Collagen Fibril Self-Assembly Simulator

Assembly Conditions

Temperature 37 °C

pH 7.4

Collagen concentration 1.5 mg/mL

Fibrillogenesis State

Lag phase (nucleation)

Assembled: 0%Free monomers: 0

Fibrils nucleated

Avg fibril length

0 nm

Elapsed (simulated)

0.0 min

Assembly rate k

0.00 /s

How it works

Collagen fibrillogenesis is the self-assembly of soluble triple-helix collagen monomers into insoluble, striated fibrils — the same process biotechnology labs drive in vitro to biofabricate collagen scaffolds, wound dressings and tissue-engineered constructs. It follows classic nucleation-growth kinetics with a sigmoidal (lag → growth → plateau) time course:

k(T,pH,c) = k0 · exp(-(T-37)²/2σT²) · exp(-(pH-7.4)²/2σpH²) · (c/c0)^1.3

dN_free/dt  = -k·N_free            (monomers consumed)
dL_fibril/dt = k·(monomers available)   (fibril elongation)

Each rate-limited step consumes a free monomer and appends it to a growing fibril tip, exactly like the nucleation-and-linear-growth model measured by turbidity assays (Kadler et al., 1996; Silver & Birk, 1983). Three conditions set the rate constant k:

Temperature — assembly is fastest near 37 °C (body temperature). Near 4 °C collagen solutions stay soluble for hours — the reason purified collagen is stored and pipetted on ice before an assay is warmed to trigger gelation.
pH — fibril formation is fastest near physiological pH 7.4; far from neutral the monomer's surface charge disrupts the lateral packing needed to nucleate a fibril.
Concentration — higher monomer concentration raises both the nucleation rate and the total material available, shortening the lag phase (visible in the readouts as more, and longer, fibrils per minute).

The alternating light/dark bands on each fibril are a stylized rendering of the real 67 nm axial D-period created by the quarter-staggered packing of collagen molecules — the same banding pattern that identifies a fibril under electron microscopy.

Free collagen monomer Fibril (overlap band) Fibril (gap band)

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