Peptide Amphiphile Nanofiber Self-Assembly

Assembly Conditions

Monomer concentration 120 monomers

Ionic strength (screens headgroup charge) 100 mM

Temperature 300 K

β-sheet H-bond propensity 0.65

Live Readouts

Nematic order S

0.00

Assembled fraction

Largest fiber (monomers)

How it works

Each rod represents a peptide-amphiphile monomer: a hydrophobic alkyl tail fused to a short β-sheet-forming peptide segment ending in a charged headgroup (the same design used in real self-assembling PA nanofibers, e.g. Stupp-lab biomaterials). Three competing pairwise forces act between monomer centers separated by distance r:

Hydrophobic core burial (Lennard-Jones):
  U_LJ(r) = 4ε[(σ/r)^12 − (σ/r)^6]      → pulls tails together, resists overlap

Screened electrostatic repulsion (Debye–Hückel / Yukawa):
  F_elec(r) ∝ exp(−r/λ_D) · (1/r² + 1/(rλ_D))
  λ_D ≈ 0.304 / √I  nm  (I = ionic strength, mol/L)

Directional H-bond alignment (β-sheet registry, nematic coupling):
  dn_i/dt ∝ β · Σ_j sign(n_i·n_j)(n_j − (n_i·n_j)n_i)

Hydrophobic collapse drives monomers to aggregate; screened electrostatic repulsion between like-charged headgroups is what self-limits the aggregate to a thin cylinder instead of a bulk droplet (this is the same curvature-selection argument used for surfactant micelles and worms); the alignment term reproduces the directional hydrogen bonding that locks β-strands into a common register, elongating the aggregate into a fiber rather than a blob. Motion is overdamped Langevin dynamics (thermal noise scales with temperature, √(2DΔt)) with a clamped, capped timestep.

Concentration — below the effective critical aggregation concentration (CAC) monomers stay dispersed; above it, nanofibers nucleate and grow.
Ionic strength — added salt shrinks the Debye length λ_D, screening headgroup repulsion so fibers assemble faster and pack thicker (as observed experimentally for PA nanofibers).
Temperature — higher T adds thermal agitation that can outrun the hydrophobic/H-bond driving forces and disassemble fibers.
β-sheet propensity — the strength of backbone hydrogen-bond registry; low values give disordered clumps, high values give long aligned fibers (teal rods = assembled, grey = free monomer).

Assembled monomer Free monomer (solution)

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