v2ecoli — composite comparison

Summary metrics

Δ% vs reference; divergence badge where a tolerance applies (within tol ≤ tol, drift ≤ 3·tol, else mismatch).

Metric	vEcoli 1.0 (vivarium) reference	v2ecoli:baseline (process-bigraph)	v2ecoli:millard_fba_bridge_harness (process-bigraph)
Performance
Load time (s)	1.7	5.8	6.6
Wall time (s)	221.5	220.0	662.7
Sim time reached (s)	2520	2450	2520
Realtime factor (×)	11.4	11.1	3.8
Runtime, per-step (v2ecoli engines)
Step time, mean (ms / sim-s)	0.0	76.0	263.8
Step time, median (ms / sim-s)	0.0	74.1	262.7
Step time, p95 (ms / sim-s)	0.0	81.1	288.9
Peak memory, RSS (MB)	0	1951	1893
Growth
Dry mass, initial (fg)	383.7	380.6within tol	380.6within tol
Dry mass, final (fg)	697.1	696.9-0.0%within tol	681.7-2.2%within tol
Dry-mass fold change	1.8168	1.8311+0.8%within tol	1.7910-1.4%within tol
Mean growth rate (1/s)	2.435e-04	2.550e-04+4.7%within tol	2.331e-04-4.3%within tol
Composition (final)
Protein mass (fg)	312.6	311.3-0.4%within tol	314.8+0.7%within tol
RNA mass, total (fg)	93.7	94.2+0.6%within tol	88.5-5.6%drift
rRNA mass (fg)	76.1	76.2+0.1%within tol	72.1-5.2%drift
tRNA mass (fg)	13.7	13.7-0.2%within tol	13.1-4.7%within tol
mRNA mass (fg)	3.86	4.35+12.7%drift	3.25-15.9%drift
DNA mass (fg)	12.3	12.2-1.0%within tol	12.2-0.8%within tol
Small-molecule mass (fg)	277.7	278.3+0.2%within tol	265.5-4.4%within tol
Water mass (fg)	1625.2	1624.8-0.0%within tol	1589.5-2.2%within tol
Cell volume (fL)	2.111	2.111-0.0%within tol	2.065-2.2%within tol
Metabolism (final)
FBA objective value	0.000e+00	8.967e-01n/a	8.279e-01n/a
Molecular species (final)
Bulk molecules, total count	54885246031	54871204569-0.0%within tol	53665817570-2.2%within tol
Bulk species present (count>0)	5160	5180+0.4%within tol	5166+0.1%within tol
Bulk species, distinct	16321	16321	16321
Unique molecules (final)
Chromosomes	2	2	2
Replication forks	4	4	4
Snapshots	51	49	52

Per-step runtime (wall ms / sim-second)

Lower is faster. A rising curve = the cell getting more expensive per sim-second as it grows (more molecules to update). Range 0…335 ms/sim-s. vEcoli engines do not emit per-step timing and are absent here.

vEcoli 1.0 (vivarium)v2ecoli:baseline (process-bigraph)v2ecoli:millard_fba_bridge_harness (process-bigraph)

FBA-bridge flux-pin diagnostics

The Millard 2017 central-carbon ODE feeds fba-flux-coupler, which pins v2ecoli FBA reactions to the ODE-derived fluxes; ecoli-metabolism relaxes any pin that makes the LP infeasible. n/a = engine has no bridge (unpinned FBA). Comparing the FBA objective pinned vs unpinned shows the cost the flux-pin imposes on the metabolic solution.

Bridge diagnostic	vEcoli 1.0 (vivarium)	v2ecoli:baseline (process-bigraph)	v2ecoli:millard_fba_bridge_harness (process-bigraph)
Reactions pinned (final tick)	n/a	n/a	24
Pins relaxed as infeasible (final)	n/a	n/a	14
Pins relaxed, peak over run	n/a	n/a	14
Non-zero pin targets (final)	n/a	n/a	24
Central fluxes non-zero (final)	n/a	n/a	66
Central flux \|mean\| (mM/s, final)	n/a	n/a	2.532e-01
FBA objective value (final)	—	8.967e-01	8.279e-01

Per-reaction flux divergence (metabolism deep-dive)

Opens up the single FBA objective / central flux |mean| numbers above: each row is a base reaction (isozyme / fwd-rev variants lumped), flux is the per-reaction signed mean over the run (mmol·gDCW⁻¹·h⁻¹). Caveat: FBA has alternate optimal solutions, so reversible reactions and TCA/PPP branch points can differ even at matched growth — a near-identical FBA objective can still hide per-pathway flux reshuffling, which is exactly what this section surfaces.

base reactions: v2ecoli:baseline (process-bigraph) 2820, v2ecoli:millard_fba_bridge_harness (process-bigraph) 2820
v2ecoli:millard_fba_bridge_harness (process-bigraph) vs v2ecoli:baseline (process-bigraph): identical reaction set

193 reactions carry materially different flux (|Δ| ≥ 0.001, rel ≥ 25%) vs v2ecoli:baseline (process-bigraph) (the reference).

Pathways with the largest flux divergence

Pathway / EC bucket	#reactions	Σ\|Δflux\|
transport (named)	18	5.07e+03
named reaction	163	3.53e+03
transferase	3	0.237
hydrolase	5	0.161
lyase	2	0.0297
oxidoreductase (redox)	2	0.0279

Sign-flipped reactions (11) — flux reverses direction

Reaction (direction differs)	v2ecoli:baseline (process-bigraph)	v2ecoli:millard_fba_bridge_harness (process-bigraph)
`PGLUCISOM-RXN`	0.264	-75.3
`GAPOXNPHOSPHN-RXN`	0.755	-74.7
`PHOSGLYPHOS-RXN`	-0.755	74.7
`2PGADEHYDRAT-RXN`	0.754	-74.7
`3PGAREARR-RXN`	-0.754	74.7
`TRIOSEPISOMERIZATION-RXN`	-0.346	75.1
`F16ALDOLASE-RXN`	0.154	-75.1
`ASPAMINOTRANS-RXN`	0.214	-0.237
`GLUTDEHYD-RXN`	0.116	-0.202
`DEOXYRIBOSE-P-ALD-RXN`	-0.00187	0.00931
`D-PPENTOMUT-RXN`	-0.0018	0.00938

Top 40 reactions by |Δflux| vs v2ecoli:baseline (process-bigraph)

Reaction	Pathway/EC	v2ecoli:baseline (process-bigraph) reference	v2ecoli:millard_fba_bridge_harness (process-bigraph)	Δ vs ref	rel
`TRANS-RXN-300`	transport (named)	0	2.3e+03	2.3e+03	100%
`TRANS-RXN-121`	transport (named)	0.000443	2.3e+03	2.3e+03	100%
`FLAVONADPREDUCT-RXN`	named reaction	-0.0206	-495	495	100%
`PYFLAVOXRE-RXN`	named reaction	-0.0193	-495	495	100%
`PYRUVDEH-RXN`	named reaction	0.0185	495	495	100%
`ATPSYN-RXN`	named reaction	-7.58	-470	463	98%
`TRANS-RXN0-277`	transport (named)	0	-420	420	100%
`F16BDEPHOS-RXN`	named reaction	0.013	313	313	100%
`6PFRUCTPHOS-RXN`	named reaction	0.169	238	237	100%
`PGLUCISOM-RXN`	named reaction	0.264	-75.3	75.5	100%
`6PGLUCONOLACT-RXN`	named reaction	0.269	75.7	75.5	100%
`GLU6PDEHYDROG-RXN`	named reaction	0.269	75.7	75.5	100%
`GAPOXNPHOSPHN-RXN`	named reaction	0.755	-74.7	75.5	101%
`PHOSGLYPHOS-RXN`	named reaction	-0.755	74.7	75.5	101%
`2PGADEHYDRAT-RXN`	named reaction	0.754	-74.7	75.5	101%
`3PGAREARR-RXN`	named reaction	-0.754	74.7	75.5	101%
`TRIOSEPISOMERIZATION-RXN`	named reaction	-0.346	75.1	75.4	100%
`KDPGALDOL-RXN`	named reaction	0	75.3	75.3	100%
`PGLUCONDEHYDRAT-RXN`	named reaction	0	75.3	75.3	100%
`F16ALDOLASE-RXN`	named reaction	0.154	-75.1	75.2	100%
`PEPSYNTH-RXN`	named reaction	0	75.1	75.1	100%
`ADENYL-KIN-RXN`	named reaction	0.546	75.7	75.1	99%
`GLUCOSE-6-PHOSPHATE-1-EPIMERASE-RXN`	named reaction	0	50.8	50.8	100%
`TRANS-RXN0-601`	transport (named)	-31	0	31	100%
`TRANS-RXN-218`	transport (named)	15.5	0	15.5	100%
`MALATE-DEH-RXN`	named reaction	-0.59	-0.121	0.469	79%
`FUMHYDR-RXN`	named reaction	0.555	0.1	0.455	82%
`ASPAMINOTRANS-RXN`	named reaction	0.214	-0.237	0.451	190%
`ASPARTASE-RXN`	named reaction	-0.587	-0.145	0.442	75%
`TRANS-RXN0-574`	transport (named)	0.554	0.151	0.403	73%
`RXN0-7077`	named reaction	0	0.354	0.354	100%
`GLUTDEHYD-RXN`	named reaction	0.116	-0.202	0.318	158%
`RXN0-313`	named reaction	0.209	-0.000548	0.209	100%
`ALDOSE-1-EPIMERASE-RXN`	named reaction	0	0.197	0.197	100%
`2.7.1.121-RXN`	transferase	0.167	0	0.167	100%
`PEPDEPHOS-RXN`	named reaction	-0.155	0	0.155	100%
`RXN-11811`	named reaction	-0.128	-0.277	0.149	54%
`RXN-20084`	named reaction	-0.0921	-0.237	0.145	61%
`ENOYL-ACP-REDUCT-NADPH-RXN`	named reaction	-0.0019	-0.127	0.125	98%
`RXN-9952`	named reaction	0.268	0.392	0.124	32%

Behavioral overlays (shared axis)

All engines on one auto-scaled axis per observable; line height is comparable across engines. Divergence between curves is real behavioral divergence.

vEcoli 1.0 (vivarium)v2ecoli:baseline (process-bigraph)v2ecoli:millard_fba_bridge_harness (process-bigraph)

Dry mass

fg · range: 0 … 697

Protein mass

fg · range: 0 … 315

RNA mass

fg · range: 0 … 94.2

DNA mass

fg · range: 0 … 12.3

Small molecules

fg · range: 0 … 278

Cell volume

fL · range: 0 … 2.11

Growth rate

1/s · range: 0 … 0.000316

Bulk total count

molecules · range: 0 … 5.49e+10

Trajectories over time

Each line spans t=0 → end of run, auto-scaled per cell (shapes comparable, absolute heights not).

Trajectory	vEcoli 1.0 (vivarium)	v2ecoli:baseline (process-bigraph)	v2ecoli:millard_fba_bridge_harness (process-bigraph)
Dry mass
Protein
RNA
DNA
Small molecules
Volume
Bulk total count

Unique molecular species (final counts)

Active count per unique-molecule type at end of run; Δ% vs the reference engine.

Unique molecule	vEcoli 1.0 (vivarium)	v2ecoli:baseline (process-bigraph)	v2ecoli:millard_fba_bridge_harness (process-bigraph)
DnaA_box	826	814-1%	820-1%
RNA	6237	6695+7%	5147-17%
active_RNAP	1331	1445+9%	1035-22%
active_replisome	4	4+0%	4+0%
active_ribosome	25434	25519+0%	24125-5%
chromosomal_segment	0	0	0
chromosome_domain	7	7+0%	7+0%
full_chromosome	2	2+0%	2+0%
gene	11772	11642-1%	11662-1%
oriC	4	4+0%	4+0%
promoter	8478	8378-1%	8390-1%