MODEL PROTEIN FOLDING · INDEX · under KEEPER ERIS

Protein Folding · Index

Dave asked for protein folding: the math and the difficulty, as edutainment, on his I-13 WASM engine. 12 pages from Levinthal’s count to AlphaFold, each one booting the engine, checking its SHA-256 and running real folding math on the VM.

Dave (t249u): "can you build some pages on protein folding, the math and the difficulty, edutaiton please, use this wasm engine"

MODEL Filter:

Levinthal’s Paradox · 3²⁰⁰ vs a Millisecond
MODEL MATH · THE COUNT
Anfinsen’s Dogma · The Sequence Knows
MODEL BIOLOGY · THERMODYNAMIC HYPOTHESIS
Energy Landscapes & Folding Funnels
MODEL PHYSICS · LANDSCAPE
The HP Lattice · Fold It Yourself
MODEL COMPUTING · INTERACTIVE FOLDER
Why Folding Is NP-Hard
MODEL MATH · COMPLEXITY
Ramachandran Plot · φ and ψ
MODEL BIOLOGY · BACKBONE ANGLES
α-Helix & β-Sheet · 3.6 per Turn
MODEL BIOLOGY · SECONDARY STRUCTURE
ΔG = ΔH − TΔS · Two-State Folding
MODEL PHYSICS · THERMODYNAMICS & KINETICS
Metropolis & Simulated Annealing
MODEL COMPUTING · MONTE CARLO
Femtoseconds vs Milliseconds · MD & Anton
MODEL PHYSICS · MOLECULAR DYNAMICS
AlphaFold2 & CASP14 · Solved and Unsolved
MODEL AI · STRUCTURE PREDICTION
Misfolding · Prions & Amyloid
MODEL BIOLOGY · WHEN IT GOES WRONG

Engine folder LIT verbatim copies of Dave’s files

Cooperative board MODEL shared across all protein-folding pages

localStorage key mayhem-protein-folding-board: each page’s CRITIC writes its best score.

    Dave’s I-13 engine on this page

    booting I-13 v0.3…

    LIT What the VM computes here: This index boots the engine like every page, then recounts the S1 optimum and checks the shared I-13 library (exp, √, ln).

    Sources (browsed Oct 2026)

    1. Protein folding (overview)

    MODEL Two agents, as Dave set for every world. The ARTIST folds the 20-residue HP chain S1 HPHPPHHPHPPHPHHPPHPH on the square (2D) lattice with pivot, corner and kink moves. The CRITIC judges each move (Metropolis at temperature T) and scores the best fold as −E/9 (E_ref = -9, proved optimal by exhaustive search here). It also has Dave’s I-13 VM recount every kept fold from raw coordinates. Rendered with Three.js r160 from a pinned CDN, devicePixelRatio capped at 2. Drag to orbit, scroll to zoom.

    LIT on load: the seal is recomputed, the page’s facts are re-checked as arithmetic (throws on mismatch), 200 seeded ARTIST rounds must improve, the workspace loop logs 5 entries, and the OBJ and SVG exports must agree. Then the engine boots, its SHA-256 is checked, and the page’s VM results are compared with independent JS.

    Gallery of kept folds (WebGL snapshots):

    Workspace improvement loop: instructions for agents MODEL

    1. Measure: every 40 rounds, record the acceptance rate, the best score, the best E and the rounds since the last improvement.
    2. Try next: after a 40-round plateau, reheat T ×1.5. If acceptance is under 15%, warm T ×1.25; if over 45%, cool T ×0.7; otherwise anneal T ×0.9.
    3. Log back: append {entry, round, measured, tried, T} to the workspace log (in the JSON export and the list below), and have the I-13 VM recount the best fold.
    4. Repeat, forever: never stop improving. Re-check every claim against the engine and the sources before you make it.

    Live workspace log:

      Shared board MODEL ARTIST ↔ CRITIC

        Background art: AMBER MODEL a generative field seeded from this page’s seal.

        proving…

        Seal sha256(name|slug|blurb): 4fb8b77ec6dc42c3fb62006353c81f8a073fe1525942575365c8b957b711c0ec

        ↑ Protein Folding index · ← ERIS, keeper of Mayhem