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Sensei Ewok Research Lab

Small tools. Careful questions. Research in the open.

  • What this isA small, independent software lab. We write research tools, test them in public, and say plainly what each one does and does not do.
  • What it is notNot a medical organization, not a clinic, and not affiliated with the Cystic Fibrosis Foundation. Nothing here is medical advice.

CFTR is a human protein, and variants of it are linked to cystic fibrosis. Structure 6MSM places 1,181 of its 1,480 amino acids. Residue 508 is present in this structure. A model fitted to electron-microscope data, not a photograph.

Structure 6MSM domain color key & provenance
  • Membrane-spanning part 1, residues 81 to 365
  • Nucleotide-binding part 1, residues 423 to 646
  • Membrane-spanning part 2, residues 859 to 1155
  • Nucleotide-binding part 2, residues 1210 to 1443
  • Gray: placed, outside the four marked parts
  • Dotted gray: not placed in this structure
  • Flat band: helix or strand, as UniProt annotates

Figure 1. The CFTR protein, drawn from structure 6MSM.

source PDB 6MSM · UniProt P13569 · method alpha-carbon trace, residues placed from the deposited coordinates · read 2026-10-15 · lock 7490af5 · not shown movement, lipids, water, or how any variant behaves in a person.

Interactive Scientific Magazine · 4 Pillars · 40 Five-Act Monographs

Read the 40 CF & Biophysics Monographs

Every monograph unfolds in five acts: a human and physical story, a plain-language derivation of the governing law, a coupled two-plate interactive laboratory you can perturb in your browser, clinical and therapeutic horizons grounded in primary DOIs, and a downloadable SKILL.md companion.

C Pillar C · C.01–C.10 · 10 Five-Act Monographs

Pillar I · The CFTR Channel: Structure, Folding & Allosteric Gating

Ten 5-Act monographs tracing human CFTR from cryo-EM atomic coordinates (PDB 5UAK, 6MSM, 8EIQ, 8EJ1) and NBD1–ICL4 folding thermodynamics to anion pore electrostatics, organoid theratyping, and TMEM16A/SLC26A9 bypass.

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C.01 · VOL. 01★ PARETO22 MIN READF508del Folding & Dual-Site Allostery (8EIQ)Tracing the 42.2 Å and 53.2 Å allosteric rescue pathways from transmembrane helices…C.02 · VOL. 01★ PARETO22 MIN READATP Dimerization, R-Domain & Ivacaftor Gating (6MSM)How PKA phosphorylation clears the regulatory R-domain from the cytosolic cleft…C.03 · VOL. 0122 MIN READAnion Pore, Bicarbonate Selectivity & Airway pHHow cationic arginine/lysine rings in the cytosolic portal and TM6 selectivity…C.04 · VOL. 0222 MIN READVanzacaftor–Tezacaftor–Deutivacaftor & Deuterium KIEHow replacing C–H with C–D bonds in deutivacaftor slows CYP3A4 oxidative clearance…C.05 · VOL. 0222 MIN READRare Missense Variants (N1303K, G85E) & Organoid SwellingWhy N1303K in NBD2 resists standard correctors differently from F508del in NBD1,…C.06 · VOL. 0322 MIN READPartial-Conductance Thresholds & Therapeutic BenchmarksSynthesizing Pillar I: why the relationship between functional CFTR expression and…C.07 · VOL. 0322 MIN READTransmembrane Helical Insertion & Hydrophobic MismatchHow charged pore-lining residues (R334, R347, K95) and polar transmembrane segments…C.08 · VOL. 0322 MIN READDistal Class I Truncations, C-Terminal PDZ Anchoring & ERAD EscapeWhy stop codons in exons 23–27 produce a partially functional channel when NMD is…C.09 · VOL. 0322 MIN READPan-Allele Deep Mutational Scanning & TheratypingHow high-throughput FRT/HBE electrophysiology, Potts co-evolutionary energy models,…C.10 · VOL. 0322 MIN READGenotype-Agnostic Anion Bypass: TMEM16A, SLC26A9 & ENaCCan alternative apical chloride/bicarbonate channels and sodium-absorption brakes…
G Pillar G · G.01–G.10 · 10 Five-Act Monographs

Pillar II · Genetic & RNA Rescue: Stop Variants, Splicing & Base/Prime Editing

Ten 5-Act monographs for the genotypes small-molecule modulators cannot reach alone: Class I nonsense readthrough, NMD attenuation, engineered suppressor tRNAs, splice-switching ASOs, ExSpeU1 snRNAs, base/prime editing, split inteins, mRNA codon velocity, and IS110 bridge recombinases.

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G.01 · VOL. 0122 MIN READClass I Premature Stop Codons (G542X, W1282X) & NMDHow the 50–55 nucleotide exon-junction complex (EJC) rule triggers UPF1/SMG1…G.02 · VOL. 01★ PARETO22 MIN READRibosomal Readthrough Competition (UGA/UAG/UAA) & ETI SynergyHow small-molecule readthrough agents shift the kinetic race between eRF1/eRF3…G.03 · VOL. 0222 MIN READEngineered Suppressor tRNAs (ACE-tRNA) for Arg, Trp & GlyHow anticodon-edited transfer RNAs charged by endogenous aminoacyl-tRNA synthetases…G.04 · VOL. 0222 MIN READSplice-Switching ASOs (3849+10kb C>T, 2789+5G>A)How 2'-O-MOE phosphorothioate oligonucleotides mask deep-intronic pseudo-exons from…G.05 · VOL. 03★ PARETO22 MIN READAdenine Base Editing (ABE8e / TadA) Without DNA BreaksHow Cas9 nickase fused to an evolved TadA deoxyadenosine deaminase converts…G.06 · VOL. 0322 MIN READPrime Editing (PEmax / epegRNA) & PassaGENE RewritingHow Cas9 H840A nickase fused to an engineered reverse transcriptase copies a…G.07 · VOL. 0322 MIN READEngineered U1 snRNA & Branchpoint Splicing RescueHow modified small nuclear RNAs (ExSpeU1) restore canonical 5' splice-site…G.08 · VOL. 0322 MIN READDual-AAV Split-Intein Reconstitution & ΔR MinigenesHow full-length 4.44 kb CFTR cDNA exceeds single-AAV promoter budgets, and how…G.09 · VOL. 0322 MIN READmRNA Codon Velocity, Poly(A) Half-Life & TLR EvasionWhy replacing every rare codon with the fastest synonymous codon causes NBD1…G.10 · VOL. 0322 MIN READIS110 Bridge-RNA Recombinases & CpG-Depleted Super-ExonsHow programmable single-protein bridge recombinases and phage integrases insert a…
D Pillar D · D.01–D.10 · 10 Five-Act Monographs

Pillar III · Airway Delivery, Mucus Biophysics & Host Defense

Ten 5-Act monographs on the physical barriers between a genetic medicine and a lung cell: MUC5B/MUC5AC gel-on-brush osmotic mechanics, SORT-LNPs, nebulizer shear, endosomal escape, basal stem cell homing, phage-biofilm dynamics, MPPs, and CD47 stealth.

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D.01 · VOL. 01★ PARETO22 MIN READMUC5B/MUC5AC Gel-on-Brush Osmotic Mechanics & Amsden MeshHow hyperconcentrated mucin polymers (above 4 to 8 percent solids) compress the…D.02 · VOL. 01★ PARETO22 MIN READLung-Targeted SORT-LNPs & Vibrating-Mesh Nebulizer ShearHow five-component Selective Organ Targeting (SORT) lipid ratios tune apparent acid…D.03 · VOL. 0222 MIN READEndosomal Escape, Ionizable Lipid pK_a & H_II FusionHow V-ATPase acidification (dropping from pH 7.4 to 5.5) protonates ionizable…D.04 · VOL. 0222 MIN READAirway Basal Stem Cells vs. Differentiated Ciliated CellsWhy mRNA in differentiated ciliated/secretory cells turns over with epithelial…D.05 · VOL. 0322 MIN READInhaled mRNA & Viral Vectors in the Clinic (VX-522, ARCT-032, Lentivirus)How Weibel bronchial branching (across generations 0 through 16), Stokes aerosol…D.06 · VOL. 0322 MIN READBiofilm Reaction-Diffusion (Thiele Φ) & Phage–Antibiotic SynergyHow oxygen-consuming bacterial biofilms and PMN neutrophils create steep hypoxic…D.07 · VOL. 0322 MIN READPericiliary Gel-on-Brush Compression & ENaC Osmotic RescueHow hyper-concentrated CF mucus (>6–8% solids) exerts osmotic pressure above the…D.08 · VOL. 0322 MIN READZwitterionic & PEG-Shedding Mucus-Penetrating NanoparticlesHow densely neutral surface coatings evade hydrophobic and electrostatic MUC5B/eDNA…D.09 · VOL. 0322 MIN READSurfactant Corona Remodeling, CD47 Stealth & Glycocalyx EntryHow SP-A and SP-D collectins opsonize inhaled nanoparticles for alveolar macrophage…D.10 · VOL. 0322 MIN READTight-Junction Paracellular Gating & Basal Stem Cell PersistenceWhy terminally differentiated ciliated cells turn over every 3–6 months, and how…
L Pillar L · L.01–L.10 · 10 Five-Act Monographs

Pillar IV · Living Proofs, Non-Equilibrium Biophysics & Global Registries

Ten 5-Act monographs uniting Lean 4 formal proof landscapes (Fermat's Last Theorem 29,500 lemmas), Schnakenberg stochastic thermodynamics, Rao–Esposito coarse-graining, AlphaEvolve Pareto regimens, trial endpoint forensics, and global CF registry mathematics.

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L.01 · VOL. 0122 MIN READLean 4 Fermat's Last Theorem Blueprint & Allosteric PatchingHow the Lean 4 formalization blueprint of Wiles and Taylor–Wiles maps deductive…L.02 · VOL. 01★ PARETO22 MIN READSchnakenberg Cycle Affinity, Entropy Production & TUR BoundsWhy CFTR breaks detailed balance via MgATP hydrolysis (driven by roughly twenty…L.03 · VOL. 0222 MIN READCoarse-Graining Hidden States, Rao–Esposito & Kemeny's ConstantWhen patch-clamp electrodes lump five microscopic CFTR states into binary 'Open'…L.04 · VOL. 02★ PARETO22 MIN READWasserstein Optimal Transport (W₂) & Thermodynamic Speed LimitsHow the Benamou–Brenier–Aurell–Dechant–Sasa inequality (linking total entropy…L.05 · VOL. 0322 MIN READGlobal Registry Denominator Math (CFFPR, ECFSPR, CCFR, ACFDR)Deconstructing the five-tier epidemiological cascade (Living → Seen → Genotyped →…L.06 · VOL. 0322 MIN READReproducible Claim Checkers & Source-Grounded Council LoopsSynthesizing Pillar IV: how Answer Tiers (T0–T3), SHA-256 evidence locks, Scite…L.07 · VOL. 0322 MIN READAlphaEvolve Program Search & the 24-Hour Six-Barrier RegimenHow FunSearch / AlphaEvolve program-synthesis loops discover non-obvious dosing…L.08 · VOL. 0322 MIN READCounterfactual Endpoint Forensics: ppFEV₁, LCI₂.₅ & Sweat Chloride PowerHow spirometry (ppFEV₁) loses statistical power in children and well-preserved…L.09 · VOL. 0322 MIN READPolygenic Modifier Loci, Epistasis & CYP3A4 SafetyHow non-CFTR modifier genes (SLC26A9, SLC6A14, EHF/APIP, MUC4/MUC20, TGFB1) reshape…L.10 · VOL. 0322 MIN READNon-Equilibrium ATP Gating Cycles & Closing the Final 8% GapWhy CFTR is an evolutionary ABC transporter turned ATP-driven non-equilibrium ion…
Sensei Ewok Research Lab · 4 Pillars · 40 Five-Act Monographs

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