Toxic, intermediate, detoxified.
Each biochemical channel maps a metal species into balanced ternary values. The processor can represent uncertainty and partial transformation directly instead of forcing every result into binary yes/no logic.
Toxic
Original hazardous or bioavailable form. Examples: methylmercury, arsenate, free cuprous copper, cadmium, chromate.
Intermediate
Reduced, oxidized, bound, or partially transported species. This middle state is the key advantage over binary biosensing.
Detoxified
Volatilized, effluxed, sequestered, precipitated, or otherwise biologically neutralized product.
Twenty operon-backed trits.
The source project maps metal-resistance operons into independent biochemical channels. Each channel provides a three-state pathway that can be read, routed, transformed, and combined.
Natural detoxification as computation.
Operations are performed by moving chemical species through enzymatic transitions. A channel becomes a physical trit register when its concentration profile is stabilized in a microfluidic compartment.
Mercury / mer
-1 toxic
demethylase
0 intermediate
reductase
+1 volatile
Arsenic / ars
-1 input
reduction
0 state
efflux
+1 removed
Copper / cop
-1 reactive
oxidation
0 bound
transport
+1 safe
Sixteen gates on biochemical states.
The original React project defines primitive, composite, arithmetic, and unary ternary gates. This static version keeps the reference table compact and readable.
| Gate | Formula | Biochemical interpretation |
|---|---|---|
| T-AND | min(A,B) | Selects the most toxic or least processed state. |
| T-OR | max(A,B) | Propagates the most detoxified state. |
| T-NOT | -A | Inverts toxic and detoxified states while neutral remains neutral. |
| T-NAND | -min(A,B) | Functionally complete gate built from cautious selection plus inversion. |
| T-CONS | A = B -> A, else 0 | Consensus voting for redundant chambers. |
| T-SUM | (A + B) mod 3 | Balanced ternary addition for biochemical counters and adders. |
| T-MED | median(A,B,0) | Neutral-clamped majority gate for noisy reaction outputs. |
| T-CYC | -1 -> 0 -> +1 -> -1 | Sequential transformation through a cyclic metal pathway. |
From sample to ternary output.
The processor combines microfluidics, immobilized engineered cells, cofactor management, biosensors, ternary ALU chemistry, and electronic readout.
Trinary Registers
Biological micro-compartments store concentration profiles for -1, 0, and +1 states using semi-permeable membranes.
Biochemical Bus
Diffusion channels and pneumatic valves route metal species between registers, sensors, and ALU chambers.
Trinary ALU
Enzymatic gates perform logical, arithmetic, and unary operations over metal-state inputs.
Control Unit
pH pulses, UV/blue light, cofactors, and thermal zones synchronize biochemical operation cycles.
FPGA Interface
Optical and electrochemical outputs are digitized into trits for electronic post-processing.
CRISPR Memory
DNA spacer arrays provide persistent ternary storage and programmable biological state history.
Quorum Network
AHL signaling synchronizes populations in distributed biofilm computing layouts.
Biocontainment
Auxotrophy, kill-switches, and waste segregation isolate engineered organisms from the environment.
Where trinary biology matters.
Three-state outputs are useful when real-world chemistry has danger, caution, and safe zones rather than binary thresholds.
Environmental Bioremediation
Autonomous colonies detect and detoxify mercury, arsenic, cadmium, and copper gradients in water or soil.
Water Quality Biosensors
Tri-level risk classification for remote monitoring: danger, caution, or compliant.
Food Safety
Rapid methylmercury screening in fish and seafood using regulatory thresholds.
Medical Diagnostics
Point-of-care heavy-metal exposure classification from blood or urine panels.
Industrial Wastewater
Adaptive treatment that responds to chemical speciation, not just total concentration.
Bio-Computing Education
Microfluidic teaching kits for non-binary logic, synthetic biology, and biochemical gates.
Ten phases from construct to processor.
This roadmap condenses the source implementation plan into a static engineering checklist.
Genetic Engineering
Clone mer, ars, cop, cad and supporting operons into stable chassis strains; verify activity assays and reporter outputs.
Microfluidic Fabrication
Design masks, fabricate SU-8 molds, cast PDMS channels, bond to glass, and condition surfaces.
Cell Immobilization
Load engineered cells into alginate or chitosan chambers and verify viability after gelation.
Calibration
Build dose-response curves, set trinary thresholds, and validate truth tables across all input combinations.
Directed Evolution
Improve enzyme turnover and thermal stability to shorten trinary operation cycles.
CRISPR & Optogenetics
Add light-controlled CRISPRi/CRISPRa to reconfigure logic without rebuilding strains.
Multi-Metal Assembly
Integrate twenty operons, test orthogonality, and quantify cross-talk across metal pairs.
Biosensor Array
Multiplex fluorescence, colorimetry, luminescence, and electrochemistry into parallel readout.
System Integration
Connect registers, ALU, valve matrix, waste manifold, FPGA interface, and dashboard.
Safety Certification
Validate containment, metal waste handling, BSL procedures, and fail-safe operating modes.
Scientific basis.
The concept draws on mercury resistance, metal efflux systems, biosensors, microfluidics, and ternary logic research.
- Ralston & O'Halloran, MerR mercury regulator binding studies.
- Barkay et al., bacterial mercury resistance and mer operon biology.
- Fox & Walsh, mercuric reductase enzymology.
- Lafrance-Vanasse et al., organomercurial lyase MerB structure and mechanism.
- Grass & Rensing, copper homeostasis and resistance systems.
- Ackerley et al., chromate reductase activity and bioremediation.
- Messens et al., arsenate reductase mechanisms.
- Microfluidic Quake valve architecture for biological processors.
- CRISPR memory and optogenetic gene regulation literature.
- Balanced ternary and trinary logic gate references.