelling device with no direct literature counterpart.

The NADH shuttles

Cytosolic NADH is handed across the inner membrane by two shuttles, both textbook [3]. Their equilibrium constants are set from thermodynamics: cytosolic malate dehydrogenase (Keq = 2.6 × 10⁻⁵) [1], the aspartate aminotransferases (Keq = 0.147, matching the standard ~0.15) [1], and the cytosolic glycerol-3-phosphate dehydrogenase (Keq = 1 × 10⁴) [1].

The electrogenic aspartate/glutamate carrier (net one negative charge exported) is what makes the malate-aspartate shuttle effectively one-way; its electrogenicity is well established [5].
The malate-aspartate carriers and dehydrogenases are scaled to roughly 5 % of a full capacity. This differs from a literature rate by design: skeletal muscle relies chiefly on the glycerophosphate shuttle [3], so the malate-aspartate route is kept minor — which also prevents the matrix dicarboxylate pool from over-filling. The 5 % figure is a modelling choice with no single literature value.

Mitochondrial transport and the adenine nucleotide translocase

AdenineNucleotideTranslocase — electrogenic ATP⁴⁻/ADP³⁻ exchange (net one negative charge out). Its electrogenicity, and the quarter of the proton-motive force it costs to export each ATP, are literature-grounded [5] and set the P/O ratio correctly [12]. The velocity is a model capacity.
PyruvateCarrier — electroneutral proton symport, the established mechanism of the mitochondrial pyruvate carrier [9]. Its capacity is reduced about threefold from a naïve setting; this differs from a literature rate deliberately, so the mitochondria do not drain cytosolic pyruvate to near-zero and prevent lactate dehydrogenase engaging under heavy demand.
PhosphateCarrier — modelled with two protons per phosphate, where the literature usually gives one [5]; see the ETC modelling-choices note for why.
MatrixProtonHomeostat — a single electroneutral proton exchange holding the matrix ~0.4 pH units alkaline. It is a lumped stand-in for the aggregate K⁺/H⁺ and Na⁺/H⁺ antiporters [10], so it has no single literature rate; the 0.4-unit gradient is set below the ~0.5–0.7 often quoted [5] so more of the proton-motive force sits in the membrane potential.
OM_* (outer-membrane porins) — fast, near-equilibrating exchange reflecting the freely permeable outer membrane [5]; the large velocity is deliberate, not a measured rate.
AdenylateKinase_c / _m (2 ADP ⇌ ATP + AMP) — Keq = 0.44 (written as its reciprocal, 2.27), which matches the standard value [7]; its near-equilibrium operation is what makes AMP a sensitive energy-stress signal.

Calcium signalling

Calcium is the feed-forward matching mitochondrial output to demand ("parallel activation"), a well-established mechanism [6].

CalciumUniporter — the membrane-potential-driven MCU (net two positive charges in). Its low calcium affinity — it engages in the micromolar range — is literature-grounded [6]; the exact Km and velocity are model capacities.
CalciumEffluxMito (lumped NCLX / mHCX) and CalciumReuptake (SERCA-like) — lumped devices with no single literature rate, sized to hold resting cytosolic calcium near 0.1 µM and matrix calcium near 0.2 µM, the measured resting levels [3].

The phosphocreatine buffer

CreatineKinase_c — the apparent equilibrium constant near 150 at pH 7 (represented as Keq = 1.5 × 10⁶ once the proton is explicit) matches the standard value [7]. Km(PCr) = 0.72 mM and Km(ADP) = 0.035 mM are within measured ranges [2]. The high velocity reflects the enzyme's fast near-equilibrium buffering — a literature-grounded property [3] — though the exact velocity is a model capacity.

Lactate export and the blood compartment

LactateTransport_c_to_b — monocarboxylate transport carrying one proton per lactate, the established MCT mechanism [9]; exporting lactate is therefore also how a working muscle exports acid. Km ≈ 1 mM is broadly consistent with reported MCT affinities [9].
BloodLactateConsumption — an artificial systemic sink standing in for lactate disposal by other tissues (the Cori cycle). It is a boundary term rather than an enzyme, so it has no literature rate by construction.
BloodLactateProduction — an artificial systemic source standing in for the constitutive resting glycolysis of the unmodeled tissues (erythrocytes above all — they have no mitochondria — plus gut, skin, brain), which hold circulating lactate near ~1 mM at rest [3]. Self-inhibited at that set point (so it is off during exercise) and acid-neutral (it carries the proton the disposal sink removes). A boundary term, so it has no literature rate by construction; the set point it targets is the measured resting arterial lactate (0.5–1.5 mM).

Proton buffering and pH regulation

Intracellular pH is tracked implicitly: each of the cytosol, intermembrane space, and matrix carries its total titratable proton as the state variable, and pH is derived each step by inverting the compartment's buffering — a generic buffer (pKa ≈ 7.3, ≈ 51 mmol H⁺ per pH unit per liter, at the upper edge of the 30–50 range reported for muscle [3]) plus a binding polynomial for every phosphate species (Pi pKa₂ ≈ 6.8, the ester phosphates ≈ 6.1–6.5). This is the standard mechanistic-model treatment [Beard/Bazil] and is what lets a reaction's fractional proton (e.g. glycogen phosphorylase releasing ≈ 0.29 H⁺ as it converts Pi to glucose-1-phosphate) fall out of the chemistry rather than being dropped by integer stoichiometry.
ProtonBuffer_b — the blood buffer stays an explicit reversible buffer at pKa ≈ 7.1, a bicarbonate-weighted value, sized to ~24 mmol titratable base so plasma holds near pH 7.4 and acidifies only modestly, consistent with measured blood buffering [3].
PlasmaProtonHomeostat — the plasma-membrane Na⁺/H⁺ exchanger, anion exchanger, and bicarbonate cotransporters, lumped into one electroneutral proton exchange that holds each cell's cytosol ≈ 0.4 pH units acid of blood, the direction and magnitude of measured resting cytosol-to-plasma pH gradients [3]. A model term, not one enzyme.
BloodAcidBaseRegulation — the lungs' and kidneys' export of the net metabolic acid-base load, holding blood at its 7.4 set point. A boundary term standing in for respiratory + renal compensation, so it has no single literature rate by construction.

Boundary conditions: supply, demand, and gas exchange

These are source/sink terms representing the cell's environment, not enzymes.

ATPConsumption — the basal ATP-demand rate, Vf = 0.026 mM/s, matches the measured resting ATP turnover of skeletal muscle (~0.02–0.05 mM/s) [3]. The guided exercises override this with their own workloads.
GlucoseSupply — the default rate (5 × 10⁻⁵ mM/s) is consistent with measured skeletal-muscle glucose uptake (~2–5 µmol/min for a working muscle) [3]. Guided exercises set their own supply.
OxygenSupply — a boundary gas-exchange term. Oxygen delivery is self-limited so matrix O₂ settles near 0.012 mM, within the measured mitochondrial range of 0.005–0.03 mM [5]; the delivery rate itself is a boundary condition, not a measured enzyme rate.
CO2Removal — a boundary gas-exchange term, made a bidirectional homeostat that holds dissolved blood CO₂ at its set point (declared Keq = 1.2 mM). This is the dissolved arterial CO₂ at pCO₂ ~40 mmHg (40 mmHg × 0.03 mmol·L⁻¹·mmHg⁻¹ = 1.2 mM) [14]; the model has no bicarbonate pool, so CO2_b is the dissolved/metabolic CO₂ (~5% of total blood CO₂), not the ~24 mM total-CO₂/bicarbonate. It lumps whole-body respiration and ventilation, standing in for respiratory control, so it has no single enzyme rate.
PhosphateSupply — a lumped homeostat standing in for the sodium-phosphate cotransporter and whole-body phosphate regulation. It is a placeholder device with no single literature rate.
AMPRecovery_c / _m, NADHConsumption, FADH2Consumption — surrogate source/sink terms (the last two default to off). They are modelling devices, not measured reactions.

Starting concentrations

The initial concentrations are measured resting-skeletal-muscle values, and match the literature [11][3]:

ATP 8 mM, phosphocreatine 30 mM, creatine 10 mM, cytosolic NAD⁺ 0.7 mM, free phosphate 3 mM, glycogen 80 mM glucosyl units [11].
Free ADP (0.015 mM) and AMP (0.002 mM) are set far below total cellular content on purpose: most adenine nucleotide is protein-bound, and the low free concentrations are what enzymes sense — a literature-grounded distinction that makes AMP a sensitive stress signal [3].
Matrix nucleotides sit near an ATP/ADP ratio of ~1 (much lower than the cytosol, because the electrogenic translocase drives export) [5] and a NAD⁺/NADH ratio near 5, both consistent with measured mitochondrial poise [8].
Resting cytosolic calcium 0.1 µM, matrix calcium 0.2 µM, and blood pH 7.4 are standard resting values [3].

References

Literature audit of the current model

This audit is a snapshot of the model definitions present in the repository on 1 October 2026. It is documentation only: no value, equation, reaction, initial condition, compartment, model file, or simulation path was changed.

Repository traceability and audit scope

Reactions, stoichiometry, Vf, Vr, Keq, Km, inhibitors, activators, Hill coefficients, charge terms, and special electron-transfer settings are defined in App/metabolism_models/*.py.
App/metabolism_types.py defines the rate laws, Haldane-derived reverse velocities, Butler-Volmer/Marcus electron-transfer law, compartment-volume conversion, membrane-potential coupling, phosphate proton binding, and the global buffer constants.
App/fluxion_core.py assembles the skeletal-muscle, liver, and erythrocyte models and defines their metabolite lists and initial conditions. App/tissue_registry.py applies tissue namespaces, scalar overrides, tissue-specific regulators, mass factors, and per-tissue compartment volumes.
Display units are defined in App/ui_qt/model_data.py: concentrations are mM unless explicitly identified otherwise; mitochondrial potential is mV and insulin/glucagon signals are pM. Simulation time is seconds. Intracellular H_* states are total titratable-proton equivalents, not free proton concentrations; blood H_b remains an explicit free-proton concentration.

The assembled default model contains 234 reaction instances and 220 starting state values across skeletal muscle, liver, erythrocyte, and the shared blood pool. Tissue-tagged copies are retained as separate audit targets; the compact register below combines only copies whose entire displayed parameter bundle is identical.

The comparison count is by evaluation statement, not by paper and not by reaction. A reaction can therefore contribute several conclusions (for example, stoichiometry matches, Keq matches, Vf is not directly comparable, and its generic Km set has insufficient assay context). Across 1,144 evaluation statements, the conservative status totals are:

Matches literature — 168
Does not match literature — 4
Not directly comparable — 490
No reliable literature value found — 93
Insufficient context — 389

How the comparison labels were assigned

Vf is a model capacity (or, for complexes I, III and IV, an exchange-current scale), not kcat and not an enzyme concentration. The register therefore marks every Vf and every Haldane-derived Vr as Not directly comparable, unless the reaction is an artificial boundary or recovery term for which No reliable literature value found is more informative. A matching Km does not validate Vf; a matching transformed equilibrium constant does not validate the chosen rate law. The kinetic-database comparison used BRENDA and SABIO-RK [17][18], but most Fluxion entries omit organism, isoform, free Mg²⁺, pH, temperature, ionic strength, enzyme concentration, and assay direction. Those numerical Km, Ki, Ka, and Hill terms are conservatively marked Insufficient context unless a close primary or curated match was available.

Chemical Keq values were compared as written, with explicit-proton reactions kept distinct from apparent transformed K′eq values. eQuilibrator [1][15] and the component-contribution framework [16], together with Rhea [19], were used for reaction identity and thermodynamic direction. This avoids treating chemical concentrations as activities or silently converting a pH-7 transformed constant into the explicit-H⁺ convention used by several Fluxion reactions.

High-confidence findings

The reversible glycolytic constants, malate dehydrogenase, aminotransferase, adenylate kinase, creatine kinase, TCA reversible steps, respiratory midpoint- potential-derived constants, and ATP-synthase 8/3 H⁺ per ATP are supported at the level claimed, subject to the chemical-versus-transformed convention stated above [1][7][15][20].
The respiratory-chain total of ten pumped charges per NADH and the resulting theoretical P/O near 2.7 are consistent with the bovine c8 ATP-synthase structure; measured mammalian P/O is lower (about 2.1–2.5 depending on preparation and workload), as expected when leak and transport costs are included [12][20][22].
Matrix Ca²⁺ half-activation at 0.001 mM (1 µM) with about two-fold activation is close to the 0.84 µM, approximately two-fold response measured at 37 °C in isolated skeletal-muscle mitochondria [21]. It is not evidence that every individual enzyme has the same Ka or Hill coefficient.
Muscle ATP 8 mM and phosphocreatine 30 mM agree with mammalian fibre data and human calibrated 31P-MRS values (ATP about 8.2 mM, PCr about 33 mM). The model's Pi 3 mM lies between fibre-type-dependent reports (about 0.8–6 mM) [11][23].
The erythrocyte G6PD/6PGD, glutathione, and 2,3-BPG modules use substrate-scale constants and pool sizes in the range of published human erythrocyte models and experiments [24][25][26]. Their simplified one-step laws are still not equivalent to the detailed pH-, Mg²⁺-, haemoglobin-binding-, and oxygen-state- dependent rate equations in those publications.

Direct mismatches and deliberate departures

PhosphateCarrier is written as two H⁺ per phosphate in both muscle and liver. The canonical mitochondrial phosphate carrier is normally represented as electroneutral Pi/H⁺ symport (one proton per phosphate). These are the two reaction-instance Does not match literature conclusions. Fluxion's value is retained because the source documents it as a deliberate reduced-model pH calibration.
Thiolase uses a first-pass apparent Keq of 0.02 for the condensation 2 acetyl-CoA → acetoacetyl-CoA + CoA. The measured equilibrium favours thiolysis far more strongly (synthesis Keq ~1e-5), but at that value the acetoacetyl-CoA pass-through pool would sit at sub-nanomolar levels and the near-equilibrium reverse velocity would be ~1000× the forward, which the reduced model cannot resolve. Because acetoacetyl-CoA is a pulled intermediate whose exact level is not load-bearing (HMG-CoA synthase sets the chain flux), the value is raised to keep the pool representable (~0.5 µM) and the solver well-conditioned while preserving the unfavourable direction and the acetyl-CoA² drive. A declared model calibration, not the measured constant.
CitrateMalateCarrier (the mitochondrial tricarboxylate carrier, SLC25A1) carries an NADPH_c product inhibitor with no real counterpart -- the carrier itself is not NADPH-regulated in vivo. It is a labeled modeling device standing in for a genuine calibration conflict: this carrier trades against MAL_c, the same tiny cytosolic malate pool the malate-aspartate shuttle maintains, so a constant Vf fast enough to sustain the cytosolic NADPH backup (ME1/IDH1) through a prolonged oxidant challenge disturbs that shuttle pool at rest well past the model's resting-stationarity tolerance, while a constant Vf slow enough to leave the shuttle undisturbed cannot sustain the backup. Gating it on the SAME NADPH signal that already throttles the two dehydrogenases it feeds (product inhibition, Ki 0.001) resolves this without inventing an unrelated fourth regulatory axis: the standing citrate/isocitrate pool alone buffers a brief demand, and this gate lets the carrier itself speed up only once that demand is sustained. A declared model calibration device, not a real mechanism of SLC25A1.
The liver's G6PDehydrogenase/PhosphogluconateDehydrogenase run at Vf 0.01, calibration-capped near muscle's own low-capacity copy (0.008) rather than the literature "major NADPH producer" scale a real liver runs. Neither enzyme touches the malate-aspartate shuttle directly, but drawing G6P_c shifts cytosolic glycolytic flux (GAPDH's NAD+/NADH turnover) enough to ripple into ASP_c/ASP_m/ AKG_m/MAL_c -- measurably, and roughly linearly in Vf (0.94% resting disturbance at a naive Vf 0.05, 0.41% at 0.01), past the 0.5% rest-disturbance bar the shuttle's own fragility already demands elsewhere (CitrateMalateCarrier above). A declared calibration limit, not a measured rate; see OPEN-WORK.md 4.2.
NADPHConsumption_liver carries an INS_b activator with no direct literature rate -- it is a labeled modeling device standing in for the liver's unmodeled lipogenesis/cholesterol synthesis (the real NADPH consumer a real liver's PPP feeds), gated on insulin because that biosynthetic program genuinely is insulin-driven (SREBP-1c) in vivo. A declared calibration device, not a mismeasured constant.
AlanineTransaminase is written as the single step alanine → pyruvate, not the real alanine + alpha-ketoglutarate ⇌ pyruvate + glutamate transamination. The model tracks no whole-body nitrogen budget (no ammonia, no urea cycle, no free amino-acid pool beyond this one boundary species), so the amino group this reaction moves is not represented at all rather than wired through the malate-aspartate shuttle's AKG_c/GLU_c pair, which would either slowly drain or flood that near-equilibrium pair for no teaching benefit. Alanine and pyruvate are both 3-carbon, so the written step is exactly carbon-conserving on its own. A declared model simplification, not a mismeasured constant.

Composite beta-oxidation, ROS formation, peroxide removal, hormone secretion/clearance, gas exchange, systemic disposal, and proton-homeostat reactions are marked Not directly comparable or No reliable literature value found, not as mismatches. They represent several enzymes, transporters, tissues, or feedback loops with a single reduced-order term, so comparison to one purified-enzyme constant would be invalid. (Ketogenesis is now resolved into its three explicit enzymes -- thiolase, HMG-CoA synthase, HMG-CoA lyase -- and the non-oxidative pentose-phosphate branch is resolved into its isomerase, epimerase, transketolase, and transaldolase steps. These appear individually in the register below rather than as composite terms.)

Literature-search limitations

Consensus was used for broad discovery and primary-paper identification [20]-[26]. The installed Elicit connector could not run because the connected account does not include API access. BRENDA, SABIO-RK, eQuilibrator, Rhea, PubMed/PMC, and primary papers were used instead. Some older kinetic measurements are paywalled or expose numerical tables only in PDFs; where assay conditions or isoform identity could not be verified, the result is Insufficient context rather than a forced match. No literature evidence was inferred from search-result snippets alone.

Exhaustive model-value register

This compact register enumerates every value in the assembled default model. Identical tissue copies are shown together only when their complete displayed bundles agree; the reaction-instance counts above remain ungrouped. Concentration-like kinetic values are in mM unless the named state is an insulin/glucagon signal (pM) or Dpsi (mV). Vf and Vr are mM s⁻¹ in the reaction's home-compartment frame. Stoichiometric coefficients and charge are per model reaction event. Keq is the model's numerical chemical equilibrium constant and can be concentration-dimensional when the written reaction changes molecularity.

Reaction and kinetic-parameter register

GlucoseSupply: stoichiometry ∅ → GLC_b — Not directly comparable; Vf 0.05 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Keq 5 — No reliable literature value found; Haldane-derived Vr used 0.05 — Not directly comparable; Km {GLC_b 5} — No reliable literature value found; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PhosphateSupply (@muscle, @liver): stoichiometry ∅ → Pi_c — Not directly comparable; Vf 0.1 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Keq 4 — No reliable literature value found; Haldane-derived Vr used 0.0025 — Not directly comparable; Km {Pi_c 0.1} — No reliable literature value found; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
ATPConsumption (@muscle, @liver): stoichiometry ATP_c + H2O_c → ADP_c + Pi_c + H_c + 0.05 Ca_c — Not directly comparable; Vf 0.026 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {ATP_c 0.2, H2O_c 1, ADP_c 0.2, Pi_c 0.2, H_c 0.0001} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
AMPRecovery_c (@muscle, @liver, @rbc): stoichiometry AMP_c + Pi_c → ADP_c — Not directly comparable; Vf 0.01 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {AMP_c 0.05, Pi_c 0.3, ADP_c 0.1} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
AMPRecovery_m (@muscle, @liver): stoichiometry AMP_m + Pi_m → ADP_m — Not directly comparable; Vf 0.01 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {AMP_m 0.05, Pi_m 0.3, ADP_m 0.1} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
NADHConsumption (@muscle, @liver): stoichiometry NADH_c + H_c → NAD_c — Not directly comparable; Vf 0 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {NADH_c 0.05, NAD_c 0.05} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
FADH2Consumption (@muscle, @liver): stoichiometry FADH2_m → FAD_m — Not directly comparable; Vf 0 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {FADH2_m 0.05, FAD_m 0.05} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
ProtonBuffer_b: stoichiometry BufferH_b → Buffer_b + H_b — Matches literature; Vf 5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 7.94328e-05 — Insufficient context; Haldane-derived Vr used 6.2946271 — Not directly comparable; Km {BufferH_b 1, Buffer_b 1, H_b 0.0001} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
BloodAcidBaseRegulation: stoichiometry ∅ → H_b — Not directly comparable; Vf 0.004 — No reliable literature value found; declared Vr 0 — No reliable literature value found; inhibitors {H_b: Ki 3.98e-05, Hill n 3} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
CreatineKinase_c (@muscle): stoichiometry PCr_c + ADP_c + H_c → Cr_c + ATP_c — Matches literature; Vf 50 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1.5e+06 — Matches literature; Haldane-derived Vr used 39.68254 — Not directly comparable; Km {PCr_c 0.72, ADP_c 0.035, H_c 0.0001, Cr_c 6, ATP_c 0.5} — Matches literature; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GlycogenPhosphorylase (@muscle): stoichiometry GLY_c + Pi_c → G1P_c — Matches literature; Vf 0.35 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {GLY_c 2, Pi_c 5, G1P_c 0.05} — Insufficient context; inhibitors {ATP_c: Ki 4, Hill n 2, G6P_c: Ki 0.5, Hill n 2} — Insufficient context; activators {AMP_c: Ka 0.05, Hill n 2, maximum fold 15} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking yes} — Not directly comparable.
PhosphoglucoMutase (@muscle, @liver): stoichiometry G1P_c → G6P_c — Matches literature; Vf 8 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 17 — Matches literature; Haldane-derived Vr used 0.94117647 — Not directly comparable; Km {G1P_c 0.05, G6P_c 0.1} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
UGPase (@muscle): stoichiometry G1P_c + UTP_c → UDPGlc_c + 2 Pi_c — Matches literature; Vf 4 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {G1P_c 0.1, UTP_c 0.1} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking yes} — Not directly comparable.
GlycogenSynthase (@muscle): stoichiometry UDPGlc_c → GLY_c + UDP_c — Matches literature; Vf 0.0055 — Not directly comparable (calibrated well below a naive reuse of the former lumped step's Vf -- moving G6P_c from co-substrate to allosteric activator removed a self-limiting throttle the old stoichiometry had, so a naive Vf ran ~5-10x too fast at rest and drove cytosolic pH to ~8.6 within 90 minutes; see the deliberate-departures note); declared Vr 0 — Not directly comparable; Km {UDPGlc_c 0.2, GLY_c 50} — Insufficient context; inhibitors {AMP_c: Ki 0.05, Hill n 2} — Insufficient context; activators {G6P_c: Ka 0.5, Hill n 1.5, maximum fold 4} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
NucleosideDiphosphateKinase (@muscle): stoichiometry UDP_c + ATP_c → UTP_c + ADP_c — Matches literature; Vf 2 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Matches literature (NDK trades nucleotides of essentially equal phosphoanhydride bond energy); Haldane-derived Vr used 2 — Not directly comparable; Km {UDP_c 0.05, ATP_c 0.5, UTP_c 0.05, ADP_c 0.5} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Hexokinase (@muscle): stoichiometry GLC_c + ATP_c → G6P_c + ADP_c + H_c — Matches literature; Vf 0.38 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {GLC_c 0.05, ATP_c 0.5, G6P_c 0.05, ADP_c 0.5} — Insufficient context; inhibitors {G6P_c: Ki 0.05, Hill n 1.2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PGI (@muscle, @liver, @rbc): stoichiometry G6P_c → F6P_c — Matches literature; Vf 2 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 0.35087719 — Matches literature; Haldane-derived Vr used 5.7 — Not directly comparable; Km {G6P_c 0.1, F6P_c 0.1} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PFK1 (@muscle): stoichiometry F6P_c + ATP_c → F16BP_c + ADP_c + H_c — Matches literature; Vf 0.68 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {F6P_c 0.1, ATP_c 0.3} — Insufficient context; inhibitors {ATP_c: Ki 2, Hill n 2, H_c: Ki 0.0001, Hill n 2.5} — Insufficient context; activators {AMP_c: Ka 0.1, Hill n 2, maximum fold 10, F26BP_c: Ka 0.015, Hill n 2, maximum fold 4} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Aldolase (@muscle, @liver, @rbc): stoichiometry F16BP_c → DHAP_c + GAP_c — Matches literature; Vf 2 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 0.08 — Matches literature; Haldane-derived Vr used 5 — Not directly comparable; Km {F16BP_c 0.05, DHAP_c 0.1, GAP_c 0.1} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
TPI (@muscle, @liver, @rbc): stoichiometry DHAP_c → GAP_c — Matches literature; Vf 5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 0.045454545 — Matches literature; Haldane-derived Vr used 110 — Not directly comparable; Km {DHAP_c 0.05, GAP_c 0.05} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GAPDH (@muscle, @liver, @rbc): stoichiometry GAP_c + Pi_c + NAD_c → BPG13_c + NADH_c + H_c — Matches literature; Vf 3.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 0.08 — Matches literature; Haldane-derived Vr used 91.145833 — Not directly comparable; Km {GAP_c 0.05, Pi_c 0.3, NAD_c 0.08, BPG13_c 0.05, NADH_c 0.05} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking yes} — Not directly comparable.
PGK (@muscle, @liver, @rbc): stoichiometry BPG13_c + ADP_c → PG3_c + ATP_c — Matches literature; Vf 5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 3300 — Matches literature; Haldane-derived Vr used 0.02020202 — Not directly comparable; Km {BPG13_c 0.05, ADP_c 0.15, PG3_c 0.2, ATP_c 0.5} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PGM (@muscle, @liver, @rbc): stoichiometry PG3_c → PG2_c — Matches literature; Vf 4 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 0.17 — Matches literature; Haldane-derived Vr used 23.529412 — Not directly comparable; Km {PG3_c 0.1, PG2_c 0.1} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Enolase (@muscle, @liver, @rbc): stoichiometry PG2_c → PEP_c + H2O_c — Matches literature; Vf 2.8 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 0.5 — Matches literature; Haldane-derived Vr used 5.6 — Not directly comparable; Km {PG2_c 0.1, PEP_c 0.1} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PyruvateKinase (@muscle, @rbc): stoichiometry PEP_c + ADP_c + H_c → PYR_c + ATP_c — Matches literature; Vf 4.4 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {PEP_c 0.08, ADP_c 0.15, H_c 0.0001} — Insufficient context; inhibitors {ATP_c: Ki 2, Hill n 2} — Insufficient context; activators {F16BP_c: Ka 0.05, Hill n 2, maximum fold 2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
LactateDehydrogenase_c (@muscle, @liver, @rbc): stoichiometry PYR_c + NADH_c + H_c → LAC_c + NAD_c — Matches literature; Vf 6 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 3.6e+08 — Matches literature; Haldane-derived Vr used 0.083333333 — Not directly comparable; Km {PYR_c 0.1, NADH_c 0.03, H_c 0.0001, LAC_c 10, NAD_c 0.15} — Insufficient context; inhibitors {LAC_c: Ki 20, Hill n 1.2} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
LactateTransport_c_to_b (@muscle, @rbc): stoichiometry LAC_c + H_c → LAC_b + H_b — Not directly comparable; Vf 0.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 2.5 — Insufficient context; Haldane-derived Vr used 0.2 — Not directly comparable; Km {LAC_c 1, LAC_b 1} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
BloodLactateConsumption: stoichiometry LAC_b + H_b → ∅ — Not directly comparable; Vf 0.04 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {LAC_b 1, H_b 1e-06, O2_b 0.003} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
BloodLactateProduction: stoichiometry ∅ → LAC_b + H_b — Not directly comparable; Vf 0.035 — No reliable literature value found; declared Vr 0 — No reliable literature value found; inhibitors {LAC_b: Ki 1, Hill n 2} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
MalateDehydrogenase_c (@muscle, @liver): stoichiometry MAL_c + NAD_c → OAA_c + NADH_c + H_c — Matches literature; Vf 0.25 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 2.6e-05 — Matches literature; Haldane-derived Vr used 4807.6923 — Not directly comparable; Km {MAL_c 0.08, NAD_c 0.1, OAA_c 0.05, NADH_c 0.08} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
AspartateAminotransferase_c (@muscle, @liver): stoichiometry ASP_c + AKG_c → OAA_c + GLU_c — Matches literature; Vf 0.25 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 0.147 — Matches literature; Haldane-derived Vr used 2.8344671 — Not directly comparable; Km {ASP_c 0.9, AKG_c 0.1, OAA_c 0.05, GLU_c 3} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
AspartateAminotransferase_m (@muscle, @liver): stoichiometry ASP_m + AKG_m → OAA_m + GLU_m — Matches literature; Vf 2.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 0.147 — Matches literature; Haldane-derived Vr used 28.344671 — Not directly comparable; Km {ASP_m 0.9, AKG_m 0.1, OAA_m 0.05, GLU_m 3} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
OxoglutarateMalateCarrier (@muscle, @liver): stoichiometry MAL_c + AKG_m → MAL_m + AKG_c — Not directly comparable; Vf 0.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 0.5 — Not directly comparable; Km {MAL_c 0.4, AKG_m 0.1, MAL_m 0.4, AKG_c 0.1} — Insufficient context; configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
AspartateGlutamateCarrier (@muscle, @liver): stoichiometry ASP_m + GLU_c + H_i + 148.14815 Dpsi_m → ASP_c + GLU_m + H_m — Not directly comparable; Vf 0.25 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 0.25 — Not directly comparable; Km {ASP_m 0.05, GLU_c 2.8, ASP_c 0.05, GLU_m 2.8} — Insufficient context; configuration {reversible yes, charge -1, home m, phosphate-proton tracking no} — Not directly comparable.
G3PDH_cyt (@muscle, @liver): stoichiometry DHAP_c + NADH_c + H_c → G3P_c + NAD_c — Matches literature; Vf 5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 10000 — Matches literature; Haldane-derived Vr used 0.041666667 — Not directly comparable; Km {DHAP_c 0.1, NADH_c 0.03, G3P_c 0.5, NAD_c 0.5} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
G3PDH_mito (@muscle, @liver): stoichiometry G3P_c + FAD_m → DHAP_c + FADH2_m — Matches literature; Vf 10 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 2 — Matches literature; Haldane-derived Vr used 1 — Not directly comparable; Km {G3P_c 0.5, FAD_m 0.05, DHAP_c 0.1, FADH2_m 0.05} — Insufficient context; configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
OM_Pyruvate (@muscle, @liver): stoichiometry PYR_c → PYR_i — Not directly comparable; Vf 10 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 10 — Not directly comparable; Km {PYR_c 0.1, PYR_i 0.1} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
OM_Pi (@muscle, @liver): stoichiometry Pi_c → Pi_i — Not directly comparable; Vf 10 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 10 — Not directly comparable; Km {Pi_c 0.18, Pi_i 0.18} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
OM_ADP (@muscle, @liver): stoichiometry ADP_c → ADP_i — Not directly comparable; Vf 10 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 10 — Not directly comparable; Km {ADP_c 0.06, ADP_i 0.06} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
OM_ATP (@muscle, @liver): stoichiometry ATP_c → ATP_i — Not directly comparable; Vf 10 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 10 — Not directly comparable; Km {ATP_c 0.06, ATP_i 0.06} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
OM_H (@muscle, @liver): stoichiometry H_c → H_i — Not directly comparable; Vf 10 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 10 — Not directly comparable; Km {H_c 0.0001, H_i 0.0001} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
MatrixProtonHomeostat (@muscle, @liver): stoichiometry H_i → H_m — Not directly comparable; Vf 50 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Keq 0.39810717 — No reliable literature value found; Haldane-derived Vr used 125.59432 — Not directly comparable; Km {H_i 0.0001, H_m 0.0001} — No reliable literature value found; configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
PlasmaProtonHomeostat (@muscle, @liver, @rbc): stoichiometry H_c → H_b — Not directly comparable; Vf 0.5 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Keq 0.39810717 — No reliable literature value found; Haldane-derived Vr used 1.2559432 — Not directly comparable; Km {H_c 0.0001, H_b 0.0001} — No reliable literature value found; configuration {reversible yes, charge 0, home c, phosphate-proton tracking no} — Not directly comparable.
PyruvateCarrier (@muscle, @liver): stoichiometry PYR_i + H_i → PYR_m + H_m — Matches literature; Vf 7.2 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 7.2 — Not directly comparable; Km {PYR_i 0.1, PYR_m 0.1} — Insufficient context; inhibitors {PYR_m: Ki 2, Hill n 1.5} — Insufficient context; configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
PhosphateCarrier (@muscle, @liver): stoichiometry Pi_i + 2 H_i → Pi_m + 2 H_m — Does not match literature; Vf 10 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 10 — Not directly comparable; Km {Pi_i 0.2, Pi_m 0.2} — Insufficient context; inhibitors {Pi_m: Ki 4, Hill n 2} — Insufficient context; configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
AdenineNucleotideTranslocase (@muscle, @liver): stoichiometry ATP_m + ADP_i + 148.14815 Dpsi_m → ATP_i + ADP_m — Not directly comparable; Vf 11 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 11 — Not directly comparable; Km {ATP_m 0.1, ADP_i 0.01, ATP_i 0.1, ADP_m 0.01} — Insufficient context; inhibitors {ATP_i: Ki 6, Hill n 2} — Insufficient context; activators {ADP_i: Ka 0.08, Hill n 1.6, maximum fold 2, Ca_m: Ka 0.001, Hill n 2, maximum fold 2} — Matches literature; configuration {reversible yes, charge -1, home m, phosphate-proton tracking no} — Not directly comparable.
AdenylateKinase_c (@muscle, @liver): stoichiometry ATP_c + AMP_c → 2 ADP_c — Matches literature; Vf 5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 2.2727273 — Matches literature; Haldane-derived Vr used 4.4 — Not directly comparable; Km {ATP_c 0.1, AMP_c 0.05, ADP_c 0.1} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
AdenylateKinase_m (@muscle, @liver): stoichiometry ATP_m + AMP_m → 2 ADP_m — Matches literature; Vf 50 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 2.2727273 — Matches literature; Haldane-derived Vr used 44 — Not directly comparable; Km {ATP_m 0.1, AMP_m 0.05, ADP_m 0.1} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
CalciumUniporter (@muscle, @liver): stoichiometry Ca_c + 296.2963 Dpsi_m → Ca_m — Matches literature; Vf 0.03 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 0.15 — Not directly comparable; Km {Ca_c 0.001, Ca_m 0.005} — Insufficient context; configuration {reversible yes, charge -2, home m, phosphate-proton tracking no} — Not directly comparable.
CalciumEffluxMito (@muscle, @liver): stoichiometry Ca_m → Ca_c — Matches literature; Vf 0.02 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {Ca_m 0.002} — Insufficient context; configuration {reversible no, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
CalciumReuptake (@muscle, @liver): stoichiometry Ca_c → ∅ — Matches literature; Vf 0.03 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {Ca_c 0.001} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PyruvateDehydrogenase (@muscle, @liver): stoichiometry PYR_m + NAD_m + CoA_m → AcCoA_m + CO2_m + NADH_m + H_m — Matches literature; Vf 22 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {PYR_m 0.08, NAD_m 0.1, CoA_m 0.05} — Insufficient context; inhibitors {NADH_m: Ki 0.02, Hill n 2, AcCoA_m: Ki 0.6, Hill n 1.5} — Insufficient context; activators {Ca_m: Ka 0.001, Hill n 2, maximum fold 2} — Matches literature; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PyruvateCarboxylase (@muscle, @liver): stoichiometry PYR_m + CO2_m + ATP_m → OAA_m + ADP_m + Pi_m — Matches literature; Vf 0.0093 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {PYR_m 0.08, CO2_m 0.02, ATP_m 0.08, OAA_m 0.05, ADP_m 0.08, Pi_m 0.2} — Insufficient context; inhibitors {OAA_m: Ki 0.8, Hill n 2, MAL_m: Ki 0.5, Hill n 2, CIT_m: Ki 1, Hill n 2} — Insufficient context; activators {AcCoA_m: Ka 0.08, Hill n 1.8, maximum fold 2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Cataplerosis (@muscle): stoichiometry CIT_m → ∅ — Matches literature; Vf 0.02 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {CIT_m 0.5} — Insufficient context; configuration {reversible no, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
CitrateSynthase (@muscle): stoichiometry AcCoA_m + OAA_m → CIT_m + CoA_m — Matches literature; Vf 24 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {AcCoA_m 0.01, OAA_m 0.005, CoA_m 0.05} — Insufficient context; inhibitors {CIT_m: Ki 5, Hill n 2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Aconitase (@muscle, @liver): stoichiometry CIT_m → ICIT_m — Matches literature; Vf 20 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 0.066666667 — Matches literature; Haldane-derived Vr used 300 — Not directly comparable; Km {CIT_m 0.08, ICIT_m 0.08} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
IsocitrateDehydrogenase (@muscle, @liver): stoichiometry ICIT_m + NAD_m → AKG_m + CO2_m + NADH_m + H_m — Matches literature; Vf 8.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {ICIT_m 0.06, NAD_m 0.1} — Insufficient context; inhibitors {ATP_m: Ki 1.5, Hill n 2, NADH_m: Ki 0.02, Hill n 2} — Insufficient context; activators {ADP_m: Ka 0.2, Hill n 2, maximum fold 2, Ca_m: Ka 0.001, Hill n 2, maximum fold 2} — Matches literature; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
AlphaKGDehydrogenase (@muscle, @liver): stoichiometry AKG_m + NAD_m + CoA_m → SucCoA_m + CO2_m + NADH_m + H_m — Matches literature; Vf 6.8 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {AKG_m 0.07, NAD_m 0.1, CoA_m 0.05} — Insufficient context; inhibitors {NADH_m: Ki 0.02, Hill n 2, SucCoA_m: Ki 0.5, Hill n 1.5} — Insufficient context; activators {Ca_m: Ka 0.001, Hill n 2, maximum fold 2} — Matches literature; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
SuccinylCoASynthetase (@muscle, @liver): stoichiometry SucCoA_m + ADP_m + Pi_m → SUC_m + ATP_m + CoA_m — Matches literature; Vf 8.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 3.8 — Matches literature; Haldane-derived Vr used 0.59649123 — Not directly comparable; Km {SucCoA_m 0.06, ADP_m 0.1, Pi_m 0.5, SUC_m 0.08, ATP_m 0.2, CoA_m 0.05} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
SuccinateDehydrogenase (@muscle, @liver): stoichiometry SUC_m + FAD_m → FUM_m + FADH2_m — Matches literature; Vf 8 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Matches literature; Haldane-derived Vr used 8 — Not directly comparable; Km {SUC_m 0.08, FAD_m 0.05, FUM_m 0.08, FADH2_m 0.05} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Fumarase (@muscle, @liver): stoichiometry FUM_m + H2O_m → MAL_m — Matches literature; Vf 44 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 4.4 — Matches literature; Haldane-derived Vr used 10 — Not directly comparable; Km {FUM_m 0.08, H2O_m 1, MAL_m 0.08} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
MalateDehydrogenase (@muscle, @liver): stoichiometry MAL_m + NAD_m → OAA_m + NADH_m + H_m — Matches literature; Vf 7 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 2.6e-05 — Insufficient context; Haldane-derived Vr used 134615 — Not directly comparable; Km {MAL_m 0.08, NAD_m 0.1, OAA_m 0.05, NADH_m 0.08} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
ComplexI (@muscle, @liver): stoichiometry NADH_m + CoQ_m + 5 H_m → NAD_m + CoQH2_m + 4 H_i + 592.59259 Dpsi_m — Matches literature; Vf 0.18 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 7.4e+11 — Matches literature; Haldane-derived Vr used 4.86486e-13 — Not directly comparable; Km {NADH_m 0.05, CoQ_m 0.05, NAD_m 0.1, CoQH2_m 0.05} — Insufficient context; configuration {reversible yes, charge 4, home inferred, phosphate-proton tracking no, electron-transfer steepness 1, cap 40} — Not directly comparable.
ComplexII (@muscle, @liver): stoichiometry FADH2_m + CoQ_m → FAD_m + CoQH2_m — Matches literature; Vf 8.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 2.85 — Insufficient context; Haldane-derived Vr used 2.9824561 — Not directly comparable; Km {FADH2_m 0.05, CoQ_m 0.05, FAD_m 0.05, CoQH2_m 0.05} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
ComplexIII (@muscle, @liver): stoichiometry CoQH2_m + 2 CytC_ox_i + 2 H_m → CoQ_m + 2 CytC_red_i + 4 H_i + 296.2963 Dpsi_m — Matches literature; Vf 0.18 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 6.3e+06 — Matches literature; Haldane-derived Vr used 2.85714e-08 — Not directly comparable; Km {CoQH2_m 0.05, CytC_ox_i 0.05, CoQ_m 0.05, CytC_red_i 0.05} — Insufficient context; configuration {reversible yes, charge 2, home m, phosphate-proton tracking no, electron-transfer steepness 1, cap 40} — Not directly comparable.
ComplexIV (@muscle, @liver): stoichiometry 2 CytC_red_i + 0.5 O2_m + 4 H_m → 2 CytC_ox_i + H2O_m + 2 H_i + 592.59259 Dpsi_m — Matches literature; Vf 0.18 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1.9e+18 — Matches literature; Haldane-derived Vr used 9.47368e-17 — Not directly comparable; Km {CytC_red_i 0.05, O2_m 0.001, CytC_ox_i 0.05} — Insufficient context; configuration {reversible yes, charge 4, home m, phosphate-proton tracking no, electron-transfer steepness 1, cap 40} — Not directly comparable.
ATPSynthase (@muscle, @liver): stoichiometry ADP_m + Pi_m + 2.6666667 H_i + 395.06173 Dpsi_m → ATP_m + H2O_m + 1.6666667 H_m — Matches literature; Vf 13.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 7.3e-06 — Matches literature; Haldane-derived Vr used 4.62329e+06 — Not directly comparable; Km {ADP_m 0.05, Pi_m 0.8, ATP_m 0.1} — Insufficient context; activators {Ca_m: Ka 0.001, Hill n 2, maximum fold 2} — Matches literature; configuration {reversible yes, charge -2.6666667, home inferred, phosphate-proton tracking no} — Not directly comparable.
ProtonLeak (@muscle, @liver): stoichiometry H_i + 148.14815 Dpsi_m → H_m — Matches literature; Vf 0.011 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {H_i 0.0001} — Insufficient context; activators {Dpsi_m: Ka 175, Hill n 4, maximum fold 25} — Insufficient context; configuration {reversible no, charge -1, home m, phosphate-proton tracking no} — Not directly comparable.
ROS_Generation_Q (@muscle, @liver): stoichiometry 2 O2_m + CoQH2_m → 2 O2super_m + CoQ_m + 2 H_m — Matches literature; Vf 0.004 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {O2_m 0.02, CoQH2_m 0.05, O2super_m 0.01, CoQ_m 0.05} — Insufficient context; activators {CoQH2_m: Ka 0.15, Hill n 2, maximum fold 2, Dpsi_m: Ka 180, Hill n 2, maximum fold 2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
SOD_m (@muscle, @liver): stoichiometry 2 O2super_m + 2 H_m → H2O2_m + O2_m — Matches literature; Vf 2.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {O2super_m 0.01, H2O2_m 0.01, O2_m 0.02} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PeroxideDetox_m (@muscle, @liver): stoichiometry 2 H2O2_m → 2 H2O_m + O2_m — Matches literature; Vf 1.8 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {H2O2_m 0.01, H2O_m 1, O2_m 0.02} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
OxygenSupply: stoichiometry ∅ → O2_b — Not directly comparable; Vf 0.02 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {O2_b 0.1} — No reliable literature value found; inhibitors {O2_b: Ki 0.06, Hill n 2} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
OxygenUptake (@muscle, @liver): stoichiometry O2_b → O2_m — Matches literature; Vf 0.8 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {O2_b 0.05} — Insufficient context; inhibitors {O2_m: Ki 0.015, Hill n 2} — Insufficient context; configuration {reversible no, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
CO2Export (@muscle, @liver): stoichiometry CO2_m → CO2_b — Matches literature; Vf 10 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 10 — Not directly comparable; Km {CO2_m 0.1, CO2_b 0.1} — Insufficient context; configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
CO2Removal: stoichiometry ∅ → CO2_b — Matches literature; Vf 0.12 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1.2 — Insufficient context; Haldane-derived Vr used 0.12 — Not directly comparable; Km {CO2_b 1.2} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GlucoseTransport_c_to_b (@muscle): stoichiometry GLC_c → GLC_b — Matches literature; Vf 0.004 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 0.004 — Not directly comparable; Km {GLC_c 5, GLC_b 5} — Insufficient context; activators {INS_b: Ka 100, Hill n 2, maximum fold 6} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
InsulinSecretion: stoichiometry ∅ → INS_b — Not directly comparable; Vf 0.6 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {INS_b 1} — No reliable literature value found; activators {GLC_b: Ka 5, Hill n 2, maximum fold 8} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
InsulinClearance: stoichiometry INS_b → ∅ — Not directly comparable; Vf 10 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {INS_b 100} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GlucagonSecretion: stoichiometry ∅ → GCG_b — Not directly comparable; Vf 2.5 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {GCG_b 1} — No reliable literature value found; inhibitors {GLC_b: Ki 5, Hill n 2} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GlucagonClearance: stoichiometry GCG_b → ∅ — Not directly comparable; Vf 5 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {GCG_b 50} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
G6PDehydrogenase (@muscle): stoichiometry G6P_c + NADP_c → P6GL_c + NADPH_c + H_c — Matches literature; Vf 0.008 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {G6P_c 0.067, NADP_c 0.0037} — Matches literature; inhibitors {NADPH_c: Ki 0.0031, Hill n 2} — Matches literature; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
G6PDehydrogenase (@liver): stoichiometry G6P_c + NADP_c → P6GL_c + NADPH_c + H_c — Matches literature; Vf 0.01 — Not directly comparable (cut from a "major producer" scale to near muscle's own low-capacity level -- see the deliberate-departures note below); declared Vr 0 — Not directly comparable; Km {G6P_c 0.067, NADP_c 0.0037} — Matches literature; inhibitors {NADPH_c: Ki 0.0031, Hill n 2} — Matches literature; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Phosphogluconolactonase (@muscle, @rbc): stoichiometry P6GL_c + H2O_c → P6G_c + H_c — Matches literature; Vf 2 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {P6GL_c 0.02, H2O_c 1} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PhosphogluconateDehydrogenase (@muscle, @rbc): stoichiometry P6G_c + NADP_c → Ru5P_c + CO2_b + NADPH_c — Matches literature; Vf 0.05 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {P6G_c 0.03, NADP_c 0.004} — Matches literature; inhibitors {NADPH_c: Ki 0.0031, Hill n 2} — Matches literature; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PhosphogluconateDehydrogenase (@liver): stoichiometry P6G_c + NADP_c → Ru5P_c + CO2_b + NADPH_c — Matches literature; Vf 0.01 — Not directly comparable (calibration-capped, see G6PDehydrogenase @liver above); declared Vr 0 — Not directly comparable; Km {P6G_c 0.03, NADP_c 0.004} — Matches literature; inhibitors {NADPH_c: Ki 0.0031, Hill n 2} — Matches literature; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
NADPHConsumption_liver (@liver): stoichiometry NADPH_c → NADP_c — Not directly comparable; Vf 0.000005 — No reliable literature value found (a labeled modeling device standing in for unmodeled hepatic lipogenesis/cholesterol synthesis, see the deliberate-departures note below); declared Vr 0 — No reliable literature value found; Km {NADPH_c 0.05} — No reliable literature value found; activators {INS_b: Ka 40, Hill n 2, maximum fold 3 — real hepatic lipogenesis is insulin-driven (SREBP-1c)} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
RibosePhosphateIsomerase (@muscle, @liver, @rbc): stoichiometry Ru5P_c → R5P_c — Matches literature; Vf 0.5 — Not directly comparable (set high so the step is never rate-limiting; the resting PPP flux is governed by G6PD); Keq 1.2 (R5P/Ru5P) — Matches literature [27] (measured at 38 °C, pH 7.0, 1 mM free Mg²⁺; older room-temperature, Mg-free measurements give ~3); Km {Ru5P_c 0.5, R5P_c 0.5} — No reliable literature value found (first-pass; no human-erythrocyte Km table was obtainable, and the measured constants found are bacterial); configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
RibulosePhosphateEpimerase (@muscle, @liver, @rbc): stoichiometry Ru5P_c → X5P_c — Matches literature; Vf 0.5 — Not directly comparable (not rate-limiting, see above); Keq 1.82 (X5P/Ru5P) — Matches literature [27] (same conditions; other measurements range 1.4–2.2); Km {Ru5P_c 0.5, X5P_c 0.5} — No reliable literature value found (first-pass; the measured constant found, 0.22 mM, is from spinach and is not adopted); configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
TransketolaseI (@muscle, @liver, @rbc): stoichiometry X5P_c + R5P_c → S7P_c + GAP_c — Insufficient context; Vf 0.5 — Not directly comparable; Keq 1.2 — Insufficient context (traces to early Racker/Horecker equilibria of about 1; the secondary tables that list these do not preserve each quotient's direction, so it is not re-confirmed); Km {X5P_c 0.2, R5P_c 0.4, S7P_c 0.2, GAP_c 0.1} — No reliable literature value found (first-pass); configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable. The two transketolase steps are one enzyme acting twice, written as two reactions because the engine keys on reaction name.
Transaldolase (@muscle, @liver, @rbc): stoichiometry S7P_c + GAP_c → E4P_c + F6P_c — Insufficient context; Vf 0.5 — Not directly comparable; Keq 1.05 — Insufficient context (matches the Venkataraman & Racker 1961 value at 37 °C, pH 7.4, no Mg²⁺; not re-confirmed against a same-direction physiological-condition measurement); Km {S7P_c 0.2, GAP_c 0.1, E4P_c 0.1, F6P_c 0.3} — No reliable literature value found (first-pass); configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
TransketolaseII (@muscle, @liver, @rbc): stoichiometry X5P_c + E4P_c → F6P_c + GAP_c — Insufficient context; Vf 0.5 — Not directly comparable; Keq 10 — Insufficient context (near the Datta & Racker 1961 value of ~11.9 at 25 °C, pH 7.6; not re-confirmed); Km {X5P_c 0.2, E4P_c 0.1, F6P_c 0.3, GAP_c 0.1} — No reliable literature value found (first-pass); configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
R5PNucleotideDrain (@muscle, @liver, @rbc): stoichiometry R5P_c → ∅ — Not directly comparable (a labeled artificial boundary standing in for unmodeled de-novo nucleotide synthesis via PRPP); Vf 0.002 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {R5P_c 0.05} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GlutathioneReductase (@muscle, @rbc): stoichiometry GSSG_c + NADPH_c + H_c → 2 GSH_c + NADP_c — Matches literature; Vf 1 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {GSSG_c 0.065, NADPH_c 0.0085} — Matches literature; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GlutathionePeroxidase (@muscle, @rbc): stoichiometry 2 GSH_c + H2O2_c → GSSG_c + 2 H2O_c — Not directly comparable; Vf 5 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {GSH_c 1.33, H2O2_c 0.005} — Matches literature; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
BasalROSProduction (@muscle): stoichiometry ∅ → H2O2_c — Matches literature; Vf 1e-06 — Not directly comparable; declared Vr 0 — Not directly comparable; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
OxidativeChallenge (@muscle, @rbc): stoichiometry ∅ → H2O2_c — Matches literature; Vf 0 — Not directly comparable; declared Vr 0 — Not directly comparable; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Catalase (@muscle, @rbc): stoichiometry H2O2_c → H2O_c + 0.5 O2_b — Matches literature; Vf 0.2 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {H2O2_c 1} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
MalicEnzyme_c (@muscle): stoichiometry MAL_c + NADP_c → PYR_c + CO2_b + NADPH_c — Matches literature; Vf 0.2 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {MAL_c 1, NADP_c 0.005} — Insufficient context; inhibitors {NADPH_c: Ki 0.0003, Hill n 2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
CitrateMalateCarrier (@muscle): stoichiometry CIT_m + MAL_c → CIT_c + MAL_m — Matches literature (the citrate/malate antiport mechanism); Vf 0.3 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Matches literature (electroneutral antiport, no chemistry); Haldane-derived Vr used 0.3 — Not directly comparable; Km {CIT_m 0.5, MAL_c 0.4, CIT_c 0.1, MAL_m 0.4} — Insufficient context; inhibitors {NADPH_c: Ki 0.001, Hill n 2} — No reliable literature value found (a labeled modeling device, not a real regulatory mechanism of SLC25A1 -- see the deliberate-departures note); configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
Aconitase_c (@muscle): stoichiometry CIT_c → ICIT_c — Matches literature; Vf 0.3 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 0.0666667 — Matches literature (same value as the matrix Aconitase, isoform-independent thermodynamics); Haldane-derived Vr used 4.5 — Not directly comparable; Km {CIT_c 0.08, ICIT_c 0.08} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
IsocitrateDehydrogenase_c (@muscle): stoichiometry ICIT_c + NADP_c → AKG_c + CO2_b + NADPH_c + H_c — Matches literature; Vf 0.2 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {ICIT_c 0.065, NADP_c 0.049} — Insufficient context; inhibitors {NADPH_c: Ki 0.0003, Hill n 2, AKG_c: Ki 0.6, Hill n 2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GlycogenPhosphorylase (@liver): stoichiometry GLY_c + Pi_c → G1P_c — Matches literature; Vf 0.35 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {GLY_c 2, Pi_c 5, G1P_c 0.05} — Insufficient context; inhibitors {ATP_c: Ki 4, Hill n 2, G6P_c: Ki 0.5, Hill n 2, INS_b: Ki 10, Hill n 2} — Insufficient context; activators {AMP_c: Ka 0.05, Hill n 2, maximum fold 15} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking yes} — Not directly comparable.
UGPase (@liver): stoichiometry G1P_c + UTP_c → UDPGlc_c + 2 Pi_c — Matches literature; Vf 4 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {G1P_c 0.1, UTP_c 0.1} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking yes} — Not directly comparable.
GlycogenSynthase (@liver): stoichiometry UDPGlc_c → GLY_c + UDP_c — Matches literature; Vf 0.0055 — Not directly comparable (see @muscle above for the calibration finding); declared Vr 0 — Not directly comparable; Km {UDPGlc_c 0.2, GLY_c 50} — Insufficient context; inhibitors {AMP_c: Ki 0.05, Hill n 2} — Insufficient context; activators {G6P_c: Ka 0.5, Hill n 1.5, maximum fold 4, INS_b: Ka 25, Hill n 2, maximum fold 4} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
NucleosideDiphosphateKinase (@liver): stoichiometry UDP_c + ATP_c → UTP_c + ADP_c — Matches literature; Vf 2 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Matches literature; Haldane-derived Vr used 2 — Not directly comparable; Km {UDP_c 0.05, ATP_c 0.5, UTP_c 0.05, ADP_c 0.5} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Hexokinase (@liver): stoichiometry GLC_c + ATP_c → G6P_c + ADP_c + H_c — Not directly comparable (idled, Vf 0 -- the liver runs Glucokinase instead, below); declared Vr 0 — Not directly comparable; Km {GLC_c 0.05, ATP_c 0.5, G6P_c 0.05, ADP_c 0.5} — Insufficient context; inhibitors {G6P_c: Ki 0.05, Hill n 1.2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Glucokinase (@liver): stoichiometry GLC_c + ATP_c → G6P_c + ADP_c + H_c — Matches literature; Vf 0.12 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {GLC_c 10, ATP_c 0.5, G6P_c 0.05, ADP_c 0.5} — Matches literature (GLC_c Km; the other two are inert Michaelis-Menten leftovers unused by this irreversible reaction, kept for parity with the enzyme it replaces); configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PFK1 (@liver): stoichiometry F6P_c + ATP_c → F16BP_c + ADP_c + H_c — Matches literature; Vf 0.4 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {F6P_c 0.1, ATP_c 0.3} — Insufficient context; inhibitors {ATP_c: Ki 2, Hill n 2, H_c: Ki 0.0001, Hill n 2.5} — Insufficient context; activators {AMP_c: Ka 0.1, Hill n 2, maximum fold 10, F26BP_c: Ka 0.015, Hill n 2, maximum fold 4} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PyruvateKinase (@liver): stoichiometry PEP_c + ADP_c + H_c → PYR_c + ATP_c — Matches literature; Vf 1.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {PEP_c 0.08, ADP_c 0.15, H_c 0.0001} — Insufficient context; inhibitors {ATP_c: Ki 2, Hill n 2, GCG_b: Ki 12, Hill n 2} — Insufficient context; activators {F16BP_c: Ka 0.05, Hill n 2, maximum fold 2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
LactateTransport_c_to_b (@liver): stoichiometry LAC_c + H_c → LAC_b + H_b — Not directly comparable; Vf 1.4 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 2.5 — Insufficient context; Haldane-derived Vr used 0.56 — Not directly comparable; Km {LAC_c 1, LAC_b 1} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Cataplerosis (@liver): stoichiometry CIT_m → ∅ — Matches literature; Vf 0 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {CIT_m 0.5} — Insufficient context; configuration {reversible no, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
CitrateSynthase (@liver): stoichiometry AcCoA_m + OAA_m → CIT_m + CoA_m — Matches literature; Vf 24 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {AcCoA_m 0.01, OAA_m 0.005, CoA_m 0.05} — Insufficient context; inhibitors {CIT_m: Ki 5, Hill n 2, CIT_m: Ki 1, Hill n 2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PyruvateCarboxylase_GNG (@liver): stoichiometry PYR_m + CO2_m + ATP_m → OAA_m + ADP_m + Pi_m — Matches literature; Vf 0.186 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {PYR_m 0.08, CO2_m 0.02, ATP_m 0.08} — Insufficient context; inhibitors {INS_b: Ki 25, Hill n 2, CIT_m: Ki 3, Hill n 2} — Insufficient context; activators {GCG_b: Ka 30, Hill n 2, maximum fold 6, AcCoA_m: Ka 0.08, Hill n 1.8, maximum fold 2} — Insufficient context; configuration {reversible no, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
PEPCK_m (@liver): stoichiometry OAA_m + ATP_m → PEP_m + ADP_m + CO2_m — Matches literature; Vf 2 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {OAA_m 0.008, ATP_m 0.1} — Insufficient context; inhibitors {INS_b: Ki 10, Hill n 2} — Insufficient context; activators {GCG_b: Ka 30, Hill n 1.5, maximum fold 4} — Insufficient context; configuration {reversible no, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
PEP_Carrier (@liver): stoichiometry PEP_m → PEP_c — Matches literature; Vf 30 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 30 — Not directly comparable; Km {PEP_m 0.05, PEP_c 0.05} — Insufficient context; configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
FructoseBisphosphatase1 (@liver): stoichiometry F16BP_c + H2O_c → F6P_c + Pi_c — Matches literature; Vf 0.15 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {F16BP_c 0.02, H2O_c 1} — Insufficient context; inhibitors {F26BP_c: Ki 0.002, Hill n 2, AMP_c: Ki 0.05, Hill n 2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Glucose6Phosphatase (@liver): stoichiometry G6P_c + H2O_c → GLC_c + Pi_c — Matches literature; Vf 0.12 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {G6P_c 0.2, H2O_c 1} — Insufficient context; inhibitors {INS_b: Ki 100, Hill n 2} — Insufficient context; activators {GCG_b: Ka 30, Hill n 1.5, maximum fold 3} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
F26BP_Synthesis (@liver): stoichiometry F6P_c + ATP_c → F26BP_c + ADP_c — Matches literature; Vf 0.3 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {F6P_c 0.1, ATP_c 0.3} — Insufficient context; inhibitors {GCG_b: Ki 30, Hill n 2, F26BP_c: Ki 0.03, Hill n 2} — Insufficient context; activators {INS_b: Ka 100, Hill n 2, maximum fold 5} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
F26BP_Degradation (@liver): stoichiometry F26BP_c + H2O_c → F6P_c + Pi_c — Matches literature; Vf 0.6 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {F26BP_c 0.01, H2O_c 1} — Insufficient context; activators {GCG_b: Ka 30, Hill n 2, maximum fold 5} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GlycerolSupply: stoichiometry ∅ → GLYC_b — Not directly comparable; Vf 0.000191 — No reliable literature value found (calibrated numerically so resting blood glycerol settles near ~0.06 mM against GlycerolKinase's draw); declared Vr 0 — No reliable literature value found; inhibitors {GLYC_b: Ki 0.1, Hill n 2; INS_b: Ki 40, Hill n 2} — No reliable literature value found; activators {GCG_b: Ka 30, Hill n 2, maximum fold 3 — the same adipose lipolytic event FattyAcidSupply stands in for} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GlycerolKinase (@liver): stoichiometry GLYC_b + ATP_c → G3P_c + ADP_c — Matches literature; Vf 0.005 — Not directly comparable (a liver-cytosol-normalised rate; a naive blood/cytosol volume match against GlycerolSupply overshoots what the liver's pyruvate/citrate sinks can absorb at rest, so this is calibrated well under that naive value -- see the code comment); declared Vr 0 — Not directly comparable; Km {GLYC_b 0.1, ATP_c 0.1} — Insufficient context; configuration {reversible no, charge 0, home c, phosphate-proton tracking no} — Not directly comparable.
AlanineSupply: stoichiometry ∅ → ALA_b — Not directly comparable; Vf 0.00021 — No reliable literature value found (calibrated numerically so resting blood alanine settles near ~0.44 mM against AlanineTransaminase's draw); declared Vr 0 — No reliable literature value found; inhibitors {ALA_b: Ki 0.5, Hill n 2; INS_b: Ki 40, Hill n 2} — No reliable literature value found; activators {GCG_b: Ka 30, Hill n 2, maximum fold 3 — the glucose-alanine cycle's fasting/exercise mobilisation} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
AlanineTransaminase (@liver): stoichiometry ALA_b → PYR_c — Does not match literature (lumped; the real reaction is ALA + AKG ⇌ PYR + GLU, see the deliberate-departures note above); Vf 0.005 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {ALA_b 1} — Insufficient context; inhibitors {INS_b: Ki 40, Hill n 2} — Insufficient context; activators {GCG_b: Ka 30, Hill n 1.5, maximum fold 3} — Insufficient context; configuration {reversible no, charge 0, home c, phosphate-proton tracking no} — Not directly comparable.
FattyAcidSupply: stoichiometry ∅ → FA_b — Not directly comparable; Vf 0.0020187 — No reliable literature value found (calibrated so the net hormone multiplier at the resting poise reproduces the previous 0.0015 supply exactly); declared Vr 0 — No reliable literature value found; inhibitors {FA_b: Ki 0.4, Hill n 2; INS_b: Ki 40, Hill n 2 — insulin is the dominant antilipolytic signal} — No reliable literature value found; activators {GCG_b: Ka 30, Hill n 2, maximum fold 3 — glucagon/fasting lipolytic drive} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
BetaOxidation (@liver): stoichiometry FA_b + CoA_m + NAD_m + FAD_m + H2O_m → AcCoA_m + NADH_m + FADH2_m + H_m — Not directly comparable; Vf 0.2 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {FA_b 0.1, CoA_m 0.1, NAD_m 0.1, FAD_m 0.05} — Insufficient context; inhibitors {INS_b: Ki 40, Hill n 2} — Insufficient context; configuration {reversible no, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
Thiolase (@liver): stoichiometry 2 AcCoA_m → AcAcCoA_m + CoA_m — Not directly comparable; Vf 10 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 0.02 — Does not match literature (first-pass; the measured synthesis equilibrium is ~1e-5, see deliberate departures above); Haldane-derived Vr used 5.55556 — Not directly comparable; Km {AcCoA_m 0.3, AcAcCoA_m 0.02, CoA_m 0.05} — Insufficient context; configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
HMGCoASynthase (@liver): stoichiometry AcAcCoA_m + AcCoA_m + H2O_m → HMGCoA_m + CoA_m — Not directly comparable; Vf 6 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {AcAcCoA_m 0.02, AcCoA_m 0.3, H2O_m 1} — Insufficient context; inhibitors {INS_b: Ki 35, Hill n 2} — Insufficient context; configuration {reversible no, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
HMGCoALyase (@liver): stoichiometry HMGCoA_m → AcAc_m + AcCoA_m — Not directly comparable; Vf 3 — Not directly comparable (retuned 10x slower than an initial 30, a numerical-conditioning fix, not a biological one: HMG-CoA's own quasi-steady-state relative to this Km was thousands of times faster than the live simulation path's ~0.1 s reporting frame, so the chunked solver could overshoot it below zero on every restart; the net ketogenesis flux, which this pass-through step does not control, is unaffected); declared Vr 0 — Not directly comparable; Km {HMGCoA_m 0.02} — Insufficient context; configuration {reversible no, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
BDH (@liver): stoichiometry AcAc_m + NADH_m + H_m → BHB_m + NAD_m — Matches literature; Vf 20 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 20.3 — Insufficient context; Haldane-derived Vr used 9.8522167 — Not directly comparable; Km {AcAc_m 0.1, NADH_m 0.05, BHB_m 0.1, NAD_m 0.5} — Insufficient context; configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
AcetoacetateExport (@liver): stoichiometry AcAc_m → AcAc_b — Matches literature; Vf 15 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 15 — Not directly comparable; Km {AcAc_m 0.2, AcAc_b 0.2} — Insufficient context; configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
BHBExport (@liver): stoichiometry BHB_m → BHB_b — Matches literature; Vf 15 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 15 — Not directly comparable; Km {BHB_m 0.2, BHB_b 0.2} — Insufficient context; configuration {reversible yes, charge 0, home m, phosphate-proton tracking no} — Not directly comparable.
AcetoacetateDisposal: stoichiometry AcAc_b → ∅ — Matches literature; Vf 0.0005 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {AcAc_b 0.2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
BHBDisposal: stoichiometry BHB_b → ∅ — Matches literature; Vf 0.0005 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {BHB_b 0.2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GlucoseTransport_c_to_b (@liver): stoichiometry GLC_c → GLC_b — Matches literature; Vf 0.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 0.5 — Not directly comparable; Km {GLC_c 17, GLC_b 17} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
Hexokinase (@rbc): stoichiometry GLC_c + ATP_c → G6P_c + ADP_c + H_c — Matches literature; Vf 0.01 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {GLC_c 0.05, ATP_c 0.5, G6P_c 0.05, ADP_c 0.5} — Insufficient context; inhibitors {G6P_c: Ki 0.05, Hill n 1.2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PFK1 (@rbc): stoichiometry F6P_c + ATP_c → F16BP_c + ADP_c + H_c — Matches literature; Vf 0.04 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {F6P_c 0.1, ATP_c 0.3} — Insufficient context; inhibitors {ATP_c: Ki 2, Hill n 2, H_c: Ki 0.0001, Hill n 2.5} — Insufficient context; activators {AMP_c: Ka 0.1, Hill n 2, maximum fold 10, F26BP_c: Ka 0.015, Hill n 2, maximum fold 4} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
GlucoseTransport_c_to_b (@rbc): stoichiometry GLC_c → GLC_b — Matches literature; Vf 0.5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 1 — Insufficient context; Haldane-derived Vr used 0.5 — Not directly comparable; Km {GLC_c 1.5, GLC_b 1.5} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
ATPConsumption (@rbc): stoichiometry ATP_c + H2O_c → ADP_c + Pi_c + H_c — Not directly comparable; Vf 0.0006 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {ATP_c 0.2, H2O_c 1, ADP_c 0.2, Pi_c 0.2, H_c 0.0001} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
PhosphateSupply (@rbc): stoichiometry ∅ → Pi_c — Not directly comparable; Vf 0.1 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Keq 1 — No reliable literature value found; Haldane-derived Vr used 0.01 — Not directly comparable; Km {Pi_c 0.1} — No reliable literature value found; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
AdenylateKinase_c (@rbc): stoichiometry ATP_c + AMP_c → 2 ADP_c — Matches literature; Vf 5 — Not directly comparable; declared Vr 0 — Not directly comparable; Keq 2.2727273 — Matches literature; Haldane-derived Vr used 11 — Not directly comparable; Km {ATP_c 0.5, AMP_c 0.1, ADP_c 0.5} — Insufficient context; configuration {reversible yes, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
NADPHConsumption (@rbc): stoichiometry NADPH_c → NADP_c — Not directly comparable; Vf 0.0001 — No reliable literature value found; declared Vr 0 — No reliable literature value found; Km {NADPH_c 0.05} — No reliable literature value found; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
BisphosphoglycerateMutase (@rbc): stoichiometry BPG13_c → BPG23_c — Matches literature; Vf 0.02 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {BPG13_c 0.05} — Insufficient context; inhibitors {BPG23_c: Ki 4.5, Hill n 2} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
BisphosphoglyceratePhosphatase (@rbc): stoichiometry BPG23_c + H2O_c → PG3_c + Pi_c — Matches literature; Vf 0.0006 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {BPG23_c 5, H2O_c 1} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
G6PDehydrogenase (@rbc): stoichiometry G6P_c + NADP_c → P6GL_c + NADPH_c + H_c — Matches literature; Vf 0.05 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {G6P_c 0.067, NADP_c 0.0037} — Matches literature; inhibitors {NADPH_c: Ki 0.0031, Hill n 2} — Matches literature; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
BasalROSProduction (@rbc): stoichiometry ∅ → H2O2_c — Matches literature; Vf 5e-05 — Not directly comparable; declared Vr 0 — Not directly comparable; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.
HemoglobinOxidation (@rbc): stoichiometry Hb_c + H2O2_c → HbOx_c + H2O_c — Matches literature; Vf 0.1 — Not directly comparable; declared Vr 0 — Not directly comparable; Km {Hb_c 5, H2O2_c 0.02} — Insufficient context; configuration {reversible no, charge 0, home inferred, phosphate-proton tracking no} — Not directly comparable.

Initial-condition register

Every assembled starting-state value follows. Labels describe evidential comparability of the numerical start state, not whether the metabolite itself is physiological.

Shared/blood

LAC_b = 0 mM — Insufficient context.
GLC_b = 5 mM — Insufficient context.
INS_b = 40 mM — Insufficient context.
GCG_b = 17 mM — Insufficient context.
O2_b = 0.1 mM — Insufficient context.
CO2_b = 1 mM — Insufficient context.
H_b = 3.98e-05 mM — Matches literature.
Buffer_b = 16 mM — Insufficient context.
BufferH_b = 8 mM — Insufficient context.
FA_b = 0.4 mM — Insufficient context.
AcAc_b = 0.05 mM — Insufficient context.
BHB_b = 0.1 mM — Insufficient context.
GLYC_b = 0.05 mM — Matches literature (fasting-human arterial glycerol, ~0.03-0.1 mM).
ALA_b = 0.4 mM — Matches literature (fasting-human plasma alanine, ~0.3-0.45 mM).

Muscle

GLY_muscle_c = 80 mM — Insufficient context.
G1P_muscle_c = 0 mM — Insufficient context.
UTP_muscle_c = 0.2 mM — Insufficient context.
UDP_muscle_c = 0.01 mM — Insufficient context.
UDPGlc_muscle_c = 0.3 mM — Insufficient context.
GLC_muscle_c = 0.1 mM — Insufficient context.
G6P_muscle_c = 0 mM — Insufficient context.
F6P_muscle_c = 0 mM — Insufficient context.
F16BP_muscle_c = 0 mM — Insufficient context.
DHAP_muscle_c = 0 mM — Insufficient context.
GAP_muscle_c = 0 mM — Insufficient context.
G3P_muscle_c = 0.08 mM — Insufficient context.
BPG13_muscle_c = 0 mM — Insufficient context.
PG3_muscle_c = 0 mM — Insufficient context.
PG2_muscle_c = 0 mM — Insufficient context.
PEP_muscle_c = 0 mM — Insufficient context.
PYR_muscle_c = 0 mM — Insufficient context.
ATP_muscle_c = 8 mM — Matches literature.
ADP_muscle_c = 0.015 mM — Insufficient context.
AMP_muscle_c = 0.002 mM — Insufficient context.
PCr_muscle_c = 30 mM — Matches literature.
Cr_muscle_c = 10 mM — Insufficient context.
NAD_muscle_c = 0.7 mM — Insufficient context.
NADH_muscle_c = 0.001 mM — Insufficient context.
LAC_muscle_c = 0 mM — Insufficient context.
MAL_muscle_c = 0.5 mM — Insufficient context.
OAA_muscle_c = 0.005 mM — Insufficient context.
ASP_muscle_c = 1.5 mM — Insufficient context.
GLU_muscle_c = 6 mM — Insufficient context.
AKG_muscle_c = 0.1 mM — Insufficient context.
Pi_muscle_c = 3 mM — Matches literature.
H2O_muscle_c = 55500 mM — Insufficient context.
H_muscle_c = 69.691435 mM — Insufficient context.
Ca_muscle_c = 0.0001 mM — Matches literature.
PYR_muscle_i = 0 mM — Insufficient context.
ATP_muscle_i = 7.8 mM — Insufficient context.
ADP_muscle_i = 0.02 mM — Insufficient context.
Pi_muscle_i = 0.5 mM — Insufficient context.
H_muscle_i = 68.626027 mM — Insufficient context.
CytC_ox_muscle_i = 0.187 mM — Insufficient context.
CytC_red_muscle_i = 0.013 mM — Insufficient context.
PYR_muscle_m = 0.05 mM — Insufficient context.
CoA_muscle_m = 0.6 mM — Insufficient context.
AcCoA_muscle_m = 0.05 mM — Insufficient context.
OAA_muscle_m = 0.005 mM — Insufficient context.
CIT_muscle_m = 0.35 mM — Insufficient context.
ICIT_muscle_m = 0.02 mM — Insufficient context.
AKG_muscle_m = 0.1 mM — Insufficient context.
SucCoA_muscle_m = 0.02 mM — Insufficient context.
SUC_muscle_m = 0.3 mM — Insufficient context.
FUM_muscle_m = 0.05 mM — Insufficient context.
MAL_muscle_m = 0.5 mM — Insufficient context.
ASP_muscle_m = 1 mM — Insufficient context.
GLU_muscle_m = 5 mM — Insufficient context.
ATP_muscle_m = 5.8 mM — Insufficient context.
ADP_muscle_m = 0.2 mM — Insufficient context.
AMP_muscle_m = 0 mM — Insufficient context.
NAD_muscle_m = 0.42 mM — Insufficient context.
NADH_muscle_m = 0.08 mM — Insufficient context.
FAD_muscle_m = 0.198 mM — Insufficient context.
FADH2_muscle_m = 0.002 mM — Insufficient context.
CoQ_muscle_m = 1.967 mM — Insufficient context.
CoQH2_muscle_m = 0.033 mM — Insufficient context.
Pi_muscle_m = 5 mM — Insufficient context.
H2O_muscle_m = 55500 mM — Insufficient context.
H_muscle_m = 45.950042 mM — Insufficient context.
CO2_muscle_m = 0.05 mM — Insufficient context.
O2_muscle_m = 0.03 mM — Insufficient context.
Ca_muscle_m = 0.0002 mM — Matches literature.
Dpsi_muscle_m = 160 mV — Insufficient context.
O2super_muscle_m = 0 mM — Insufficient context.
H2O2_muscle_m = 0 mM — Insufficient context.
NADP_muscle_c = 0.166 mM — Insufficient context.
NADPH_muscle_c = 0.164 mM — Insufficient context.
GSH_muscle_c = 1 mM — Insufficient context.
GSSG_muscle_c = 0.005 mM — Insufficient context.
P6GL_muscle_c = 0.001 mM — Insufficient context.
P6G_muscle_c = 0.025 mM — Insufficient context.
Ru5P_muscle_c = 0.008 mM — Insufficient context.
H2O2_muscle_c = 1e-07 mM — Insufficient context.
CIT_muscle_c = 0.35 mM — Insufficient context.
ICIT_muscle_c = 0.033 mM — Insufficient context.

Liver

GLY_liver_c = 200 mM — Insufficient context.
G1P_liver_c = 0 mM — Insufficient context.
UTP_liver_c = 0.2 mM — Insufficient context.
UDP_liver_c = 0.01 mM — Insufficient context.
UDPGlc_liver_c = 0.3 mM — Insufficient context.
GLC_liver_c = 5 mM — Insufficient context.
G6P_liver_c = 0.12 mM — Insufficient context.
F6P_liver_c = 0.055 mM — Insufficient context.
F16BP_liver_c = 0.01 mM — Insufficient context.
DHAP_liver_c = 0 mM — Insufficient context.
GAP_liver_c = 0 mM — Insufficient context.
G3P_liver_c = 0.08 mM — Insufficient context.
BPG13_liver_c = 0 mM — Insufficient context.
PG3_liver_c = 0 mM — Insufficient context.
PG2_liver_c = 0 mM — Insufficient context.
PEP_liver_c = 0.01 mM — Insufficient context.
PYR_liver_c = 0.04 mM — Insufficient context.
ATP_liver_c = 4.8 mM — Matches literature.
ADP_liver_c = 0.015 mM — Insufficient context.
AMP_liver_c = 0.003 mM — Insufficient context.
NAD_liver_c = 0.7 mM — Insufficient context.
NADH_liver_c = 0.001 mM — Insufficient context.
LAC_liver_c = 0.7 mM — Insufficient context.
MAL_liver_c = 0.5 mM — Insufficient context.
OAA_liver_c = 0.005 mM — Insufficient context.
ASP_liver_c = 1.5 mM — Insufficient context.
GLU_liver_c = 6 mM — Insufficient context.
AKG_liver_c = 0.1 mM — Insufficient context.
Pi_liver_c = 3 mM — Matches literature.
H2O_liver_c = 55500 mM — Insufficient context.
H_liver_c = 68.978518 mM — Insufficient context.
Ca_liver_c = 0.0001 mM — Matches literature.
PYR_liver_i = 0 mM — Insufficient context.
ATP_liver_i = 7.8 mM — Insufficient context.
ADP_liver_i = 0.02 mM — Insufficient context.
Pi_liver_i = 0.5 mM — Insufficient context.
H_liver_i = 68.626027 mM — Insufficient context.
CytC_ox_liver_i = 0.187 mM — Insufficient context.
CytC_red_liver_i = 0.013 mM — Insufficient context.
PYR_liver_m = 0.05 mM — Insufficient context.
CoA_liver_m = 0.6 mM — Insufficient context.
AcCoA_liver_m = 0.05 mM — Insufficient context.
OAA_liver_m = 0.005 mM — Insufficient context.
CIT_liver_m = 0.35 mM — Insufficient context.
ICIT_liver_m = 0.02 mM — Insufficient context.
AKG_liver_m = 0.1 mM — Insufficient context.
SucCoA_liver_m = 0.02 mM — Insufficient context.
SUC_liver_m = 0.3 mM — Insufficient context.
FUM_liver_m = 0.05 mM — Insufficient context.
MAL_liver_m = 0.5 mM — Insufficient context.
ASP_liver_m = 1 mM — Insufficient context.
GLU_liver_m = 5 mM — Insufficient context.
ATP_liver_m = 5.8 mM — Insufficient context.
ADP_liver_m = 0.2 mM — Insufficient context.
AMP_liver_m = 0 mM — Insufficient context.
NAD_liver_m = 0.42 mM — Insufficient context.
NADH_liver_m = 0.08 mM — Insufficient context.
FAD_liver_m = 0.198 mM — Insufficient context.
FADH2_liver_m = 0.002 mM — Insufficient context.
CoQ_liver_m = 1.967 mM — Insufficient context.
CoQH2_liver_m = 0.033 mM — Insufficient context.
Pi_liver_m = 5 mM — Insufficient context.
H2O_liver_m = 55500 mM — Insufficient context.
H_liver_m = 45.951679 mM — Insufficient context.
CO2_liver_m = 0.05 mM — Insufficient context.
O2_liver_m = 0.03 mM — Insufficient context.
Ca_liver_m = 0.0002 mM — Matches literature.
Dpsi_liver_m = 160 mV — Insufficient context.
O2super_liver_m = 0 mM — Insufficient context.
H2O2_liver_m = 0 mM — Insufficient context.
F26BP_liver_c = 0.008 mM — Insufficient context.
PEP_liver_m = 0.02 mM — Insufficient context.
AcAcCoA_liver_m = 0.001 mM — Insufficient context (trace ketogenesis intermediate; seed only, settles ~5e-4 mM).
HMGCoA_liver_m = 0.001 mM — Insufficient context (trace ketogenesis intermediate; seed only, settles ~2e-5 mM).
AcAc_liver_m = 0.02 mM — Insufficient context.
BHB_liver_m = 0.05 mM — Insufficient context.
NADP_liver_c = 0.166 mM — Insufficient context.
NADPH_liver_c = 0.164 mM — Insufficient context.
P6GL_liver_c = 0.001 mM — Insufficient context.
P6G_liver_c = 0.025 mM — Insufficient context.
Ru5P_liver_c = 0.008 mM — Insufficient context.
R5P_liver_c = 0.01 mM — Insufficient context.
X5P_liver_c = 0.01 mM — Insufficient context.
S7P_liver_c = 0.008 mM — Insufficient context.
E4P_liver_c = 0.005 mM — Insufficient context.

Rbc

GLC_rbc_c = 5 mM — Insufficient context.
G6P_rbc_c = 0.06 mM — Insufficient context.
F6P_rbc_c = 0.015 mM — Insufficient context.
F16BP_rbc_c = 0.01 mM — Insufficient context.
DHAP_rbc_c = 0.02 mM — Insufficient context.
GAP_rbc_c = 0.01 mM — Insufficient context.
BPG13_rbc_c = 0.002 mM — Insufficient context.
PG3_rbc_c = 0.05 mM — Insufficient context.
PG2_rbc_c = 0.01 mM — Insufficient context.
PEP_rbc_c = 0.02 mM — Insufficient context.
PYR_rbc_c = 0.06 mM — Insufficient context.
BPG23_rbc_c = 4.5 mM — Insufficient context.
ATP_rbc_c = 1.5 mM — Matches literature.
ADP_rbc_c = 0.3 mM — Insufficient context.
AMP_rbc_c = 0.015 mM — Insufficient context.
NAD_rbc_c = 0.12 mM — Insufficient context.
NADH_rbc_c = 0.002 mM — Insufficient context.
LAC_rbc_c = 1.5 mM — Insufficient context.
Pi_rbc_c = 1 mM — Matches literature.
H2O_rbc_c = 55500 mM — Insufficient context.
H_rbc_c = 67.45544 mM — Insufficient context.
NADP_rbc_c = 0.166 mM — Insufficient context.
NADPH_rbc_c = 0.164 mM — Insufficient context.
GSH_rbc_c = 3.2 mM — Insufficient context.
GSSG_rbc_c = 0.016 mM — Insufficient context.
P6GL_rbc_c = 0.001 mM — Insufficient context.
P6G_rbc_c = 0.025 mM — Insufficient context.
Ru5P_rbc_c = 0.008 mM — Insufficient context.
H2O2_rbc_c = 1e-07 mM — Insufficient context.
Hb_rbc_c = 5 mM — Insufficient context.
HbOx_rbc_c = 0 mM — Insufficient context.

Global constants, compartments, and proton bookkeeping

Compartment-volume fractions: c 0.7, i 0.02, m 0.07, b 1; matrix capacity scale 10 — Not directly comparable (the fractions are modelling geometry; the scale is derived).
Thermal voltage 26.71 mV — Matches literature at the model temperature; inner-membrane capacitance 0.00675 mM charge mV⁻¹ — Insufficient context; proton reference 0.0001 mM — Not directly comparable.
Generic intracellular buffer total 100 mM and pKa 7.3 — Matches literature at the stated reduced-model buffer-capacity level; pH inversion bounds 2–12 and tolerance 1e-13 — Not directly comparable.
Phosphate-group pKa values: Pi 6.82, ATP 6.48, ADP 6.38, AMP 6.22, G1P 6.11, G6P 6.11, F6P 6.11, F16BP 6.05/6.65, F26BP 6.05/6.65, GAP 6.45, DHAP 6.45, G3P 6.66, BPG13 6.6, PG3 6.21, PG2 7, PEP 6.35 — Matches literature for the stated physiological-ionic-strength convention.
Numerical guards: positivity smoothing 1e-09, logarithm floor 1e-30, maximum electrical exponent 200, mechanistic-argument clamp 30 — Not directly comparable.

Register interpretation

The register is deliberately conservative. “Matches literature” means the value or relation is supportable within the explicit convention shown; it does not imply that a reduced rate law reproduces a full enzyme mechanism. “Insufficient context” means the literature contains potentially comparable numbers but Fluxion lacks one or more required qualifiers. “No reliable literature value found” is reserved mainly for artificial boundary/control capacities. “Not directly comparable” covers fitted capacities, Haldane consequences, numerical settings, and lumped reactions whose model variable is not a single measurable biochemical constant.

Source bibliography

[1] eQuilibrator — biochemical equilibrium constants (Flamholz, A., Noor, E., Bar-Even, A. & Milo, R., 2012, Nucleic Acids Research 40, D770–D775).
[2] BRENDA — the comprehensive enzyme database; Michaelis constants (Schomburg, I. et al., Nucleic Acids Research).
[3] Nelson, D.L. & Cox, M.M. Lehninger Principles of Biochemistry — pathway free energies, enzyme regulation, and standard resting concentrations.
[4] Berg, J.M., Tymoczko, J.L. & Stryer, L. Biochemistry — allosteric regulation of glycolysis and glycogen metabolism.
[5] Nicholls, D.G. & Ferguson, S.J. Bioenergetics — midpoint potentials, proton and charge stoichiometry, the electrogenic carriers, and the membrane potential.
[6] McCormack, J.G., Halestrap, A.P. & Denton, R.M. (1990). Role of calcium ions in the regulation of mammalian intramitochondrial metabolism. Physiological Reviews 70, 391–425.
[7] Lawson, J.W.R. & Veech, R.L. (1979). Effects of pH and free Mg²⁺ on the Keq of the creatine kinase reaction and other phosphate hydrolyses and transfers. Journal of Biological Chemistry 254, 6528–6537.
[8] Williamson, D.H., Lund, P. & Krebs, H.A. (1967). The redox state of free nicotinamide-adenine dinucleotide in the cytoplasm and mitochondria of rat liver. Biochemical Journal 103, 514–527.
[9] Halestrap, A.P. & Price, N.T. (1999). The proton-linked monocarboxylate transporter (MCT) family. Biochemical Journal 343, 281–299. (Mitochondrial pyruvate carrier: Halestrap, A.P., 1975; molecular identity, Bricker, D.K. et al., 2012, Science 337, 96–100.)
[10] Garlid, K.D. & Paucek, P. (2003). Mitochondrial potassium transport: the K⁺ cycle. Biochimica et Biophysica Acta 1606, 23–41.
[11] Kushmerick, M.J., Moerland, T.S. & Wiseman, R.W. (1992). Mammalian skeletal muscle fibers distinguished by contents of phosphocreatine, ATP, and Pi. Proceedings of the National Academy of Sciences 89, 7521–7525.
[12] Hinkle, P.C. (2005). P/O ratios of mitochondrial oxidative phosphorylation. Biochimica et Biophysica Acta 1706, 1–11.
[13] Rolfe, D.F.S. & Brand, M.D. (1996). Contribution of mitochondrial proton leak to skeletal-muscle respiration. American Journal of Physiology 271, C1380–C1389.
[14] West, J.B. Respiratory Physiology: The Essentials — arterial pCO₂ ~40 mmHg and the CO₂ solubility coefficient (0.03 mmol·L⁻¹·mmHg⁻¹) giving dissolved arterial CO₂ ~1.2 mM.
[15] Flamholz, A., Noor, E., Bar-Even, A. & Milo, R. (2012). eQuilibrator—the biochemical thermodynamics calculator. Nucleic Acids Research 40, D770–D775. Calculations require an explicit pH, ionic strength, temperature, Mg²⁺ convention, and reaction proton convention.
[16] Noor, E. et al. (2012). An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. Bioinformatics 28, 2037–2044.
[17] Schomburg, I. et al. (2013). BRENDA in 2013: integrated reactions, kinetic data, enzyme function data. Nucleic Acids Research 41, D764–D772. Database: BRENDA.
[18] Wittig, U. et al. (2018). SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. Nucleic Acids Research 46, D656–D660. Database: SABIO-RK.
[19] Lombardot, T. et al. (2022). Rhea, the reaction knowledgebase in 2022. Nucleic Acids Research 50, D693–D700. Database: Rhea.
[20] Watt, I.N., Montgomery, M.G., Runswick, M.J., Leslie, A.G.W. & Walker, J.E. (2010). Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria. PNAS 107, 16823–16827. Bovine mitochondrial ATP synthase has a c8 ring and therefore requires 8/3 translocated protons per ATP at the synthase itself.
[21] Glancy, B., Willis, W.T., Chess, D.J. & Balaban, R.S. (2013). Effect of calcium on the oxidative phosphorylation cascade in skeletal muscle mitochondria. Biochemistry 52, 2793–2809. At 37 °C, 840 nM Ca²⁺ produced about a two-fold increase in maximal oxidative-phosphorylation velocity, with ADP affinity near 43 µM.
[22] Lark, D.S. et al. (2016). Direct real-time quantification of mitochondrial oxidative phosphorylation efficiency in permeabilized skeletal muscle myofibers. American Journal of Physiology—Cell Physiology 311, C239–C245. ATP/O was 2.09 ± 0.251 in permeabilized fibres and 2.44 ± 0.124 in isolated mitochondria under the reported conditions.
[23] Kemp, G.J., Meyerspeer, M. & Moser, E. (2007). Absolute quantification of phosphorus metabolite concentrations in human muscle in vivo by 31P MRS. NMR in Biomedicine 20, 555–565. Reported values were PCr 33 ± 2 mM, Pi 4.5 ± 0.2 mM, and ATP 8.2 ± 0.4 mM.
[24] Yachie-Kinoshita, A. et al. (2010). A metabolic model of human erythrocytes: practical application of the E-Cell simulation environment. Journal of Biomedicine and Biotechnology 2010, 642420. The model compiles glycolytic, PPP, nucleotide, glutathione, membrane-transport, pH, Mg²⁺, and haemoglobin-binding kinetics from experimental literature.
[25] Mulquiney, P.J. & Kuchel, P.W. (1999). Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte: computer simulation and metabolic control analysis. Biochemical Journal 342, 597–604; PMID 10477270. The companion 13C/31P-NMR study estimated about 19% of normal glycolytic carbon flux through the 2,3-BPG shunt and showed that in-vivo and in-vitro BPG mutase/phosphatase constants differ materially.
[26] Raftos, J.E., Whillier, S. & Kuchel, P.W. (2010). Glutathione synthesis and turnover in the human erythrocyte. Journal of Biological Chemistry 285, 23557–23567. The authors explicitly distinguish isolated-enzyme constants from parameters refined against intact-cell behaviour.
[27] Casazza, J.P. & Veech, R.L. (1986). The interdependence of glycolytic and pentose cycle intermediates in ad libitum fed rats. Journal of Biological Chemistry 261, 690–698; PMID 3079759. Measured equilibrium constants of the pentose-phosphate interconversions at 38 °C, pH 7.0, 1 mM free Mg²⁺ and ionic strength 0.25 M, including ribose-5-phosphate isomerase (R5P/Ru5P 1.20 ± 0.02) and ribulose-5-phosphate 3-epimerase (X5P/Ru5P 1.82 ± 0.02). Values were read from the BioNumbers compilation of equilibrium constants; the original paper's full text was not directly readable.