vEcoli vs v2ecoli — Runtime & Behavior

Runtime and growth-behavior comparison of vEcoli — the established vivarium-based E. coli whole-cell model — and v2ecoli, the current process-bigraph baseline. Each engine runs from its own ParCa-generated sim_data (vEcoli's regenerated from current master; v2ecoli's from its own cache) over the same simulated duration, so the comparison reflects engine and runtime differences rather than a re-parameterization of the biology.

Performance

vEcoli (vivarium)
12.2x
206s wall for 2520s sim
v2ecoli (process-bigraph)
15.5x
163s wall for 2520s sim
MetricvEcoli (vivarium)v2ecoli (process-bigraph)
EnginevEcoli 1.0 (vivarium)v2ecoli (process-bigraph)
Load time1.68s5.15s
Sim duration2520s (42.0 min)2520s (42.0 min)
Wall time205.9s162.9s
Speed12.2x15.5x
Final dry mass707.2 fg705.3 fg
Chromosomes22
Forks44

Growth Comparison

Dry Mass
Cell Mass
Growth Rate
Volume

Chromosome Replication

Chromosomes
Replication Forks

Mass Components (side-by-side)

Mass Components
RNA Breakdown
Structural Components

Dry Mass Comparison Table (fg)

TimevEcoli (vivarium)v2ecoli (process-bigraph)
0 min383.7379.7
1 min383.7382.7
5 min406.4405.3
10 min436.9436.0
20 min507.9512.0
30 min589.1592.3
40 min686.0684.7
Generated 2026-05-31 21:27 EDT · git c6fbba2 · eranagmon@LT-0919936 · python 3.12.12 · Darwin