The 3D companion shows a single N-body block being eaten in real time. This 2D version keeps the same lattice-erosion mechanic in a cheaper top-down cross-section, but plots the two numbers the 3D scene never graphs over time: the depolymerization rate and the cumulative monomer yield, as rolling strip charts under the block. It also adds a control the 3D scene has no equivalent for — protein-engineering level, which models what real directed-evolution campaigns (FAST-PETase, LCC-ICCG) actually changed: a higher melting-equilibrium temperature and a boosted catalytic prefactor, not just "more enzyme".
The 3D scene's thermal term also had its equilibrium sign flipped — its activity rose monotonically with temperature instead of the bell-shaped optimum its own on-page description promised. This 2D engine uses the corrected form of the Daniel–Danson equilibrium model, so raising temperature past the effective melting point genuinely costs you activity again:
k_cat(T) = A_eff · exp(−Ea / R·T) (Arrhenius catalytic step)
K_eq(T) = exp[(ΔH_eq/R) · (1/T_eq,eff − 1/T)] (unfolding equilibrium)
F_active(T) = 1 / (1 + K_eq(T)) (fraction correctly folded)
rate(T) = k_cat(T) · F_active(T) → bell-shaped optimum near T_eq,eff
Engineering level m (0–1):
T_eq,eff = T_eq + m·ΔT_shift (higher thermostability)
A_eff = A · (1 + m·boost) (higher intrinsic turnover)
- Temperature — raises the raw catalytic rate constant (Arrhenius), but past the enzyme's effective melting equilibrium an increasing fraction of the population reversibly unfolds and stops working, producing a genuine thermal optimum.
- Enzyme concentration — sets how many enzyme molecules are hunting the surface at once; throughput rises roughly linearly at low concentration, then saturates as the shrinking exposed surface itself becomes the bottleneck — the same Michaelis-Menten-shaped saturation real heterogeneous biocatalysis shows with respect to enzyme loading.
- Protein-engineering level — shifts the melting equilibrium to a higher temperature and boosts the catalytic prefactor, matching how real thermostabilized PETase variants shift their optimum right and raise their ceiling rather than simply working "faster at every temperature".
- Crystallinity is held fixed here (roughly a third of the lattice) so the charts isolate the effect of temperature, concentration and engineering — the 3D scene is the place to explore crystallinity itself.