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Home / Docs / Parameters

Parameter Reference

Each module documents its own parameters with defaults, units, and literature sources in its README. This page provides a central index and explains the configuration layering system.

For configuration layering and profiles, see Guide. For architecture details, see Architecture.

Configuration layering

Parameters are layered at runtime:

  1. bdm.core.toml contains core tissue parameters under [skin] and visualization/simulation settings
  2. modules/*/config.toml contains per-module parameters under [skin.modulename]
  3. profiles/*.toml provides skin phenotype overlays (normal, aged, diabetic, aged_diabetic, rheumatoid, burn, pressure, surgical, tumor, tumor_wound)
  4. studies/*/preset.toml provides study experiment configs (wound, diabetic-wound, tumor, tumor-wound, burn, pressure-ulcer, surgical, rheumatoid, baseline, full-model)

The merge script (scripts/config/merge_config.py) combines layers 1 and 2 into bdm.toml (gitignored). Profiles and study configs are applied as sparse overrides via scripts/config/apply_preset.py.

Module parameter index

Module Config file Parameters
Tissue bdm.core.toml [skin] Cell cycle, division, calcium, differentiation, KGF, O2, water, mechanics, shedding
Wound modules/wound/config.toml Wound geometry, trigger time, inward bias, resolution
Inflammation modules/inflammation/config.toml Diffusion/decay, Hill thresholds, wound source, split mode
Perfusion modules/perfusion/config.toml Per-layer profiles, angiogenesis rate/delay
Immune modules/immune/config.toml Neutrophil/macrophage timing, cytokine rates, efferocytosis, chemotaxis
Fibroblast modules/fibroblast/config.toml State machine thresholds, TGF-beta/collagen PDE, recruitment waves
MMP modules/mmp/config.toml MMP diffusion/decay/production, TIMP dynamics, MMP*TIMP neutralization rates
Fibronectin modules/fibronectin/config.toml Deposition, serum leakage, migration boost
Scar modules/scar/config.toml Collagen threshold, proportional mode, accumulation rate
Angiogenesis modules/angiogenesis/config.toml VEGF diffusion/decay/production, hypoxia threshold
Dermis modules/dermis/config.toml Sub-layer densities, collagen recovery, MMP degradation
Diabetic modules/diabetic/config.toml 16 scaling factors across all systems
Biofilm modules/biofilm/config.toml Growth, clearance, seeding, M1 block threshold
Tumor modules/tumor/config.toml BCC cycle factor, soft CI, apoptosis, handoff
Elastin modules/elastin/config.toml Sub-layer densities, production, MMP degradation
Hyaluronan modules/hyaluronan/config.toml Sub-layer densities, water retention, migration scaffold
Hemostasis modules/hemostasis/config.toml Fibrin deposition, platelet activation, clot dissolution
Glucose modules/glucose/config.toml Supply, consumption, diabetic hyperglycemia threshold
Temperature modules/temperature/config.toml Q10 factors, wound surface, body core
Lactate modules/lactate/config.toml Hypoxia production, VEGF boost, perfusion clearance
Nitric Oxide modules/nitric_oxide/config.toml iNOS/eNOS production, vasodilation, antimicrobial
pH modules/ph/config.toml Wound bed pH, acid mantle, enzyme activity
Senescence modules/senescence/config.toml DNA damage, SASP output (inflammation, MMP, TGF-beta)
Neuropathy modules/neuropathy/config.toml Nerve density, Wallerian degeneration, neuropeptide signaling
ROS modules/ros/config.toml Oxidative stress, mitochondrial superoxide, antioxidant defense
Bioelectric modules/bioelectric/config.toml Transepithelial potential, galvanotaxis
Lymphatic modules/lymphatic/config.toml Lymphangiogenesis, interstitial fluid dynamics
Mechanotransduction modules/mechanotransduction/config.toml Tissue stiffness, wound contraction
Body Site modules/body_site/config.toml Anatomical region scaling factors (opt-in)
Photon modules/photon/config.toml SLM light transport, opsin kinetics, phototoxicity
Burn modules/burn/config.toml Jackson's thermal injury, stasis zone, TEWL, contracture
Pressure modules/pressure/config.toml Ischemia-reperfusion, compression, shear, repositioning
Blood modules/blood/config.toml Hematocrit, platelet aggregation
Scab modules/scab/config.toml Eschar formation, provisional wound cover

Simulation settings

These parameters live in bdm.core.toml under [skin] and control simulation infrastructure:

Parameter Default Description
duration_days 30 Simulation duration in days
tissue_min -20 Min x/y for boundary removal
tissue_max 20 Max x/y for boundary removal
metrics_interval_h 10 Hours between CSV rows (0 = disabled)
metrics_autoopen true Open CSV in default app after simulation
subcycle_slow 10 PDE sub-cycling for slow fields (water, hyaluronan, vascular)
subcycle_medium 5 PDE sub-cycling for medium fields (inflammation, TGF-beta, MMP, VEGF)
hot_reload false Watch bdm.toml for runtime parameter changes

Mechanistic toggles

Optional biophysical replacements for simplified parametric models. All default to false.

Toggle Config section Description
mech_immune_recruitment skin.immune Gradient-driven monocyte extravasation (Michaelis-Menten)
mech_m1_m2_transition skin.immune Efferocytosis engulfment count drives M1 to M2
mech_collagen_deposition skin.fibroblast Constitutive basal + TGF-beta receptor occupancy collagen
mech_vegf_production skin.angiogenesis HIF-1alpha stabilization drives VEGF production

See each module's README for parameter details. Enable via studies/full-model/preset.toml for testing.

Debug flags

Under [skin.debug] in bdm.core.toml:

Flag Default What it enables
immune false Immune cell spawning, migration, state transitions
fibroblast false Collagen, TGF-beta, state transitions
wound false Wound creation, resolution, coverage
scaled_grid false ScaledGrid initialization diagnostics
perf false Wall-clock timing of major operations