wound

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Wound

Circular punch biopsy event that initiates the wound healing cascade.

Biology

A punch biopsy creates a full-thickness circular wound that destroys the epithelium and damages the underlying dermis and vasculature. This technique is the standard clinical and experimental model for studying wound healing because it produces a reproducible, well-defined lesion with clean margins. Removing a cylinder of tissue eliminates the protective stratum corneum, disrupts calcium gradients that maintain barrier homeostasis, and severs dermal capillaries to create a hypoxic wound bed.

The wound event serves as the trigger for the entire healing cascade. Loss of the epithelial barrier exposes underlying tissue to the environment, releasing damage-associated molecular patterns (DAMPs) that recruit neutrophils and macrophages. Keratinocytes at the wound margin activate, lose their cell-cell adhesion, and begin migrating inward to re-cover the wound surface. These marginal cells also proliferate to supply additional daughter cells, which are biased toward the wound center. As the migrating sheet advances and cells stack vertically through crowding-driven extrusion, the wound gradually closes with a stratified epithelium that matures into a functional barrier.

Model

• WoundEvent zeros Stratum, Calcium, O2 fields in the wound cylinder at the configured trigger step
• Spawns basal keratinocytes at the wound margin, spacing them by one cell diameter around the perimeter
• Inward division bias (wound_inward_bias) preferentially directs daughter cells toward the wound center, reproducing the centripetal migration sheet observed in vivo
• Crowding-driven vertical extrusion builds stratified layers as the wound bed fills
• WoundResolution provides a safety timeout that removes residual agents 200 steps before simulation end or at greater than 90% Stratum coverage, whichever comes first

Parameters

From modules/wound/config.toml:

Parameter	Default	Units	Description	Source
enabled	true	bool	Master switch	Convention
center_x	15.0	um	X-center of punch biopsy	Convention
center_y	15.0	um	Y-center of punch biopsy	Convention
radius	5.0	um	Radius of circular wound	Convention
trigger_h	0	hours	Hours at which wound fires	Convention
inward_bias	0.3	0 to 1	Division bias toward wound center	Calibrated
vascular_damage	0.5	fraction	Legacy vascular damage (superseded by perfusion module)	Calibrated

Coupling

Reads

Field	Source module	How used
Stratum	tissue	Coverage check for wound closure percentage

Writes

Field	Consumer modules	What is written
Stratum	tissue, scar	Zeros in wound cylinder
Calcium	tissue	Zeros in wound cylinder
O2	tissue	Zeros in wound cylinder
Vascular	perfusion	Damage proportional to vascular_damage

Validation

Dataset	Observable	Sources	Notes
closure_kinetics_punch_biopsy	Wound closure percentage over time	Eaglstein 1978, Cukjati 2000, Pastar 2014	Sigmoid closure curve, approximately 22 days to 90%

Literature data

Reference curves for validation (full citations in SOURCES.yaml):

Dataset	File	Normalization
Closure kinetics (punch biopsy)	closure_kinetics_punch_biopsy.csv	Absolute 0 to 100%

Raw digitized data (3 papers)

File	Source
eaglstein1978_closure.csv	Eaglstein et al. 1978
cukjati2000_closure.csv	Cukjati et al. 2000
pastar2014_closure.csv	Pastar et al. 2014

Metrics

Column	Units	Description
wound_closure_pct	%	Fraction of wound voxels with Stratum > 0.5

Source files

File	Purpose
wound_event.h	Wound creation, field zeroing, agent spawning, resolution
config.toml	Module configuration