Crate rasayan 

Rasayan — Biochemistry Engine

Rasayan (Sanskrit: रसायन — alchemy, chemistry of life) provides computational models of biochemistry for the AGNOS ecosystem. Enzyme kinetics, metabolic pathways, signal transduction, protein structure, membrane transport, and bioenergetics.

Architecture

Twenty-five core modules (plus optional logging, mcp, ai):

• enzyme — Michaelis-Menten kinetics, competitive/uncompetitive/mixed inhibition, substrate inhibition, allosteric regulation (Hill equation), reversible reactions (Haldane), multi-substrate kinetics (ping-pong, sequential), temperature dependence (Arrhenius, Q10), linearization transforms (Lineweaver-Burk, Eadie-Hofstee), enzyme database.
• metabolism — Metabolic state: ATP/ADP balance, energy charge, aerobic/anaerobic yield, oxygen-dependent ATP regeneration, metabolic rate.
• signal — Signal transduction: ligand-receptor binding, dose-response (Hill function), second messengers (cAMP, Ca2+, IP3), Gs/Gq/Gi pathway activation, messenger decay.
• protein — Protein analysis: 20 amino acid properties (molecular weight, hydrophobicity, pKa), sequence molecular weight, composition, isoelectric point (pI), extinction coefficient (280nm), Chou-Fasman secondary structure prediction.
• alignment — Sequence alignment scoring: BLOSUM62/PAM250 substitution matrices, pairwise alignment scoring, Needleman-Wunsch global alignment.
• ptm — Post-translational modification site prediction: N-glycosylation, phosphorylation (Ser/Thr/Tyr), PKA/CK2 sites, disulfide bonds, myristoylation.
• domain — Protein domain classification: zinc finger (C2H2), leucine zipper, EF-hand, Walker A/P-loop, RGD, DEAD-box, NLS, KDEL motifs.
• neurotransmitter — Neurotransmitter synthesis: serotonin (TPH), dopamine (TH), norepinephrine (DBH), GABA (GAD), glutamate, ACh (ChAT), endorphins (POMC). Bridge functions for mastishk/bhava.
• hormonal — Hormonal pathways: HPA axis cortisol (CRH→ACTH→cortisol, negative feedback), melatonin (serotonin→melatonin, light suppression), oxytocin, BDNF. Bridge functions for bhava.
• pathway — Metabolic network: unified simulation connecting all pathways with shared cofactor pools, steady-state flux analysis, respiratory quotient.
• membrane — Membrane transport: Nernst potential, Goldman-Hodgkin-Katz equation, Fick’s first law diffusion, ionic state.
• glycolysis — 10-step glycolytic pathway with individual enzyme kinetics, regulatory checkpoints (hexokinase, PFK, pyruvate kinase), configurable parameters, and per-tick ATP/NADH flux accounting.
• tca — TCA (Krebs) cycle: pyruvate dehydrogenase + 8 cycle steps, regulatory checkpoints (citrate synthase, isocitrate DH, α-KG DH), NADH/FADH2/GTP/CO2 flux output.
• etc — Electron transport chain: complexes I-IV, ATP synthase, proton motive force, respiratory control, ubiquinone and cytochrome c carrier pools.
• amino_catabolism — Amino acid catabolism: transamination, oxidative deamination (GDH), carbon skeleton routing to TCA entry points, NH4+ clearance.
• beta_oxidation — Fatty acid beta-oxidation: acyl-CoA activation, CPT-I malonyl-CoA regulation, spiral producing acetyl-CoA/NADH/FADH2.
• energy — Bioenergetics: ATP hydrolysis, phosphocreatine system, anaerobic/aerobic thresholds, metabolic equivalent (MET).
• constants — Shared physical constants (gas constant, Faraday constant).
• [mcp] — MCP tool definitions via bote (feature-gated: mcp): 8 tools for enzyme kinetics, metabolism, signaling, protein, membrane, alignment, PTM, and domain analysis.
• [ai] — Hoosh client for LLM-powered biochemistry queries (feature-gated: ai): BiochemClient with enzyme, pathway, and protein query helpers.

Relationship to Other Crates

rasayan (this) — enzyme kinetics, metabolism, signal transduction
  | metabolic state feeds into
mastishk — neuroscience (neurotransmitter synthesis depends on precursors)
  | neurotransmitter levels feed into
bhava — emotion/personality
  also:
kimiya — general chemistry (rasayan uses reaction kinetics from kimiya)
jivanu — microbiology (microbial metabolism, pharmacokinetics)
sharira — physiology (muscle bioenergetics, fatigue)

Re-exports

pub use error::RasayanError;

Modules

alignment

Sequence alignment scoring — substitution matrices and pairwise scoring.

amino_catabolism

Amino acid catabolism — transamination, deamination, and carbon skeleton routing.

beta_oxidation

Beta-oxidation of fatty acids — breakdown of acyl-CoA to acetyl-CoA.

calcium

Calcium oscillation dynamics — IP3R-mediated Ca2+ signaling.

constants

Physical constants used across rasayan modules.

domain

Protein domain classification — motif-based domain detection.

energy

Bioenergetics — ATP hydrolysis, phosphocreatine, anaerobic/aerobic thresholds.

enzyme

Enzyme kinetics — Michaelis-Menten, inhibition, allosteric regulation, multi-substrate kinetics, linearization transforms, and enzyme database.

error

Error types for rasayan.

etc

Electron transport chain (ETC) — oxidative phosphorylation model.

glycolysis

Glycolysis pathway — 10-step enzymatic conversion of glucose to pyruvate.

hormonal

Hormonal pathway models — HPA axis, melatonin, oxytocin, BDNF.

jak_stat

JAK-STAT pathway — cytokine receptor signaling.

mapk

MAPK cascade — Ras/Raf/MEK/ERK signaling pathway.

membrane

Membrane transport — diffusion, Nernst potential, Goldman equation.

metabolism

Metabolic pathways — glycolysis, TCA, oxidative phosphorylation, ATP balance.

neurotransmitter

Neurotransmitter synthesis and degradation pathways.

nuclear_receptor

Nuclear receptor signaling — ligand-activated transcription factors.

pathway

Metabolic pathway network — unified simulation and flux analysis.

pi3k

PI3K/Akt/mTOR pathway — growth, survival, and metabolism signaling.

protein

Protein structure primitives — amino acid properties, molecular weight, pI.

ptm

Post-translational modification (PTM) site prediction.

receptor

Receptor desensitization and internalization.

signal

Signal transduction — receptor binding, second messengers, dose-response.

signaling

Signaling network — unified intracellular signaling with crosstalk.

tca

TCA (Krebs) cycle — 8-step oxidation of acetyl-CoA with regulatory checkpoints.