Minimal Genome Designer: Synthetic Cell Viability

Gene Modules

Replication & Repair 70%

DNA polymerase, ligase, mismatch repair — essential floor 35%

Core Metabolism 75%

Glycolysis, ATP synthase, nucleotide synthesis — essential floor 50%

Membrane & Transport 55%

Lipid synthesis, ion pumps, nutrient import — essential floor 30%

Stress & Repair Buffer 30%

Chaperones, oxidative defence — no strict essential floor

Genome Readout

Viability0%

Genome size

0 genes

Doubling time

—

Robustness

0.0×

Colony size

1 / 24

—

How it works

Every deletable gene module has an essential floor — the fraction below which the module can no longer sustain life at all, echoing how real minimal-genome projects (JCVI-syn3.0, ~473 genes) found genes fall into essential, quasi-essential, and dispensable classes rather than a single "needed / not needed" line.

viability = Π clamp01((f_i − floor_i) / (1 − floor_i))^0.6   over 4 modules
doubling time (min) = 60 / (0.25 + Σ f_i · growthWeight_i)
robustness = Σ f_i · robustWeight_i   (lowers per-division death chance)
genome size = 60 (fixed core) + Σ f_i · fullGeneCount_i

Sliders — set each module's completeness as a fraction of its full wild-type gene complement. Drop any module under its essential floor and viability collapses toward zero.
Colony — a founder cell divides into up to 24 fixed lattice slots. Division rate follows the doubling-time formula above; each division carries a small death chance set by robustness — a genome stripped of stress/repair genes divides fast but is fragile.
Trade-off — maximum growth speed and maximum robustness pull sliders in opposite directions, exactly the tension synthetic biologists face when engineering a minimal chassis cell: smaller genomes replicate faster but tolerate less.

Real-world relevance: this is the same design trade-off behind minimal synthetic genomes used as engineering chassis for biofuels, biosensors and drug production — remove everything not load-bearing, but keep enough of a buffer that the cell survives real-world stress.

Living cell Dividing Empty slot

t = 0.0s
gen = 0

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