L1 ⚛ L1-306 ⊙ Testnet

Coarse-Grained Molecular Dynamics (MARTINI, Dry-MARTINI)

Computational Chemistry · Multi-atom grouping force fields

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⬇ L1-306.md

# ⚛ L1 Principle — Coarse-Grained Molecular Dynamics (MARTINI, Dry-MARTINI) **ID:** `L1-306` · **Status:** ⊙ Testnet (genesis catalog) > **🌐 Domain:** Computational Chemistry — *Multi-atom grouping force fields* > **🎯 Problem class:** nonlinear inverse · **🧮 Solution space:** coarse grained trajectory > **📡 Carrier:** none · **🌫 Noise:** thermal langevin > **⚖ Difficulty (δ):** 3 · **⛓ Block:** 41554115 --- ## 🧠 1. Introduction **Coarse-Grained Molecular Dynamics (MARTINI, Dry-MARTINI)** is a **nonlinear inverse problem** whose unknown lives in **coarse grained trajectory** space, within the **Multi-atom grouping force fields** sub-domain of **Computational Chemistry**. Measurements consist of none via a **md observable** sensing mechanism. The forward operator applies, in order: E · bead mapping operator; E · CG forcefield operator; D · time · symplectic operator; O · mesoscale observable operator. Observations are corrupted by Langevin-type thermal fluctuations. Well-posed forward; transferability limited to similar chemistries. ## ⚙ 2. Forward Model Physical chain: **x** → E · bead mapping → E · CG forcefield → D · time · symplectic → O · mesoscale observable → **y** (detector). ``` y = `O.mesoscale_observable` `D.time.symplectic` `E.CG_forcefield` `E.bead_mapping` x ``` **Measurement DAG:** | Primitive | What it does | |---|---| | `E.bead_mapping` | E · bead mapping operator | | `E.CG_forcefield` | E · cg forcefield operator | | `D.time.symplectic` | D · time · symplectic operator | | `O.mesoscale_observable` | O · mesoscale observable operator | ## 🔬 3. Physics Fingerprint | Property | Value | |---|---| | Domain | Computational Chemistry | | Sub domain | Multi-atom grouping force fields | | Carrier | none | | Problem class | nonlinear_inverse | | Solution space | coarse_grained_trajectory | | Noise model | thermal_langevin | | Integration axis | time | | Difficulty delta | 3 | | L dag | 3.1 | ## 📡 4. Measurement Model Well-posed forward; transferability limited to similar chemistries. | Metric | Value | |---|---| | Metric | rdf_L2_CG | | Secondary | membrane_thickness_error_nm | ## 📏 5. Operating Range (Ω) **Center problem class:** `coarse_grained_md` · **Forward operator:** `cg_md_forward` **Center point:** | Parameter | Unit | Value | |---|---|---| | Ff | — | MARTINI_v3 | | T k | — | 310 | | Dt fs | — | 20 | | N beads | — | 10000 | | N steps | — | 1e+07 | **Allowed bounds:** | Parameter | Unit | Range | |---|---|---| | Ff | — | MARTINI_v2, MARTINI_v3, MSCG, PRIME20 | | T k | — | 200 – 400 | | Dt fs | — | 5 – 50 | | N beads | — | 100 – 100000000.0 | | N steps | — | 10000 – 10000000000.0 | ## 🎯 6. Tolerance (ε) **Center tolerance:** g(r) L2 <= 0.03 | Metric | Range | |---|---| | Rdf l2 cg | 0.01 – 0.3 | ## ⚖ 7. Hardness Function Hardness scales as **`epsilon_fn`** on **rdf_L2_CG**, with κ = `150` and δ = `3`. ## 💾 8. Reference Dataset - **primary** · weight 1.0 · IPFS _(not pinned yet)_ ## 9. On-chain Registration - **Chain hash:** `0x2c7de354450547ba2ee4f3024bf4dfbea9b78b02af114ceccda8d2c41e97e88f` - **Chain tx hash:** `0xa5bc62992a36e99f8831ac3e6343326edc7a72b100b9fcdbfc85e204d6d1358e` - **Chain block:** `41554115` --- ## File Mapping This bundle consists of: `L1-306.md`, `L1-306.json`. | File | Role | How to regenerate | |------|------|-------------------| | `L1-306.md` | Source of truth — edit this | Human or LLM | | `L1-306.json` | Structured metadata for the registry | LLM regenerates from the sections above | **Prompt for your LLM after editing this Markdown:** > Read the attached Markdown. Regenerate the sibling `.json` so every field matches. > Preserve the schema documented in the rows above. > Output each file in its own fenced code block tagged with the filename. > Output only the JSON object. _This Markdown was auto-synthesized from the catalog row for `L1-306`._ _Edit it, regenerate the JSON, and submit at [/submit](/submit) to claim the artifact._

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Read the attached Markdown (L1-306.md).
Regenerate L1-306.json so every field matches the Markdown.
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L2-306-001 Coarse-Grained Molecular Dynamics (MARTINI, Dry-MARTINI) Mismatch-Only Spec

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📋 JSON metadata

{
  "artifact_id": "L1-306",
  "chain_block": 41554115,
  "chain_hash": "0x2c7de354450547ba2ee4f3024bf4dfbea9b78b02af114ceccda8d2c41e97e88f",
  "chain_tx_hash": "0xa5bc62992a36e99f8831ac3e6343326edc7a72b100b9fcdbfc85e204d6d1358e",
  "domain": "Computational Chemistry",
  "hardness_fn": {
    "delta": 3,
    "kappa": 150,
    "metric": "rdf_L2_CG",
    "type": "epsilon_fn"
  },
  "initiator_dataset": [
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      "license_hash": null,
      "name": "primary",
      "weight": 1.0
    }
  ],
  "layer": "L1",
  "observable_profile": {
    "metric": "rdf_L2_CG",
    "regime": "Well-posed forward; transferability limited to similar chemistries.",
    "secondary": "membrane_thickness_error_nm"
  },
  "physics_fingerprint": {
    "L_DAG": 3.1,
    "carrier": "none",
    "difficulty_delta": 3,
    "domain": "Computational Chemistry",
    "integration_axis": "time",
    "noise_model": "thermal_langevin",
    "primitives": [
      "E.bead_mapping",
      "E.CG_forcefield",
      "D.time.symplectic",
      "O.mesoscale_observable"
    ],
    "problem_class": "nonlinear_inverse",
    "sensing_mechanism": "md_observable",
    "solution_space": "coarse_grained_trajectory",
    "sub_domain": "Multi-atom grouping force fields",
    "title": "Coarse-Grained Molecular Dynamics (MARTINI, Dry-MARTINI)"
  },
  "size_tiers": {
    "allowed_forward_operators": [
      "cg_md_forward"
    ],
    "allowed_omega_dimensions": [
      "N_beads",
      "T_K",
      "N_steps",
      "dt_fs",
      "ff"
    ],
    "allowed_problem_classes": [
      "coarse_grained_md"
    ],
    "center_spec": {
      "epsilon_fn_center": "g(r) L2 \u003c= 0.03",
      "forward_operator": "cg_md_forward",
      "input_format": "measurement_only",
      "omega": {
        "N_beads": 10000,
        "N_steps": 10000000.0,
        "T_K": 310,
        "dt_fs": 20,
        "ff": "MARTINI_v3"
      },
      "problem_class": "coarse_grained_md"
    },
    "epsilon_bounds": {
      "rdf_L2_CG": [
        0.01,
        0.3
      ]
    },
    "omega_bounds": {
      "N_beads": [
        100,
        100000000.0
      ],
      "N_steps": [
        10000,
        10000000000.0
      ],
      "T_K": [
        200,
        400
      ],
      "dt_fs": [
        5,
        50
      ],
      "ff": [
        "MARTINI_v2",
        "MARTINI_v3",
        "MSCG",
        "PRIME20"
      ]
    }
  },
  "staked_pwm": 0.0,
  "status": "testnet",
  "sub_domain": "Multi-atom grouping force fields",
  "title": "Coarse-Grained Molecular Dynamics (MARTINI, Dry-MARTINI)"
}

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