Skip to content

diffusiophoresis_Claude_memory.md

Latest commit

 

History

History
155 lines (125 loc) · 12.1 KB

diffusiophoresis_Claude_memory.md

File metadata and controls

155 lines (125 loc) · 12.1 KB

Working Memory: diffusiophoresis (parallel)

Regime Comparison

Regime mesh_model particle_model n_types n_particles Best Score Key Insight
1-type weak Diffusiophoresis_Mesh PDE_ParticleField_D 1 9600 7/10 A=5.5,B=7.5 + M1=-8 + 150x150 mesh → sharp dispersed spot array (Iter 39)
1-type high-density Diffusiophoresis_Mesh PDE_ParticleField_D 1 14400 7/10 14400 particles → denser spots but lower entropy, no quality gain (Iter 62)
2-type opposing Diffusiophoresis_Mesh PDE_ParticleField_D 2 9600 7/10 A=5.5/B=7.5 + opposing + adhesion → hexagonal core-ring array (Iter 23)
2-type same-sign Diffusiophoresis_Mesh PDE_ParticleField_D 2 9600 7/10 same-sign moderate coupling → core-shell micro-clusters (Iter 12)
3-type opposing Diffusiophoresis_Mesh PDE_ParticleField_D 3 9600 8/10 opposing + cross-type adhesion → flower/mandala tissue morphology (Iters 14 & 45, BEST but TIME-LIMITED)
3-type same-sign Diffusiophoresis_Mesh PDE_ParticleField_D 3 9600 6/10 same-sign → nested co-localization, less complex (Iters 16, 24)
GS any-type Diffusiophoresis_Mesh_GrayScott PDE_ParticleField_D 2-3 9600 6/10 GS + particles → radial-locked at ANY coupling (Iters 33-40)
FHN 3-type PDE_Diffusiophoresis_FHN PDE_ParticleField_D 3 9600 7/10 FHN + 3-type opposing → concentric type-segregated rings (Iter 46)
GM 2-type PDE_Diffusiophoresis_GM PDE_ParticleField_D 2 9600 5/10 Stabilized; radial morphology (Iter 47)
Schnakenberg 2-type PDE_Diffusiophoresis_Schnakenberg PDE_ParticleField_D 2 9600 5/10 gamma=60 → radial concentric (Iter 51)
1-type NLD labyrinth Diffusiophoresis_Mesh (+NLD) PDE_ParticleField_D 1 9600 7/10 A=3.0/B=5.5 + NLD delta=2.0 → LABYRINTHINE Turing (Iter 83, NOVEL)
3-type NLD labyrinth Diffusiophoresis_Mesh (+NLD) PDE_ParticleField_D 3 9600 7/10 A=3.0/B=5.5 + NLD + 3-type → branching tissue on labyrinthine scaffold (Iter 85)
1-type NLD vermiform Diffusiophoresis_Mesh (+NLD) PDE_ParticleField_D 1 9600 7/10 A=2.0/B=5.0 + NLD → VERMIFORM filamentary chains, strongest fields ever (Iter 87, NOVEL)

Knowledge Base

Established Principles

  1. Moderate coupling is a UNIVERSAL HARD stability limit: |M1| <= 10 and consumption <= 100 for FHN; |M1| <= 12 and consumption <= 120 for Brusselator hexagonal; |M1| <= 8 and consumption <= 80 for Brusselator labyrinthine (tighter limit). (Evidence: Iters 4,7,32,48,81,88)
  2. D1 >= 0.05 required: D1 < 0.05 causes numerical crash. (Evidence: Iters 1, 2)
  3. Mobility sign determines pattern type, not stability: Opposing-sign → segregation. Same-sign → co-localized. Across Brusselator, GS, FHN. (Evidence: Iters 3,8,10,14,23,46)
  4. Plateau=0 is universal: All models under continuous injection drive non-equilibrium dynamics. (88 iterations, 5 PDE models).
  5. 1-type sweet spot is |M1|=8, consumption=80, A=5.5/B=7.5 at 150x150: Robust across sigma [0.005, 0.008] and particle counts [9600, 14400]. (Iters 11,15,19,39,62,76)
  6. Cross-type adhesion enhances OPPOSING-SIGN morphology specifically: p[2,5]=0.3 sharpens boundaries. Negligible on same-sign. (Evidence: Iters 10,14,17,23,24,45,46,85)
  7. Opposing-sign 3-type beats same-sign 3-type: Opposing → 7-8/10; same-sign → 6/10. (Evidence: Iters 8/9/14/21/22/45/46 vs 16/24)
  8. Iter 14 is a TIME-LIMITED local optimum with CONSUMER-DOMINANT asymmetry: 30+ perturbations scored ≤7/10, and config BLOWS UP at 4000 frames (Iter 84). The chi=-16 regime is marginally unstable. (CONFIRMED DOWNGRADED: Iters 84, 81)
  9. A=5.5/B=7.5 produces more/smaller Turing spots: Key for 1-type and 2-type, not 3-type. (Evidence: Iters 19, 23, 39, 56)
  10. Chirality has NO sweet spot: 0.3+ suppresses patterns strongly. 0.1 is neutral. (Evidence: Iters 25, 27, 64, 75)
  11. Iter 23's hexagonal regime is 2-type specific: 3-type in same params → not superior. (Evidence: Iters 26, 29)
  12. Weber-Fechner suppresses hexagonal at ANY K>0: K=0.15 already forces radial/bullseye. NO useful regime. (Iters 18, 31, 80)
  13. Michaelis-Menten is a secondary lever: Km=0.2-0.5 near-neutral. (Evidence: Iters 22, 30)
  14. Gray-Scott is fundamentally radial-locked with particles. (Evidence: Iters 33,34,38,40)
  15. 150x150 mesh (22500 nodes) is OPTIMAL for 9600 particles: 200x200 degrades all configs. (Evidence: Iters 39,41,45,49,54,55,72)
  16. Non-Brusselator PDE models are radial-locked with particles: ALL alternatives (GS, FHN, Schnakenberg, GM) produce radial morphology. Only Brusselator achieves hexagonal multi-spot arrays. (Evidence: 12+ iterations across 4 non-Brusselator models)
  17. NLD delta=2.0 + high B/A ratio → labyrinthine Turing patterns: A=3.0/B=5.5 (B/A=1.83) + NLD delta=2.0 breaks hexagonal symmetry into labyrinthine/vermiform. A=2.0/B=5.0 (B/A=2.5) pushes further into fragmented vermiform. (NEW: Evidence: Iters 83, 85, 87)
  18. NLD delta=3.0 OVER-DAMPS hexagonal at A=5.5/B=7.5: Higher NLD weakens field contrast. delta=2.0 is optimal for hexagonal regime. (NEW: Evidence: Iter 86)
  19. NLD is INCOMPATIBLE with strong coupling (chi=-16): NLD delta=1.0+ at chi=-16/consumption=100 → blowup. NLD requires moderate coupling (chi=-8). (NEW: Evidence: Iters 81, 84)
  20. ALL 8 PDE_D particle features exhausted: W-F, M-M, chirality, durotaxis, pp_field_mod, DDM, alignment, sigma — only adhesion worked. (Evidence: 80 iterations, Blocks 1-10)

Open Questions

  • Would ASYMMETRIC diffusion (D1 anisotropic) create stripe selection in Brusselator?
  • Would durotaxis on MULTI-TYPE (2 or 3-type) create boundary-sensing effects? (1-type was neutral)
  • Would NLD at LOWER delta (0.5-1.0) at A=3.0/B=5.5 still produce labyrinthine, or is delta=2.0 required?
  • Is the labyrinthine regime (A=3.0/B=5.5 + NLD) more TIME-STABLE than the hexagonal regime (A=4.5/B=6.5)?
  • Can 2-type opposing particles on the labyrinthine regime (A=3.0/B=5.5 + NLD) create core-shell vermiform filaments?
  • Can 3-type on vermiform regime (A=2.0/B=5.0 + NLD) create novel tissue morphology?
  • Would A=2.5/B=5.5 (B/A=2.2, intermediate) bridge labyrinthine and vermiform regimes?
  • Would CROSS-DIFFUSION (chi parameter in mesh model, not mobility) + NLD create coupled multi-scale patterns?
  • Can we find a TRULY TIME-STABLE 8/10 pattern using the labyrinthine regime at moderate coupling?

Failed Configurations

  • D1=0.03/0.01 + high Da_c → crash (Iters 1, 2)
  • 3-type with M1=-24, consumption=250 → all escape (Iter 4)
  • 1-type with |M1|=16, consumption=180 → all escape (Iter 7)
  • 3-type M1=-14, consumption=140 → NaN blow-up (Iter 32)
  • Avoid D1 < 0.05, |M1| > 12 (Brusselator hex), |M1| > 8 (Brusselator labyrinthine), |M1| > 10 (FHN)
  • Avoid Weber-Fechner K > 0, chirality >= 0.3
  • Gray-Scott, Schnakenberg gamma=200, GM without stabilization → all fail or radial-locked
  • 200x200 mesh at 9600 particles → dead end (Iters 49,54,55)
  • pp_field_mod → neutral (Iters 61, 63)
  • DDM → neutral on multi-type, harmful on 1-type (Iters 65-72)
  • Velocity alignment → cosmetic (Iters 73-79). HURTS 2-type.
  • NLD delta=1.0 + chi=-16 → blowup (Iter 81). NLD incompatible with strong coupling.
  • Iter 14 at 4000 frames → blowup (Iter 84). chi=-16 regime is marginally unstable.
  • NLD delta=3.0 at A=5.5/B=7.5 → over-damps fields (Iter 86, 6/10)
  • chi=-10 + consumption=100 on labyrinthine → degrades coherence (Iter 88, 5/10)

Code Insights

  • PDE_D.py features: W-F (p[2,4]), adhesion (p[2,5]), M-M (p[1,2]), durotaxis (p[1,3]), chirality (p[1,4]), pp_field_mod (p[2,6]), DDM (p[1,5]), alignment (p[2,7]) — all backward-compatible
  • Cross-type adhesion p[2,5]=0.3 is the ONLY PDE_D feature that improved scores (7→8/10)
  • ALL 8 PDE_D features tested: only adhesion worked
  • Block 11 code change: NLD in Brusselator — D1(C1) = D1_base*(1+delta*(C1-A)^2/A^2). Enabled labyrinthine and vermiform patterns.
  • Brusselator is the ONLY mesh model producing non-radial patterns; NLD extends it to labyrinthine/vermiform
  • Next code lever for Block 12: Consider CUBIC autocatalysis modification, substrate inhibition, or time-delayed feedback in Brusselator to find new pattern regimes

PDE Variants

Variant Model Literature Status Best Score
Diffusiophoresis_Mesh Brusselator Prigogine (1968) active (BEST) 8/10 (Iters 14,45,53) but TIME-LIMITED
Diffusiophoresis_Mesh (+ NLD) Brusselator + nonlinear diffusion Gambino et al. (2013) active (PROMISING) 7/10 (Iters 83, 85, 87 — labyrinthine+vermiform)
Diffusiophoresis_Mesh_GrayScott Gray-Scott Pearson (1993) FAILED 6/10 radial-locked
PDE_Diffusiophoresis_FHN FHN FitzHugh (1961) radial-locked 7/10 (Iter 46)
PDE_Diffusiophoresis_Schnakenberg Schnakenberg Schnakenberg (1979) radial-locked 5/10 (Iter 51)
PDE_Diffusiophoresis_GM Gierer-Meinhardt Gierer & Meinhardt (1972) radial-locked 5/10 (Iter 47)

Previous Block Summaries

Blocks 1-7 (Iters 1-56)

  • Global best: Iter 14/45/53 (3-type opposing Brusselator 150x150, 8/10) — flower/mandala tissue morphology
  • Best 2-type: Iter 23 (7/10) — hexagonal core-ring array
  • Best 1-type: Iter 39 (7/10) — dispersed spot array at 150x150
  • 56 iterations across 5 PDE mesh models, 6 PDE_D code features, resolutions 100x100 to 200x200
  • Brusselator is the only model producing hexagonal patterns; all others radial-locked
  • Cross-type adhesion p[2,5]=0.3 is the only code feature that improved scores

Block 8 (Iters 57-64)

  • No 8/10 ceiling broken. Best: 7/10 (Iters 61, 62, 64).
  • pp_field_mod=0.5 NEUTRAL. 14400 particles same 7/10. Chirality=0.1 neutral.

Block 9 (Iters 65-72) — DDM FAILED

  • No 8/10 ceiling broken. Best: 7/10 (Iters 70, 72). Average: 6.25/10.
  • DDM tested across full range [0.15-1.0]: NEUTRAL on multi-type, HARMFUL on 1-type.

Block 10 (Iters 73-80) — ALIGNMENT COSMETIC + W-F DEAD END

  • No 8/10 ceiling broken. Scores: 7,6,6,7,7,7,7,5. Average: 6.5/10.
  • All 8 PDE_D features exhaustively tested. Only adhesion helped. Strategy shift to mesh model.

Block 11 (Iters 81-88) — NLD: LABYRINTHINE BREAKTHROUGH

  • Scores: 1, 7, 7, 1, 7, 6, 7, 5 → Average: 5.1/10, Best: 7/10 (Iters 82, 83, 85, 87)
  • NLD + high B/A ratio → LABYRINTHINE Turing (Iter 83, NOVEL): First non-hexagonal Brusselator pattern in 83 iters
  • B/A=2.5 + NLD → VERMIFORM filaments (Iter 87, NOVEL): Strongest fields ever (pattern_growth=294)
  • 3-type on labyrinthine produces branching tissue (Iter 85, 7/10) — promising hybrid
  • NLD delta=3.0 over-damps hexagonal (Iter 86, 6/10). delta=2.0 optimal.
  • Labyrinthine has tighter coupling limit: |chi|<=8 (vs hexagonal |chi|<=12)
  • Iter 14 confirmed TIME-LIMITED (blows up at 4000 frames). No 8/10 ceiling broken but 2 novel pattern types.

Current Block (Block 12)

Block Info

Parameters: Brusselator + NLD, exploring labyrinthine+vermiform regime in depth mesh_model_name: Diffusiophoresis_Mesh (with NLD toggle via params_mesh[1][3]) Iterations: 89-96 (parallel, 4 slots per batch) Starting from: Iter 85 (3-type labyrinthine 7/10), Iter 87 (1-type vermiform 7/10), Iter 83 (1-type labyrinthine 7/10) Code modification: Consider substrate inhibition or saturation kinetics in Brusselator reaction terms

Hypothesis

The labyrinthine (Iter 83/85, A=3.0/B=5.5) and vermiform (Iter 87, A=2.0/B=5.0) regimes are the most significant discoveries since Iter 14. They produce qualitatively NEW pattern types that no parameter tuning on standard Brusselator achieved. Key priorities:

  1. Can multi-type particles on labyrinthine/vermiform fields break the 8/10 ceiling?
  2. What B/A ratio and NLD delta give the richest patterns?
  3. Is a code modification (substrate inhibition/saturation) needed to get beyond 7/10 in these regimes?
  4. Test intermediate A values (A=2.5) to bridge labyrinthine and vermiform.

Iterations This Block

(Block 12 starts at Iter 89)

Emerging Observations

(To be filled as Block 12 progresses)