mirror of
https://github.com/allaunthefox/Research-Stack.git
synced 2026-07-31 03:05:21 +00:00
92 lines
3.5 KiB
Markdown
92 lines
3.5 KiB
Markdown
# First Principles Molecular Derivation: Architectural Intent Map
|
|
|
|
**Status:** CONCEPTUAL — This DAG maps the intended first-principles derivation path. It identifies the provenance of atomic weights and the required manifold constraints. It does NOT yet execute these calculations.
|
|
|
|
```mermaid
|
|
graph TD
|
|
N0["Load IUPAC Standard<br/><i>Read data/atomic_weights.csv</i>"]
|
|
N1["Extract H<br/><i>Mean Weight: 1.00798</i>"]
|
|
N2["Extract C<br/><i>Mean Weight: 12.01060</i>"]
|
|
N3["Extract O<br/><i>Mean Weight: 15.99940</i>"]
|
|
N4["Extract N<br/><i>Mean Weight: 14.00685</i>"]
|
|
N5["Extract P<br/><i>Mean Weight: 30.97376</i>"]
|
|
N6["H2O Composition Schema<br/><i>Intent: First-Principles Water</i>"]
|
|
N7["Proposed Geometry Search<br/><i>Conceptual Sweep Angle 90-120</i>"]
|
|
N8["Coulombic Term (Assumption)<br/><i>q=0.41, r_HH</i>"]
|
|
N9["Pauli/VdW Term (Assumption)<br/><i>1/r^12</i>"]
|
|
N10["AMMR Phase-Gate (Constraint)<br/><i>Golden Ratio scaling</i>"]
|
|
N11["Theoretical Manifold Energy<br/><i>Target Functional Sum</i>"]
|
|
N12["Optimization Logic (Pending)<br/><i>Minimization via AMMR</i>"]
|
|
N13["Expected Result: H2O<br/><i>Reference Angle: 104.5 degrees</i>"]
|
|
N14["CO2 Composition Schema<br/><i>Intent: First-Principles Carbon Dioxide</i>"]
|
|
N15["Proposed Geometry Search<br/><i>Conceptual Sweep Angle 100-180</i>"]
|
|
N16["Coulombic Term (Assumption)<br/><i>O-O Repulsion</i>"]
|
|
N17["AMMR sp Hybridization<br/><i>Linear phase-lock</i>"]
|
|
N18["Theoretical Manifold Energy<br/><i>Target Functional Sum</i>"]
|
|
N19["Optimization Logic (Pending)<br/><i>Minimization via AMMR</i>"]
|
|
N20["Expected Result: CO2<br/><i>Reference Angle: 180.00 degrees</i>"]
|
|
N21["CH4 Composition Schema<br/><i>Intent: First-Principles Methane</i>"]
|
|
N22["Proposed Geometry Search<br/><i>Conceptual Tetrahedral sweep</i>"]
|
|
N23["Coulombic Term (Assumption)<br/><i>H-H Repulsion</i>"]
|
|
N24["AMMR sp3 Hybridization<br/><i>Phi-neutral symmetry</i>"]
|
|
N25["Theoretical Manifold Energy<br/><i>Target Functional Sum</i>"]
|
|
N26["Optimization Logic (Pending)<br/><i>Minimization via AMMR</i>"]
|
|
N27["Expected Result: CH4<br/><i>Reference Angle: 109.47 degrees</i>"]
|
|
N28["DNA Strand Schema<br/><i>Intent: B-DNA Assembly</i>"]
|
|
N29["Nucleotide Bases (Proposed)<br/><i>A, T, C, G resonance</i>"]
|
|
N30["Watson-Crick Pairing (Proposed)<br/><i>Hydrogen Bond resonance</i>"]
|
|
N31["Backbone Model (Proposed)<br/><i>Sugar-Phosphate chain</i>"]
|
|
N32["Helical Torsion (Proposed)<br/><i>3.4nm pitch model</i>"]
|
|
N33["Phi-Manifold (Proposed Constraint)<br/><i>Golden Ratio groove ratio</i>"]
|
|
N34["Theoretical Manifold Stability<br/><i>Target Functional Sum</i>"]
|
|
N35["Optimization Logic (Pending)<br/><i>Global minimum search</i>"]
|
|
N36["Expected Result: B-DNA<br/><i>Reference: 10.5 bp/turn</i>"]
|
|
N0 --> N1
|
|
N0 --> N2
|
|
N0 --> N3
|
|
N0 --> N4
|
|
N0 --> N5
|
|
N1 --> N6
|
|
N3 --> N6
|
|
N6 --> N7
|
|
N7 --> N8
|
|
N7 --> N9
|
|
N7 --> N10
|
|
N8 --> N11
|
|
N9 --> N11
|
|
N10 --> N11
|
|
N11 --> N12
|
|
N12 --> N13
|
|
N2 --> N14
|
|
N3 --> N14
|
|
N14 --> N15
|
|
N15 --> N16
|
|
N15 --> N17
|
|
N16 --> N18
|
|
N17 --> N18
|
|
N18 --> N19
|
|
N19 --> N20
|
|
N2 --> N21
|
|
N1 --> N21
|
|
N21 --> N22
|
|
N22 --> N23
|
|
N22 --> N24
|
|
N23 --> N25
|
|
N24 --> N25
|
|
N25 --> N26
|
|
N26 --> N27
|
|
N5 --> N28
|
|
N3 --> N28
|
|
N2 --> N28
|
|
N4 --> N28
|
|
N1 --> N28
|
|
N28 --> N29
|
|
N29 --> N30
|
|
N28 --> N31
|
|
N30 --> N32
|
|
N31 --> N32
|
|
N32 --> N33
|
|
N33 --> N34
|
|
N34 --> N35
|
|
N35 --> N36
|
|
```
|