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Research-Stack/obsidian-vault/01-LAYERS/00-Overview.md
Brandon Schneider 7c02104e43 Setup Obsidian Knowledge Base for Research Stack 
Created comprehensive Obsidian vault for managing Research Stack knowledge:

Core Structure:
- 00-MAP/ - Navigation, Dashboard, Core Concepts, Glossary, Getting Started
- 01-LAYERS/ - All 7 USTSM layers (L0-L6) with formal proofs, docs, receipts, hardware
- 07-RESEARCH/ - Milestones, Attack Plans, Conjectures, Experiments
- 08-TOOLS/ - Templates, Workflows, Scripts
- 09-REFERENCES/ - External resources
- 10-ARCHIVE/ - Completed items

Configuration Files:
- .obsidian/app.json - Vault settings
- .obsidian/community-plugins.json - Plugin configuration
- .obsidian/snippets/research-stack.css - Custom theme with layer colors
- .obsidian/plugins/ - Templater, QuickAdd, Dataview settings
- .obsidian/workspaces.json - Pre-configured workspaces

Templates Created:
- Formal Proof - For Lean theorem documentation
- Attack Plan - For research initiatives
- Milestone - For project milestones
- Receipt - For validation receipts
- Daily Standup - For daily progress tracking

Features:
- Dataview dashboard queries for system health
- Layer-specific color coding (L0-L6)
- Receipt styling and validation status
- Graph view customization
- QuickAdd commands for rapid note creation
- Templater automation with research helpers
- Pre-configured workspaces for different activities

Documentation:
- README.md - Complete vault guide
- Getting Started.md - Step-by-step tutorial
- Core Concepts.md - Fundamental principles
- Glossary.md - Research Stack terminology

Burgers 4-Theorem Attack Plan documented:
- Energy Dissipation theorem
- CFL Stability theorem
- Mass Conservation theorem
- Complexity Regularization theorem

Generated with [Devin](https://cli.devin.ai/docs)

Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
2026-05-19 14:40:41 +00:00

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Layer Overview - USTSM Architecture

Universal Substrate Topological State Machine

The Research Stack is organized into 7 layers following the USTSM architecture, from fundamental mathematics to meta-cognitive systems.

Layer Structure

Layer L0: Primordial 🟥

Domain: Pure mathematics, fixed-point arithmetic, braid fields
Status: ✅ Implemented (746 modules, 3529 build jobs, 0 errors)
Key Components:

  • Q16_16 FixedPoint arithmetic
  • Q0_64 Scalar system
  • PIST/DIAT Shell
  • BraidField operations
  • SSMS_nD state machine
  • EigensolidConvergence

Formal Proofs:

Documentation:

Layer L1: Geometric 🟩

Domain: Shape-aware topology, coupling geometry
Status: 🟡 Partial (docs migrated, partial Lean)
Key Components:

  • GWL 5-factor Coupling
  • TorsionalPIST (quaternion)
  • HybridTSMPISTTorus
  • GWL Throat
  • BodegaFlow horn-fiber

Formal Proofs:

Milestones:

Layer L2: Biological 🟦

Domain: Genetic codes, spiking neurons, STDP
Status: 🟡 Speculative (docs exist, minor Lean)
Key Components:

  • 30+ Genetic Code Tables
  • Codon Optimization
  • SpikingDynamics (Izhikevich)
  • GenomicCompression

Formal Proofs:

Layer L3: Thermodynamic 🟨

Domain: Energy-aware quality, homeostatic governance
Status: 🟡 Speculative (docs migrated)
Key Components:

  • Trixal Quality (thermal/work/irreversibility)
  • Homeostatic Governor
  • HyperFlow (Navier-Stokes)

Formal Proofs:

Layer L4: Security 🟧

Domain: Attack-aware gating, frustration memory
Status: 🟡 Partial (AngrySphinx in Lean)
Key Components:

  • AngrySphinx (exponential PoD)
  • FAMM Frustration
  • ASICTopology

Formal Proofs:

Layer L5: Semantic 🟪

Domain: Meaning-aware filtering, manifold routing, compression governance
Status: 🟡 Partial (projection receipts exist)
Key Components:

  • CrossDimensionalFilter (12 semantic primes)
  • Manifold Networking
  • BracketedCalculus
  • CompressionControl
  • RRC Equation Projection

Formal Proofs:

Layer L6: Meta 🟫

Domain: Self-aware adaptation, cognitive routing, auto-adaptive metatyping
Status: 🟡 Partial (cognitive receipts + projection holds)
Key Components:

  • Cognitive Load Decomposition (5-factor)
  • Adaptation
  • DynamicCanal
  • CompressionMechanics
  • Connectome-Protective Load Reweighting

Formal Proofs:

Layer Interactions

Upward Dependencies

L0 (Primordial) → L1 (Geometric) → L2 (Biological) → L3 (Thermodynamic)
  ↓                    ↓                   ↓                    ↓
L4 (Security) → L5 (Semantic) → L6 (Meta)

Cross-Layer Receipt Flow

  1. L0 Formal Proofs generate mathematical receipts
  2. L1-L3 consume L0 receipts for geometric/biological/thermodynamic operations
  3. L4 validates security invariants across all lower layers
  4. L5 filters semantic content using L4 security receipts
  5. L6 adapts meta-parameters based on L5 semantic analysis

Receipt Dimensions Across Layers

Dimension L0 L1 L2 L3 L4 L5 L6
C (Crossing) ✅ ✅ 🟡 🟡 ✅ ✅ ✅
σ (Sidon) ✅ ✅ 🟡 🟡 ✅ ✅ ✅
k (Steps) ✅ 🟡 🟡 🟡 ✅ ✅ ✅
ε (Residual) ✅ ✅ 🟡 🟡 ✅ ✅ ✅
t (Timing) ✅ ✅ 🟡 🟡 ✅ ✅ ✅
∅ (Scars) ✅ ✅ 🟡 🟡 ✅ ✅ ✅

Progress Summary

Implementation Status

Layer Formal Proofs Documentation Hardware Receipts
L0 ✅ Complete ✅ Complete ✅ Verified ✅ Operational
L1 🟡 Partial ✅ Complete 🟡 In Progress 🟡 Partial
L2 🟡 Minimal ✅ Complete ❌ Not Started ❌ Not Started
L3 🟡 Minimal ✅ Complete ❌ Not Started ❌ Not Started
L4 🟡 Partial ✅ Complete 🟡 In Progress 🟡 Partial
L5 🟡 Partial ✅ Complete 🟡 In Progress 🟡 Partial
L6 🟡 Partial ✅ Complete 🟡 In Progress 🟡 Partial

Next Steps

Priority 1: Complete L0 Proofs

  • Remove remaining 173 TODO(lean-port) items
  • Verify all Q16.16 arithmetic operations
  • Generate comprehensive receipt coverage

Priority 2: L1-L3 Formalization

  • Migrate geometric proofs to Lean
  • Implement biological models
  • Formalize thermodynamic equations

Priority 3: L4-L6 Integration

  • Complete security proofs
  • Implement semantic filtering
  • Develop meta-adaptive algorithms

#layer-overview #ustsm #architecture #system-design