Run provenance · 2026-04-12 13:15:12 EDT · nutrient-growth@43a3ab7 [uncommitted changes] · eranagmon@LT-0919936 · Darwin 24.2.0 arm64 (16 cores) · Python 3.12.9

E. coli Whole-Cell Simulation Comparison

Three-way comparison of vEcoli 1.0 (vivarium engine), vEcoli 2.0 (composite migration), and v2ecoli (pure process-bigraph). All use the same ParCa parameters, initial state, and biological process logic.

Performance

vEcoli 1.0 (vivarium)

11.5x

219s wall for 2520s sim

vEcoli 2.0 (composite)

11.0x

228s wall for 2520s sim

v2ecoli (pure PBG)

11.7x

216s wall for 2520s sim

Metric	vEcoli 1.0	vEcoli 2.0	v2ecoli
Engine	vEcoli 1.0 (vivarium)	vEcoli (vivarium/composite)	v2ecoli (process-bigraph)
Load time	1.95s	2.32s	3.19s
Sim duration	2520s (42.0 min)	2520s (42.0 min)	2520s (42.0 min)
Wall time	218.9s	228.1s	215.6s
Speed	11.5x	11.0x	11.7x
Final dry mass	707.2 fg	707.2 fg	696.6 fg
Chromosomes	2	2	2
Forks	4	4	4

Growth Comparison

Chromosome Replication

Mass Components (side-by-side)

Dry Mass Comparison Table (fg)

Time	vEcoli 1.0	vEcoli 2.0	v2ecoli
0 min	383.7	380.9	380.9
1 min	383.7	383.7	383.9
5 min	406.4	406.4	407.7
10 min	436.9	436.9	437.7
20 min	507.9	507.9	506.7
30 min	589.1	589.1	586.7
40 min	686.0	686.0	677.3