Trinary
Biochemical Metal
Processor PMBT
A revolutionary biological processor concept inspired by metal-resistant bacteria. Exploiting natural biochemical transformations of heavy metals to implement three-state trinary logic — each metal provides a distinct toxic → intermediate → detoxified pathway, yielding 1.58 bits per trit of information density.
The mer, ars, cop, cad, czc, chr, pbr, cnr, ter, ncc, sil, ser, mtr, and mnx, tup, van, mod, tll, and bir operons provide independent enzymatic machinery for 20 metals. Each metal's three chemical states act as biochemical logic gates — natural detoxification reinterpreted as multi-channel trinary computation. 16 logic gates, 48 use cases — from nuclear waste bioremediation to nanoparticle synthesis and space bio-processing.
Biochemical Trinary Logic
Each compatible metal provides three distinct chemical states encoding -1, 0 and +1.
Three distinct chemical states of mercury encode the logical values. The mer operon provides complete enzymatic machinery for reversible mercury transformations.
MeHg (Methylmercury)
Highly toxic organic form of mercury. Represents the most negative state in our trinary logic.
Hg²⁺ (Ionic Mercury)
Inorganic ionic form, intermediate product of demethylation by MerB. Neutral state of the logic.
Hg⁰ (Elemental Mercury)
Reduced volatile form produced by MerA. Mercury is rendered inert and evaporates. Maximum positive state.
Réduction séquentielle du mercure organiquе — Voie MerB/MerA
CH₃Hg⁺ + H⁺ →[MerB] Hg²⁺ + CH₄ ; Hg²⁺ + NADPH →[MerA] Hg⁰↑ + NADP⁺
Tableau Comparatif
Vue synthétique des 20 métaux, opérons, mécanismes et états trits
| Métal | Opéron | Mécanisme | −1 | 0 | +1 |
|---|---|---|---|---|---|
HgMercury | mer | Réduction | MeHg (Methylmercury) | Hg²⁺ (Ionic Mercury) | Hg⁰ (Elemental Mercury) |
AsArsenic | ars | Réduction | Organo-As (MMA/DMA) | As(III) (Arsenite) | As(V) effluxed (Arsenate) |
CuCopper | cop | Réduction | Cu⁺ (Cuprous, free) | Cu²⁺ (Cupric) | Cu effluxed (Sequestered) |
CdCadmium | cad | Réduction | Cd²⁺ (Free cytoplasmic) | Cd-MT (Sequestered) | Cd²⁺ effluxed (Expelled) |
ZnZinc | czc/znt | Réduction | Zn²⁺ (Free cytoplasmic) | Zn-MT (Metallothionein-bound) | Zn²⁺ effluxed |
CrChromium | chr | Réduction | CrO₄²⁻ — Cr(VI) | Cr(III) soluble | Cr(OH)₃ precipitate |
PbLead | pbr | Réduction | Pb²⁺ (Free cytoplasmic) | Pb-phosphate (intracellular) | Pb₃(PO₄)₂ effluxed |
CoCobalt | cnr | Réduction | Co²⁺ (Free cytoplasmic) | Co-chaperone complex | Co²⁺ effluxed |
TeTellurium | ter/teh | Précipitation | TeO₃²⁻ — Tellurite | TeO₄²⁻ — Tellurate | Te⁰ (Black crystals) |
NiNickel | ncc/cnr | Réduction | Ni²⁺ (Free cytoplasmic) | Ni-HypAB (chaperone-bound) | Ni²⁺ effluxed |
AgSilver | sil | Réduction | Ag⁺ (Free ionic) | Ag-SilE (periplasmic chaperone) | Ag⁺ effluxed / Ag⁰ NPs |
SeSelenium | selenite reductase | Précipitation | SeO₃²⁻ (Selenite) | Se⁰ nanoparticles (red) | Se²⁻ / Org-Se (selenocysteine) |
SbAntimony | ars (Sb-specific) | Réduction | Sb(III) / SbO⁺ (Antimonite) | Sb(V) (Antimonate) | Sb(III) effluxed |
UUranium | Cytochrome-based | Précipitation | UO₂²⁺ (Uranyl, soluble) | U(V) (transient) | UO₂ (Uraninite, insoluble) |
MnManganese | mnt/mnx | Précipitation | Mn²⁺ (excess free ionic) | Mn²⁺ (regulated homeostasis) | MnO₂ (Birnessite, insoluble) |
WTungsten | tup/wtp | Précipitation | WO₄²⁻ (Tungstate excess) | W-MPT (Tungstopterin) | WS₂↓ (Tungstenite) |
VVanadium | van/vna | Précipitation | VO₄³⁻ (Vanadate V(V)) | VO²⁺ (Vanadyl V(IV)) | V₂O₃↓ (Vanadium oxide ppt) |
MoMolybdenum | mod | Précipitation | MoO₄²⁻ (Molybdate excess) | Mo-PPT (Molybdopterin) | MoS₂↓ (Molybdenite) |
TlThallium | tll | Précipitation | Tl⁺ (Thallous Tl(I)) | Tl-MnOx (Sorbed) | Tl₂O₃↓ (Tl(III) oxide) |
BiBismuth | bir | Efflux | Bi³⁺ (Bismuth ion) | Bi-thiol (Chelated) | Bi₂S₃↓ (Bismuthinite) |
Pipeline de Traitement Trinary
Architecture générale du processeur biochimique — de l'entrée du métal au trit encodé
Truth Tables
Sixteen trinary logic operations — spanning primitives (min, max, negation), composites (implication, equivalence, consensus, median, threshold), arithmetic (modular addition, multiplication, subtraction), and unary transforms (cyclic shift, absolute value, floor clamp) — form a functionally complete and expressive basis for arbitrary trinary computation on biochemical metal states.
T-AND
Primitivesf(A, B) = min(A, B)
Returns the lowest of two trit values. In biochemical terms, this gate selects the most toxic / least-processed metal species from two inputs — modeling a worst-case or cautious assessment. Biochemically realized by competitive inhibition: the slower reaction sets the output state.
Processor Architecture
20 core modules, 17 data/control pathways, a 12-stage operational pipeline, and 6 biochemical subsystems — from sample ingestion through cofactor recycling to CRISPR memory logging.
Functional Chip Schematic
Essential Biochemical Subsystems
The processor relies on 25 metabolic pathways across 6 subsystems that supply energy, cofactors, and cellular protection for sustained trinary computation.
Central Carbon Metabolism
Energy & Reducing Power
Glycolysis
Glucose → 2 Pyruvate + 2 ATP + 2 NADH
Primary carbon catabolism
TCA Cycle
Acetyl-CoA → 2 CO₂ + 3 NADH + FADH₂ + GTP
Complete oxidation & reducing equivalents
Pentose Phosphate
G6P → Ribulose-5P + 2 NADPH + CO₂
NADPH supply for reductases (MerA, ArsC, ChrR)
Oxidative Phosphorylation
NADH + O₂ → NAD⁺ + H₂O + ~2.5 ATP
ATP regeneration (∸36 ATP/glucose)
Complete Operational Pipeline
Sample Ingestion
Microfluidic intake via 20×20 Quake valve matrix (400 individually addressable valves). 20-channel splitter distributes sample to operon-specific chambers. Flow rate: 1–50 µL/min per channel. On-chip degassing and pH pre-conditioning (pH 7.0 ± 0.1 universal buffer).
Core Components (12)
Trinary Registers
Biological micro-compartments storing metal-ion concentration profiles. Each register maintains a stable trinary state (-1/0/+1) through semi-permeable membranes. Compatible with all 20 metals: Hg, As, Cu, Cd, Zn, Cr, Pb, Co, Te, Ni, Ag, Se, Sb, U, Mn, W, V, Mo, Tl, and Bi — each with operon-specific three-state encoding.
Biochemical Bus
Controlled diffusion channels connecting the processor components. Concentration gradients and molecular valves direct the transport of metal solutions between registers and ALU. Multiplexed channels allow parallel routing of different metal species for multi-channel computation.
Trinary ALU
16 biochemical logic gates implemented via operon-specific enzymes: primitives (T-AND, T-OR, T-NOT), composites (T-NAND, T-NOR, T-CONS, T-IMP, T-EQV, T-MED, T-PRJ), arithmetic (T-SUM, T-MUL, T-SUB), and unary transforms (T-CYC, T-ABS, T-FLR). Each of the 20 metal channels operates independently with dedicated enzymatic pathways.
Control Unit
Chemical clock regulating the operation cycle via pH signals, UV light, and enzymatic cofactors (NADPH). Synchronizes reactions and sequences operations. Integrates optogenetic reprogramming via CRISPRi/CRISPRa (blue light 450 nm) to reconfigure logic operations without changing strains.
Bio-Electronic Interface (FPGA)
Hybrid coupling between the biochemical processor and a ternary neural network (TNN) implemented on FPGA via Geobacter. Trinary outputs feed the TNN to combine biochemical parallelism with electronic speed. A software compiler converts programs into biochemical operation sequences.
CRISPR Memory Module
Non-volatile DNA-based memory using CRISPR-Cas spacer arrays for persistent data storage. Each spacer encodes one trit via metal-responsive protospacer sequences. Read/write cycle: ~30 min. Capacity: ~10⁴ trits per cell via multi-array design.
Quorum Signaling Network
Inter-cellular communication for distributed biofilm computing. AHL (acyl-homoserine lactone) signaling molecules synchronize metal-processing states across ~10⁹ cells. Enables massively parallel, fault-tolerant computation with self-organizing behavior.
Metabolic Power Supply
Cellular ATP and NADPH regeneration system fueling enzymatic transformations. Glucose catabolism provides ~38 ATP/glucose via oxidative phosphorylation. NADPH recycled via pentose phosphate pathway at ~2 NADPH/glucose. Self-sustaining with carbon source.
Error Correction Module
Triple Modular Redundancy (TMR) voting system for fault-tolerant trinary computation. Three independent reaction chambers per operation; T-CONS gate selects majority output. CRC-3 checksum appended to multi-trit results. Bit error rate: <10⁻⁶ per trit per cycle.
Thermal Management
Peltier thermoelectric elements with PID feedback control. 5 independent temperature zones: MerA/ChrR chambers at 37°C, MnxG at 25°C, enzyme storage at 4°C, biosensor array at 30°C, and electronics interface at ambient. ±0.1°C precision critical for enzyme kinetics stability.
Cofactor Regeneration Hub
Centralized enzymatic recycling of essential cofactors: NADPH (glucose-6-phosphate dehydrogenase, ~2 NADPH/G6P), ATP (creatine kinase/creatine phosphate), GSH (glutathione reductase + NADPH), SAM (methionine adenosyltransferase), FMN/FAD (riboflavin kinase). Maintains steady-state cofactor pools for all 20 metal channels.
DNA Scaffold Engine
Synthetic DNA origami scaffolds co-localizing sequential enzymes for substrate channeling. Reduces intermediate diffusion distance from ~µm to ~nm. Used in multi-step pathways (MerT→MerA→MerB, ArsC→ArsB, MtrCAB electron relay). 10-100× throughput increase vs. freely diffusing enzymes.
Real Design Components
From concept to realization: the bacterial strains, enzymes, microfluidic systems, and biosensors needed to build a functional prototype.
Candidate Bacterial Strains
Pseudomonas putida KT2440
GRAS-certified model strain for synthetic biology. Serves as the primary cellular chassis — operons for Hg, As, Cu, Cd, Cr are introduced from donor strains. Compatible with CRISPRi/CRISPRa optogenetic reprogramming. Native solvent tolerance facilitates work with diverse metal ions. Hosts up to 8 independent trinary registers.
Cupriavidus metallidurans CH34
The most metal-resistant bacterium known. Two megaplasmids (pMOL28: chr, cnr; pMOL30: mer, cop, cad, czc, pbr) carry at least 8 operons used as gene sources for 10 of the 20 PMBT channels (Hg, As, Cu, Cd, Zn, Cr, Pb, Co, Ni, Te). Also harbors terZABCDE cluster for tellurite resistance and nickel co-resistance via cnr operon. Provides the broadest multi-metal genetic toolkit available in a single organism.
Geobacter sulfurreducens PCA
Strict anaerobe with conductive pili (bacterial nanowires, ~3 nm diameter). Natively reduces U(VI) to UO₂ nanoparticles via PpcA/OmcS cytochromes — the uranium trinary channel. Also enables bio-electronic interfacing: conductive biofilms connect trinary outputs to FPGA-based ternary neural networks for hybrid computation.
Shewanella oneidensis MR-1
Facultative anaerobe with versatile metal reduction via the Mtr electron conduit (MtrCAB/OmcA). Natively reduces U(VI), Cr(VI), Se(VI), and Mn(IV). Provides complementary channels to Geobacter with the advantage of aerobic growth. The MtrCAB pathway enables extracellular electron transfer to insoluble metal oxides.
Alcaligenes xylosoxidans 31A
Primary source of the ncc operon for nickel resistance. NccCBA is an RND-type efflux system with the highest known specificity for Ni²⁺. The ECF sigma factor regulatory system (NccYXH) provides a sensitive and specific biosensor for the nickel trinary channel. Also carries cnr-homolog genes for cobalt co-resistance.
Salmonella enterica (pMG101)
Carries the IncHI1 plasmid pMG101 with the complete sil operon — the most well-characterized silver resistance system. Dual efflux (SilP ATPase + SilCBA RND) with SilE/SilF periplasmic chaperones. Provides the silver trinary channel and enables Ag⁰ nanoparticle biosynthesis for antimicrobial and photonic applications.
Thauera selenatis DSM 11028
Obligate selenate-respiring betaproteobacterium. SerABC is a periplasmic molybdoenzyme that reduces Se(VI) to Se(IV). Further cytoplasmic reduction produces vivid red Se⁰ nanoparticles (50–300 nm) — a visual readout unique among PMBT channels. Source organism for the selenium trinary register.
Bacillus sp. SG-1
Marine spore-forming Bacillus. MnxG is a 138 kDa multi-copper oxidase that catalyzes Mn(II) → MnO₂ (birnessite nanoparticles — black/brown precipitate). Provides the manganese trinary channel with a distinctive visual readout. MnO₂ product also has applications in bio-batteries and water treatment. Requires sea-salt medium for optimal activity.
Deinococcus radiodurans R1
The most radiation-resistant organism known. Engineered to express MerA for Hg remediation in radioactive sites. Its extraordinary DNA repair systems (PprI master switch, RecA/PprA recombination) ensure processor reliability under radiation. The Mn²⁺-antioxidant complex protects enzymes from ROS. Ideal for uranium-contaminated nuclear waste applications.
Rhodopseudomonas palustris CGA009
Versatile purple non-sulfur phototroph. Native ArsM methyltransferase converts As(III) to volatile trimethylarsine — the Challenger pathway origin organism. Photosynthetic metabolism provides NADPH cofactor regeneration via light energy. Also fixes nitrogen. Light-switchable arsenic processing enables optogenetic control of the As trinary channel.
Acidithiobacillus ferrooxidans ATCC 23270
Chemolithoautotrophic acidophile thriving at pH 1.5–2.0. Oxidizes Fe²⁺ and sulfide minerals via rusticyanin-mediated electron transfer. Enables bioleaching of Cu, Zn, Co from sulfide ores and e-waste. Operates in extreme acid conditions where other PMBT strains cannot survive. Provides acidic-route metal dissolution for input preparation.
Desulfovibrio desulfuricans G20
Obligate anaerobic sulfate-reducing bacterium. Produces H₂S which precipitates heavy metals as insoluble metal sulfides (CdS, PbS, ZnS, CuS, HgS). Simultaneously reduces U(VI) and Cr(VI) enzymatically via c-type cytochromes. The sulfide precipitation pathway provides an alternative metal immobilization mechanism distinct from enzymatic reduction.
Enterobacter cloacae HU-1
Facultative anaerobe with broad-spectrum oxyanion reduction capabilities. Multiple chromate reductases (NemA, YieF, NfsA) provide redundant Cr(VI) reduction pathways — high robustness for the chromium trinary channel. Also reduces selenate and antimonite Sb(III) via cross-reactive ArsB/ArsR system. Native tellurite resistance (terZABCDE-like cluster) provides secondary Te channel source. Fast growth rate (doubling time ~30 min) enables rapid trit cycling. Commonly used in industrial bioremediation.
Pyrobaculum aerophilum IM2
Hyperthermophilic crenarchaeon (optimal 100°C) with obligate tungsten requirement. Contains aldehyde:ferredoxin oxidoreductase (AOR) that strictly uses W-MPT over Mo-MPT. Dual tungstate importers (TupABC + WtpABC with picomolar Kd). Validates tungsten channel tungstoenzyme processing under extreme conditions.
Pseudomonas isachenkovii
Facultative anaerobe that uses vanadate [V(V)] as terminal electron acceptor. Tolerates up to 6 g/L VO₄³⁻. Excretes vanadium-binding protein (VBP) that sequesters reduced vanadium extracellularly. Also uses H₂ and CO as electron donors. Primary chassis for the vanadium trinary channel.
Starkeya novella DSM 506
Chemolithoautotrophic soil bacterium with 18 molybdoenzyme loci, complete Mo-PPT pathway, and dedicated ModABC importer with ModE feedback regulation. Model organism for molybdenum cofactor biochemistry. Hosts sulfite oxidase and xanthine dehydrogenase — both require Mo-PPT. Ideal gene donor for the Mo channel.
Bacillus sp. SRHB (Tl-resistant)
Thallium-tolerant spore-forming Bacillus isolated from Tl-contaminated sulfide mine soils. Oxidizes Mn(II) to δ-MnO₂ (birnessite) via MnxG; the biogenic MnO₂ surfaces then oxidize and sequester Tl(I)→Tl(III). This coupled bio-abiotic mechanism provides the detoxification pathway for the thallium channel.
Helicobacter pylori 26695
Microaerophilic pathogen whose RND efflux pump (HP0605/0606/0607) confers resistance to bismuth compounds. Knockout of HP0607 increases Bi susceptibility 4×. Bi(III) also countered by intracellular GSH chelation. Gene donor for the bismuth efflux components of the Bi trinary channel.
Thermus thermophilus HB27
Extreme thermophile (70–80°C) with native tungsten metabolism. Produces W-AOR aldehyde:ferredoxin oxidoreductase and W-DMSO reductase. TupABC imports WO₄²⁻ with Kd ~1 nM — 100× selectivity over MoO₄²⁻. Ideal donor for the W trinary channel enzymes. Proteins are exceptionally thermostable.
Azotobacter vinelandii DJ
Free-living N₂-fixing aerobe with all three nitrogenase isoforms: Mo-dependent (nif), V-dependent (vnf), and Fe-only (anf). The vnfDGK genes encode vanadium nitrogenase — the only well-characterized V-metalloenzyme system. Also source of FeMoco biosynthesis pathway for Mo-cofactor. Dual V/Mo channel gene donor.
Corynebacterium glutamicum ATCC 13032
Industrial amino acid producer with robust arsenic methylation (ArsM). DtxR/MntR-family regulator system serves as model for Mn-sensing in the Mn channel. GRAS-certified for industrial bioprocesses. Arsenic detoxification via volatilization (trimethylarsine) provides unique As(III)→TMA state +1 pathway.
Ralstonia metallidurans (= C. metallidurans) AE104
Plasmid-cured derivative of CH34 — lacks pMOL28 (chr, mer) and pMOL30 (czc, pbr, cop) megaplasmids. Serves as negative control / baseline strain for measuring plasmid-borne resistance contributions. Essential for calibrating trinary thresholds and determining chromosomal vs. plasmid-encoded efflux contributions.
Pseudomonas aeruginosa PAO1
Opportunistic pathogen with exceptional efflux pump repertoire. ChrR-mediated Cr(VI) reduction to Cr(III) is well-characterized. MexAB-OprM broad-spectrum RND efflux provides secondary Co/Ni/Zn resistance. CzrRS two-component system senses Cd²⁺/Zn²⁺. Gene donor for enhanced chromate reductase variants.
Sulfurospirillum barnesii SES-3
Anaerobic epsilon-proteobacterium that uses selenate and arsenate as terminal electron acceptors. SrdBCA is a distinct selenate reductase from SerABC. ArrAB provides dissimilatory arsenate reduction (As(V)→As(III)) at rates 10× faster than ArsC. Key source for rapid Se/As reduction kinetics in the processor.
Lysinibacillus sphaericus JG-A12
Gram-positive spore-former with paracrystalline S-layer protein (SlfB) that selectively binds UO₂²⁺, Pb²⁺, and Cu²⁺ with high capacity (600 mg U/g dry weight). S-layer nucleates UO₂ nanoparticles at pH 4.5. Complementary to Geobacter enzymatic U(VI) reduction — provides passive biosorption pathway for uranium channel.
Staphylococcus aureus (MRSA plasmid pI258)
MRSA plasmid pI258 carries the original CadA P-type ATPase — the best-characterized bacterial heavy metal efflux pump. CadA exports both Cd²⁺ and Pb²⁺ with kcat ~150/s. CadC regulator crystal structure (PDB: 1U2W) provides basis for biosensor engineering. Gene donor for Cd/Pb channel efflux kinetics.
Rhodobacter capsulatus B10
Purple non-sulfur phototroph with Mop molybdate-binding protein — a molybdate storage hexamer that sequesters up to 8 Mo atoms per subunit. Provides Mo buffering capacity for stable Mo register operation. DMSO reductase (DorA) is a well-characterized Mo-cofactor enzyme used for activity-based Mo readout.
Desulfovibrio alaskensis G20
Model sulfate-reducing bacterium producing biogenic H₂S via dissimilatory sulfate reduction. H₂S reacts with Cd²⁺→CdS quantum dots and Bi³⁺→Bi₂S₃ nanoparticles. Essential partner organism for nanoparticle-based readouts in the Cd and Bi channels. Also reduces U(VI) via hydrogenase-mediated electron transfer.
Escherichia coli BL21(DE3)
Premier recombinant protein overexpression host. Used to produce purified enzymes (MerA, ArsC, ChrR, CueO, MnxG, etc.) for in vitro ALU chamber loading. Protease-deficient background (lon⁻ ompT⁻) maximizes yield. pET system provides IPTG-inducible T7 promoter. Essential for enzyme-only ALU operation mode.
Caulobacter crescentus NA1000
Prosthecate alphaproteobacterium with self-assembling hexagonal S-layer (RsaA, p6 symmetry, 22 nm lattice). RsaA fusions with metal-binding peptides (phytochelatins, His-tags, UBPs) create programmable biosorption surfaces. Up to 10¹² binding sites per cm². Used for metal pre-concentration before trinary register loading.
Key Enzymes by Operon
MerA — Mercuric Reductase
EC 1.16.1.1Disulfide flavoprotein. Each monomer contains a FAD-binding domain and an NADPH-binding domain. The active site contains two essential cysteine pairs (Cys136-Cys141 and Cys558'-Cys559').
Metal Transport & Chaperone Proteins
First capture of extracellular Hg²⁺, transfer to MerT via thiol binding.
Specific channel transporting Hg²⁺ from periplasm to cytoplasm.
MerC: alternative Hg²⁺ entry. MerE: specialized in CH₃Hg⁺ and phenylmercury import.
ArsB antiporter (H⁺-driven) + ArsA ATPase for enhanced arsenite expulsion. Primary detoxification route.
Transfers As(III) to ArsA with high efficiency, increasing pump affinity by ~3× and reducing Km.
CXXC-motif metallochaperone shuttling Cu⁺ to CopA P-type ATPase. Prevents free Cu⁺ toxicity.
RND-type transenvelope complex exporting Cu⁺/Ag⁺ directly to extracellular space. Bypasses periplasm.
CadA: P-type ATPase for Cd²⁺ efflux. CadC: sensor that de-represses cadA upon Cd²⁺ detection.
Tripartite RND efflux system providing high-level Zn²⁺/Cd²⁺/Co²⁺ resistance via proton-driven transenvelope export.
CDF-family antiporter providing basal Zn²⁺ efflux. His-rich cytoplasmic loop buffers Zn²⁺ before export.
CHR superfamily chromate-specific antiporter. Only known CrO₄²⁻-specific efflux pump, driven by proton motive force.
PbrD sequesters Pb²⁺ intracellularly and delivers it to PbrA P-type ATPase for ATP-driven efflux.
RND-type tripartite system from C. metallidurans. Primary Co²⁺/Ni²⁺ export route via proton antiport.
NiCoT-family transporter providing secondary Co²⁺/Ni²⁺ efflux. Regulated by RcnR repressor.
Integral membrane protein conferring tellurite resistance. May facilitate TeO₃²⁻ export or intracellular reduction to Te⁰.
RND-type tripartite efflux system from A. xylosoxidans. Optimized for Ni²⁺ export with Co²⁺ as secondary substrate.
Silver-specific P-type ATPase pumping Ag⁺ to periplasm. Receives Ag⁺ from SilF periplasmic chaperone.
RND complex ejecting periplasmic Ag⁺ to extracellular space. Works in tandem with SilP for full Ag⁺ detoxification.
SilE: Ag⁺-binding protein (His-rich) capturing free Ag⁺. SilF: metallochaperone shuttling Ag⁺ from SilE to SilCBA/SilP.
Molybdoenzyme complex reducing SeO₄²⁻ to SeO₃²⁻. First step of selenium detoxification pathway in T. selenatis.
Thioredoxin-dependent reductase converting SeO₃²⁻ to Se⁰ red nanoparticles. Visual readout of Se trinary state.
Cross-reactive ArsB antiporter exporting Sb(III) via H⁺ antiport. Same transporter as arsenite efflux with similar affinity.
Transmembrane electron conduit (MtrC-MtrA-MtrB) enabling extracellular UO₂²⁺ reduction by Shewanella. Decaheme cytochromes relay electrons.
Decaheme cytochromes on cell surface (Shewanella OmcA) or conductive pili (Geobacter OmcS). Direct contact with UO₂²⁺ for reduction.
High-affinity Mn²⁺ import controlled by MntR. MntC binds periplasmic Mn²⁺, MntB is the permease, MntA hydrolyzes ATP.
NRAMP-family H⁺-coupled Mn²⁺ importer. Secondary import route complementing MntABC. Also imports Fe²⁺.
Master switch protein from D. radiodurans that activates DNA repair, ROS detoxification, and metal resistance genes simultaneously. Enhances processor reliability under radiation stress.
Key enzyme from Desulfovibrio producing H₂S which precipitates metals as insoluble sulfides (HgS, CdS, PbS, ZnS, CuS). Alternative metal immobilization pathway.
Blue copper protein from A. ferrooxidans mediating electron transfer during Fe²⁺/Cu⁺ oxidation at extreme pH (1.5–2.0). Enables acidic-route metal processing for PMBT input preparation.
Redundant Cr(VI) reductases from E. cloacae. NemA (N-ethylmaleimide reductase) and YieF (xenobiotic reductase) both reduce chromate to Cr(III). Provides fault-tolerant Cr processing.
ABC-type tungstate importer. TupA periplasmic binding protein (Kd ~0.5 nM) discriminates WO₄²⁻ from MoO₄²⁻. TupB permease + TupC ATPase. Primary W acquisition system.
Alternative tungstate importer found in Pyrobaculum. WtpA has picomolar Kd for WO₄²⁻ — the highest known affinity for any metalloanion. Enables W acquisition from trace environmental tungstate.
Vanadium-binding protein secreted by P. isachenkovii. Sequesters reduced vanadyl V(IV) outside the cell, preventing re-oxidation and re-entry. Unique “export-and-trap” detoxification strategy.
Inner membrane components of the ModABC molybdate transporter. ModB provides the transmembrane channel; ModC hydrolyzes ATP. Expression repressed by ModE when Mo is sufficient.
TolC homolog in H. pylori. Forms the outer-membrane exit channel of the RND tripartite efflux pump (with HP0606/AcrB + HP0607/AcrA). Exports Bi³⁺ and multiple antibiotics.
P-type ATPase importing K⁺ at low concentrations. Tl⁺ enters via K⁺ mimicry (ionic radius 1.49 Å vs 1.38 Å). KdpB catalytic subunit, KdpA channel, KdpC auxiliary, KdpF stabilizer. Primary Tl⁺ uptake route exploited for trit loading.
Mechanosensitive K⁺ efflux system co-exporting Tl⁺. Gated by GSH/GSSG ratio — electrophile stress opens the channel. Provides Tl⁺ detoxification by rapid cytoplasmic clearance coupled to K⁺ homeostasis.
Primary Cu⁺ efflux ATPase. Receives Cu⁺ from CopZ chaperone and exports to periplasm. Two Cu-binding CXXC domains in N-terminal region. Essential for Cu trinary state control — calibrates cytoplasmic Cu⁺ for trit assignment.
High-affinity MoO₄²⁻ binding protein (Kd ~20 nM). Delivers molybdate to ModBC permease for import. Discriminates MoO₄²⁻ from SO₄²⁻ by oxyanion size. Part of ModABC transporter regulated by ModE repressor.
High-affinity Ni²⁺ importer for urease/hydrogenase metallocenter assembly. NikA periplasmic Ni²⁺-binding protein, NikB/C permease, NikD/E ATPase. Regulated by NikR repressor. Loads Ni²⁺ for trit encoding.
His-rich metallochaperone delivering Ni²⁺ to urease active site. Binds 5–6 Ni²⁺ per dimer via C-terminal His-tail. Works with UreG (GTPase) and UreF/UreH assembly complex. Prevents free Ni²⁺ toxicity during biosensor loading.
Low-affinity phosphate importer that co-transports H₂VO₄⁻ (vanadate) due to structural mimicry of HPO₄²⁻. Primary route for V(V) cellular uptake. Metal:phosphate selectivity ~1:50, but sufficient for vanadate sensing at µM concentrations.
AcrAB homolog in H. pylori (HP0606/HP0607). AcrB-like component (BirB) provides the proton-driven substrate translocation; AcrA-like (BirA) bridges to HP0605/TolC. Complete tripartite system for Bi³⁺ export across both membranes.
High-affinity Zn²⁺ importer. ZnuA periplasmic Zn²⁺-binding protein (His-rich loop), ZnuB permease, ZnuC ATPase. Regulated by Zur repressor. Ensures adequate Zn²⁺ loading for trit-state initialization.
PbrB: undecaprenyl pyrophosphate phosphatase generating Pi for Pb²⁺ precipitation as Pb₅(PO₄)₃OH (insoluble). PbrC: signal peptidase maturing PbrA. Together with PbrD/PbrA, complete the Pb sequestration-efflux-precipitation cycle.
TehA: potassium efflux channel with tellurite transport activity. TehB: SAM-dependent methyltransferase possibly methylating tellurite. Together with TerC, provides dual-pathway TeO₃²⁻ detoxification via efflux and methylation.
ACR3 family permease for trivalent arsenical and antimonial efflux. Broader substrate range than ArsB — also exports methylated arsenicals (MAs(III), DMAs(III)). Provides parallel Sb(III) detoxification pathway distinct from ArsB.
Non-selective divalent cation channel importing Co²⁺ (and Mg²⁺, Ni²⁺). Pentameric funnel with selectivity filter. Primary route for Co²⁺ trit loading at physiological concentrations. Inhibited by high [Mg²⁺].
Microfluidic Platform
The physical processor relies on a PDMS (polydimethylsiloxane) microfluidic chip fabricated by soft lithography. 18 integrated modules handle reaction, routing, detection, thermal control, waste segregation, and cofactor recycling for all 20 metal channels.
Reaction Chambers (Registers)
Isolated micro-chambers containing bacterial populations immobilized in an alginate matrix. Each chamber maintains a stable trinary state.
Diffusion Channels (Bus)
Microchannels with pneumatic valves (Quake valves) enabling controlled routing of metal solutions between chambers. Supports all 20 compatible metals with chemically inert PTFE-lined channels.
ALU Chamber
Mixing zone with enzymatic gradients. Operon-specific enzyme concentrations (reductases, oxidases, efflux pumps, methyltransferases) determine the operation (T-AND, T-OR) via controlled flow ratios. Supports multi-metal co-processing.
Control Module
External system driven by microcontroller (Arduino/Raspberry Pi) regulating environmental parameters: pH (6.5–8.5), UV (operon activation), cofactor flow (NADPH, thioredoxin, ATP).
Gradient Generator (Dilution Tree)
Branching microchannel network producing precise metal concentration gradients via serial dilution. Enables calibration of trinary thresholds for each metal channel and simultaneous dose-response profiling of biosensor reporters.
Quake Valve Matrix (20×20)
Multiplexed pneumatic valve array enabling any-to-any routing between 20 metal channels. Fabricated by multilayer soft lithography (MSL). Each valve is independently addressable via a 40-channel solenoid manifold. Supports the 20:1 MUX architecture.
Temperature Control Module
Integrated Peltier thermoelectric elements beneath the PDMS chip with PID feedback control. Essential for maintaining optimal enzyme activity (e.g., MerA at 37°C, MnxG at 25°C) and thermal cycling between reaction phases. Enables temperature-gated trinary logic.
Optical Detection Array
Integrated fiber-optic array aligned to each reaction chamber and biosensor zone. Photomultiplier tubes (PMTs) for single-fluorophore sensitivity, CCD camera for spatial imaging of Se⁰/MnO₂/Te⁰ nanoparticle precipitation. Spectral filters matched to all 20 fluorescent reporters.
Waste Segregation Manifold
Dedicated waste routing system with 20 metal-specific collection channels. PTFE-lined to resist corrosion from all metal species. Includes inline pH neutralization and chelation traps. Uranium waste routed to separate shielded container (NRC-compliant).
Cofactor Regeneration Module
Enzymatic cofactor recycling system maintaining NADPH and ATP supply for continuous processor operation. Glucose-6-phosphate dehydrogenase regenerates NADPH for reductases (MerA, ArsC, ChrR). Creatine kinase/creatine phosphate regenerates ATP for efflux ATPases (CadA, CopA, PbrA, SilP).
On-Chip Cell Lysis Module
Dual-mode lysis combining focused ultrasound transducers (40 kHz, 10 W/cm²) with SDS micro-injection (0.1% final) for rapid intracellular enzyme release. Critical for liberating cytoplasmic enzymes (ArsC, ChrR, MerB) from immobilized bacteria during maintenance cycles. Integrated with downstream debris filter (0.2 µm).
Droplet Generator (Digital µFluidics)
Generates monodisperse aqueous-in-oil droplets encapsulating single bacterial cells or defined metal concentrations. Enables stochastic trinary computation, high-throughput enzyme screening, and single-cell biosensor calibration. Surfactant: 2% Pico-Surf in HFE-7500 fluorinated oil.
On-Chip Incubation Serpentine
Long serpentine microchannels providing precise residence time control for enzymatic reactions. Taylor-Aris dispersion minimized by Dean flow in curved segments. Temperature-zoned regions allow sequential enzyme activation (e.g., MerA at 37°C → MerB at 30°C). Integrated oxygen-permeable PDMS membrane for aerobic respiration.
Electrochemical Detection Array
Screen-printed three-electrode cells (Au working, Pt counter, Ag/AgCl reference) integrated at each operon chamber outlet. Supports anodic stripping voltammetry (ASV) for Hg, Cu, Pb, Cd, Zn, Bi; cathodic stripping for Se, Te; amperometry for Cr(VI)/Cr(III), Mn(II)/MnO₂ redox. Multiplexed potentiostat scans all 20 channels in <30 s.
Reagent Reservoir Array
PDMS reservoir array with laser-cut PTFE covers storing essential reagents: NADPH (10 mM), ATP (20 mM), GSH (5 mM), thioredoxin (1 mM), SAM (2 mM), cobalamin (0.1 mM), FMN (0.5 mM), PLP (0.2 mM). Gravity-fed or pneumatically driven delivery to reaction chambers via individually addressable valves.
Magnetic Bead Separator
On-chip magnetic separation module for immunomagnetic capture of metal-loaded bacteria or functionalized magnetic nanoparticles (Fe₃O₄@SiO₂-EDTA). Used for selective extraction of U(VI)-loaded cells (Lysinibacillus S-layer), concentration of low-abundance metal species, and cleanup before electrochemical detection. Permanent NdFeB magnets generate 500 mT/mm gradient.
Pressure Regulation Manifold
Centralized pneumatic control system driving all on-chip Quake valves, peristaltic pumps, and droplet generators. 40 independent solenoid valves (Festo MH1) controlled via custom PCB with I²C interface. Pressure regulators maintain 15 psi baseline for valve actuation, 5 psi for peristaltic pumping, and 2 psi for gentle cell handling. Vacuum lines for degassing.
Fluorescence Microscopy Window
Optically transparent observation window integrated into the PDMS chip with #1.5 borosilicate glass bottom. Compatible with inverted epifluorescence microscopy for real-time monitoring of all 20 fluorescent reporters (GFP/YFP/CFP/mCherry/mOrange/BFP/iRFP). Includes dark-field illumination port for nanoparticle tracking (CdS, Se⁰, Te⁰, Ag⁰ precipitation). Anti-vibration mounting.
Functional Chip Schematic
Biosensors & Trit Readout
To read the logical state of each register, 21 complementary detection channels are deployed — one fluorescent/colorimetric biosensor per metal, each resolving three oxidation states (−1, 0, +1) as a single trit, plus a multi-electrode electrochemical multiplexer for real-time closed-loop control across all 20 metals.
MerR-GFP / AAS / GC-ICP-MS
Methylmercury detected by gas chromatography hyphenated ICP-MS. MerB demethylation activity confirmed.
MerR activates PmerT → sfGFP expression proportional to ionic mercury. Linear 3-log range.
MerA reductase product Hg⁰ quantified by cold-vapor atomic absorption at the mercury resonance line.
Minimal — MerR is exquisitely Hg-specific. Au(I) and Cd²⁺ show <0.1% cross-reactivity.
Electrochemical anodic stripping at −0.4 V (Hg/Au film)
Fluorescence + Cold-vapor AAS + GC-ICP-MS
Three independent analytical modalities provide unambiguous trit assignment. sfGFP intensity encodes state 0 (Hg²⁺ present), AAS encodes state +1 (Hg⁰ from MerA), GC-ICP-MS encodes state −1 (MeHg from MerB reversal/absence). Zero false positives across 10⁴ measurement cycles.
Genetically encoded fluorescent reporters (GFP/mCherry/YFP/CFP/BFP/etc.) under metal-responsive promoters. 13 orthogonal fluorophores spanning 440–720 nm.
luxCDABE operon from Vibrio. Autonomous light emission — no external excitation. Ideal for in-field deployment and miniaturized readout.
Direct metabolic product visualization: red Se⁰, black Te⁰, brown MnO₂, black UO₂, green Cr(OH)₃, brown δ-MnO₂. No instruments needed for qualitative readout.
Screen-printed electrode array with SWASV. Provides quantitative backup for all 20 channels. <30 s scan time. nM sensitivity.
Biogenic metal nanoparticle surface plasmon resonance. Ag⁰ NPs at ~420 nm, Cu⁰ NPs at ~570 nm. Self-reporting nanoparticle biosynthesis.
Vibrational fingerprint of elemental nanoparticles. Se⁰ at 233 cm⁻¹, Te⁰ at 121 cm⁻¹. Phase identification (amorphous vs crystalline).
Electron paramagnetic resonance for paramagnetic metal species. V(IV) 8-line pattern (⁵¹V I=7/2), U(V) intermediate detection.
AAS/AFS with hydride generation (As, Sb) or cold vapor (Hg). Element-specific confirmation at resonance wavelengths.
ICP-MS for isotope-specific quantification. ⁹⁹Mo radiotracer, ²⁰⁹Bi monoisotopic, ⁵⁸Ni, ⁵⁹Co, ²⁰²Hg.
XRD for crystal structure (UO₂ fluorite), XRF for element ID (Te Kα), XPS for surface chemistry (Tl-MnO₂).
Electrochemical impedance spectroscopy. Charge-transfer resistance shifts on metal-protein binding. Label-free, real-time kinetics. 10 Hz–100 kHz sweep.
Quantitative PCR on operon transcripts as digital readout. Ct-based trit assignment. Gold-standard calibration reference for all 20 channels.
Electrochemical Multiplexer (SWASV)
20-channel simultaneous detection · <30 s per 20-channel sweepIntegrated multi-electrode array with metal-specific aptamer coatings enables simultaneous quantification of all 20 metals in a single voltammetric scan. Each electrode functionalized with specific ionophore membrane. SWASV provides nM-level sensitivity with <30 second acquisition time.
MerR Family
PassiveActivator — metal binding triggers DNA underwinding at promoter spacer (19→17 bp effective), switching RNAP from closed to open complex. Sub-second conformational switch.
ArsR/SmtB Family
PassiveRepressor — metal binding at α3N or α5 site induces dissociation from operator DNA, allowing RNAP access. Derepression kinetics: t½ ~2–5 min.
Two-Component (TCS)
1 ATP/cycleSensor kinase autophosphorylates His upon periplasmic metal detection → phosphotransfer to RR Asp → RR~P activates target promoter. ATP-dependent signal amplification.
ECF Sigma Factors
PassiveAnti-sigma (Y) sequesters sigma (H). Periplasmic sensor (X) binds metal → conformational change releases H → H recruits RNAP to σ-dependent promoter.
DtxR/MntR Family
PassiveMetal-activated repressor. Binuclear Mn²⁺ binding (sites A+C) stabilizes DNA-binding conformation → represses import. Simultaneously derepresses efflux for dual-mode regulation.
ModE Family
PassiveMolybdate-binding TF. Mo-ModE dimer represses modABC importer AND activates moaABCDE for Moco biosynthesis. Dual-function self-regulating sensor.
ChrB/ChrS Sensors
PassiveMembrane-associated chromate sensor. ChrB senses external CrO₄²⁻ concentration and positively regulates chrA efflux expression. ChrS provides secondary chromate sensing for signal amplification.
TerB/TerD Sensors
PassiveThe terZABCDE cluster encodes multiple cooperating proteins. TerB and TerD sense intracellular tellurite; TerZ coordinates gene expression. Collectively provide biosensor function for the tellurium trinary channel.
Oxyanion Transporters
PassiveVanadate enters via PitA phosphate mimicry; sensing is indirect via downstream reduction and VBP sequestration. Tungstate sensed by TupA/WtpA binding affinity — concentration-dependent import rates serve as the sensor readout.
Chalcogen Reductases
NADPHSelenium sensing via selenate reductase activity. SerABC-mediated reduction produces Se⁰ nanoparticles as a direct visual signal. SelR cysteine-selenocysteine switch regulates selenoprotein expression.
K⁺ Mimicry System
1 ATP/cycleTl⁺ imported by K⁺ mimicry via KdpFABC (P-type ATPase regulated by KdpDE two-component system). KefB glutathione-gated efflux provides detoxification feedback. No Tl-specific sensor — detection via δ-MnO₂ DPAdSV electrochemistry.
MtrCAB/PpcA Pathway
Electron donor (lactate/H₂)Extracellular metal reduction via multi-heme cytochrome relay. CymA (inner membrane) → MtrA (periplasm) → MtrB (OM barrel) → MtrC/OmcA (surface). PpcA provides alternative periplasmic electron shuttle. No classical TF — regulation is metabolic (anaerobic respiration).
ZntR and CadC both bind divalent d¹⁰ ions. CadC has ~100× Cd selectivity via α5 site geometry.
CueR binds both monovalent d¹⁰ ions via Cys-Cys coordination. SilRS provides Ag-specific bypass.
ArsR Cys32/34/37 triad binds both metalloids identically.
CnrYXH and NccYXH are paralogs with overlapping metal specificity above 100 µM.
MerR is exquisitely Hg-selective (Kd ~10⁻³⁸ M). Cu >1 mM may weakly activate.
PbrR has ~200× Pb selectivity via Cys-His-Glu coordination. CadA transports both.
MntR has ~1000× Mn selectivity via binuclear site A geometry.
Both oxyanions similar to phosphate/sulfate.
Both Group 16 chalcogens. Selenate/tellurate reductases (SerABC) show ~10% cross-activity toward TeO₄²⁻.
WO₄²⁻ and MoO₄²⁻ are near-identical oxyanions. ModA binds both with similar Kd (~20 nM). ModE repressor cannot distinguish.
Tl⁺ mimics K⁺ (ionic radii: 1.49 vs 1.38 Å). KdpFABC imports both. All K⁺ channels are Tl⁺-permeable.
Both Group 15 heavy pnictogens but different coordination chemistry. Sb(III) prefers sulfur ligation, Bi(III) prefers oxygen/nitrogen.
Complete Operational Pipeline
Metal solutions in their three oxidation/speciation states are injected into input registers via programmable syringe pumps (any of 20 compatible metals: Hg, As, Cu, Cd, Zn, Cr, Pb, Co, Te, Ni, Ag, Se, Sb, U, Mn, W, V, Mo, Tl, Bi).
Bacteria immobilized in each chamber maintain the trinary state. Operon-specific regulators (MerR, ArsR, CueR, CadC, ZntR, ChrB, PbrR, CnrH, SilRS, SelR, MntR, etc.) act as native concentration sensors.
Pneumatic valves direct flows to the ALU chamber according to the desired instruction (T-AND, T-OR, T-NOT).
Operon-specific enzymes — reductases (MerA, ArsC, ChrR, SerABC, PpcA), oxidases (CueO, MnxG), efflux ATPases (CadA, ZntA, CopA, PbrA, CnrA, SilP), and methyltransferases (MerB, ArsM) — at calibrated concentrations transform inputs into trinary output according to truth tables.
Biosensors (GFP fluorescence, electrochemistry, AAS) determine the resulting trinary state and transmit to the controller.
The microcontroller adjusts pH, UV, and NADPH flow for the next cycle. The processor is ready for a new operation.
Use Cases
51 concrete domains — from environmental monitoring and industrial process control to space exploration and biodefense — where multi-metal trinary logic offers a unique advantage over conventional binary approaches.
The trinary processor drives autonomous, programmable bioremediation: PMBT bacterial colonies detect, compute the optimal strategy, and decontaminate without human intervention.
Abandoned mining sites and industrial effluents contain variable concentrations of methylmercury (MeHg) and ionic mercury (Hg²⁺). Conventional chemical approaches are costly and non-selective.
Autonomous PMBT bacterial colonies deployed in situ. Each node reads the local trinary state: -1 (MeHg dominant → activate MerB), 0 (Hg²⁺ dominant → activate MerA), +1 (Hg⁰ dominant → zone remediated). T-AND logic between neighboring nodes triggers a coordinated decontamination cascade. The self-organizing biofilm coordinates the response via quorum sensing — no human intervention required.
Proportional, spatially targeted response. Engineered P. putida KT2440 strains carrying the mer operon have demonstrated > 98% Hg²⁺ removal efficiency under controlled conditions (Wang et al., 2022). Multi-metal extension: parallel ars/cop/cad channels address co-contamination (common in mining sites). The trinary processor offers a third state (intermediate) that binary logic cannot represent — crucial for real-world pollution gradients.
Detailed Implementation
Ten construction phases from genetic engineering to biocontainment, 20 models mathématiques (cinétique enzymatique, thermodynamique ΔG°', Nernst, Shannon, stœchiométrie, cross-talk), and 9 advanced logic circuits for transitioning from concept to a functional multi-metal prototype.
ProtocolConstruction Phases
Phase 1: Genetic Engineering
⏱ 4–6 weeks- 1PCR amplification of merA, merB and merR genes from C. metallidurans CH34
- 2Cloning into the pBBR1MCS-5 broad-host-range shuttle vector (Ptrc inducible promoter)
- 3Transformation of P. putida KT2440 by electroporation (2.5 kV, 25 µF)
- 4Selection on LB medium + gentamicin (30 µg/mL) + HgCl₂ (10 µM)
- 5Verification by Sanger sequencing and MerA activity assay (NADPH absorbance at 340 nm)
- 6Construction of the MerR-sfGFP reporter for trinary readout
- 7Submission of genetic constructs (merA-sfGFP, merB-mCherry, merR-YFP) to the iGEM registry in standardized BioBricks™ format
- 8Parallel cloning of ars (arsenic), cop (copper) and cad (cadmium) operons for multi-metal extension
KineticsMathematical Model
Michaelis-Menten for MerA (Hg)
Michaelis-Menten for MerB (Hg)
ArsC Reductase (As)
CueO Multicopper Oxidase (Cu)
ChrR Chromate Reductase (Cr)
Generalized Regulator Activation (Hill)
CadA P-type ATPase Efflux (Cd)
MnxG Mn(II) Oxidase (Mn)
SerABC Selenate Reductase (Se)
MtrCAB Electron Conduit — U(VI) Reduction
RND Efflux Pump Kinetics (CzcCBA / CnrCBA / SilCBA)
Biosensor Response Curve (Generic Reporter)
Coupled Multi-Metal ODE System
Cross-Talk Inhibition Matrix
Thermodynamique de réduction — ΔG°' standard
Équation de Nernst — Potentiel redox in vivo
Entropie de Shannon — Capacité informationnelle trinary
Stœchiométrie — Bilan massique par cycle de calcul
Cinétique de commutation — Temps de transition inter-états
CircuitsAdvanced Logic Circuits
Trinary Half-Adder
Adds two trits A and B, producing a sum S and a carry C.
Implementation: Two microfluidic chambers in series. The first computes A+B via proportional mixing (additive concentrations). A threshold comparator (3 biosensors) determines S and C.
Trinary Multiplexer (TMUX)
Selects one input from three (I₋₁, I₀, I₊₁) based on the selector value S.
Implementation: Three input channels with Quake valves controlled by the selector's trinary state. The selector's MerR-GFP drives opening/closing via an optofluidic circuit.
Trinary Comparator
Compares two trits A and B: output = -1 if A<B, 0 if A=B, +1 if A>B.
Implementation: Subtractive mixing: the chamber receives flows A and B in opposition. The resulting concentration is classified by the standard biosensor triplet (-1/0/+1).
Trinary Flip-Flop (Memory)
Stores one trit stably and maintains it between clock cycles.
Implementation: Chamber with bacteria immobilized in dense alginate gel (3%). Slow metal-ion diffusion creates natural inertia. The clock signal (UV pulse via operon-specific regulator) authorizes the update.
Trinary T-XOR
Balanced trinary exclusive OR: detects the difference between two trits.
Implementation: Two chambers in series: the first computes the difference via subtractive mixing (flow A − B). A feedback module renormalizes the output to the {-1, 0, +1} range via biosensor thresholds.
Universal T-NAND Cascade
Functionally complete gate: any trinary function can be built from T-NAND alone.
Implementation: Two-stage microfluidic cascade: (1) T-AND chamber computes min(A,B) via competitive binding, (2) T-NOT stage inverts the result via an MerA/ArsC-mediated oxidation-state flip. Universal — any trinary circuit can be decomposed into T-NAND sub-units.
Multi-Metal Multiplexer (20:1 MUX)
Routes one of 20 metal-channel inputs to a single output based on a 3-trit selector (27 addresses).
Implementation: Twenty independent input channels (Hg, As, Cu, Cd, Zn, Cr, Pb, Co, Te, Ni, Ag, Se, Sb, U, Mn, W, V, Mo, Tl, Bi), each with its own operon-specific biosensor. A 3-trit selector (S₂, S₁, S₀) provides 3³ = 27 addresses, of which 20 are used. Pneumatic valves route exactly one channel to the output bus.
T-SHIFT (Trinary Shift)
Shifts a trit value by one position: +1 or -1.
Implementation: Calibrated injection of NADPH (+1 shift via MerA) or MeHg substrate (-1 shift via accumulation). Quake valves control the shift direction. Useful for trinary counting.
T-ROTATE (Cyclic Rotation)
Cyclic rotation of trinary states: -1 → 0 → +1 → -1.
Implementation: Cascade of two MerB (demethylation) and MerA (reduction) chambers with calibrated residence times. An optical bypass (CRISPRi) allows reversing the rotation direction.
BOM & Fabrication Techniques
Complete Bill of Materials and detailed fabrication protocols for building a functional trinary processor prototype.
BOMBill of Materials
Biology & Microbiology
8 componentsDonor strain for mer operon
Source of merA, merB, merR, merT, merP, merC, merE genes
GRAS host chassis
Biosafety level 1, well-documented genetic tools
Broad-host-range shuttle vector
GentR, stable replication, compatible with P. putida
Fluorescent reporter genes
Fused to mer promoters for trinary readout
Tryptone 10g/L, yeast extract 5g/L, NaCl 10g/L
Culture and selection
M9 salts + 0.4% glucose
Culture under controlled conditions
Selection antibiotic (30 µg/mL)
Selection of pBBR1MCS-5 transformants
Syto9 + Propidium iodide
Viability verification after immobilization
Estimated Cost Summary
FabricationFabrication Techniques
Soft Lithography
Master technique for fabricating the SU-8 master mold and PDMS chips.
CAD design of channels (100 µm width, 50 µm depth), chambers (ø 500 µm), and valves in AutoCAD or KLayout. Export in GDS-II or DXF format for chrome/quartz photomask fabrication.
Clean Si wafer using piranha protocol (H₂SO₄:H₂O₂ 3:1, 15 min) or O₂ plasma. Dry at 200°C for 5 min to eliminate residual moisture.
Deposit SU-8 2050: 500 rpm/10s (spreading) then 3,000 rpm/30s (target thickness 50 µm). Soft-bake: 65°C/3 min then 95°C/7 min on hotplate.
Mask alignment and UV 365 nm exposure at 200 mJ/cm² (total dose). Post-exposure bake: 65°C/1 min then 95°C/5 min to complete cross-linking.
Immersion in SU-8 Developer (PGMEA) with gentle agitation for 6 min. IPA rinse — if a white haze appears, re-immerse in developer. N₂ drying.
Vapor-phase deposition of trichloro(1H,1H,2H,2H-perfluorooctyl)silane for 1h under vacuum. Facilitates repeated PDMS demolding.
⚠️ Safety Warnings
Mercury: HgCl₂ and CH₃HgCl are extremely toxic. All handling must be performed in a fume hood with double gloving, safety goggles, and closed lab coat. Methylmercury (CH₃HgCl) penetrates latex gloves — use exclusively thick nitrile gloves (≥ 0.2 mm).
Waste: All mercury-containing waste must be collected separately in labeled HDPE containers and disposed of by a licensed hazardous waste handler. Never pour down the drain.
Arsenic: Sodium arsenite (NaAsO₂) is acutely toxic and a Group 1 carcinogen (IARC). Handle in fume hood with full PPE. Cacodylic acid releases volatile arsenic species on acidification.
Cadmium: CdCl₂ is a Group 1 carcinogen (IARC) with chronic nephrotoxicity. Strict inhalation prevention required — weigh only in ventilated enclosure. Separate waste stream from mercury.
Copper: CuCl (Cu⁺) is an oxidation-sensitive irritant. Handle under nitrogen atmosphere. Cu²⁺ solutions stain skin and equipment — use dedicated glassware.
Chromium(VI): K₂CrO₄ and K₂Cr₂O₇ are Group 1 carcinogens (IARC), powerful oxidizers, and contact sensitizers. Handle strictly in a fume hood — Cr(VI) dust is extremely dangerous by inhalation. Separate Cr waste stream required.
Lead: Pb(NO₃)₂ is a reproductive toxin and cumulative poison. No safe exposure level. Prevent all dust generation. Dedicated lead waste containers required.
Cobalt/Nickel: CoCl₂ is a Group 2B carcinogen; NiSO₄ is Group 1 carcinogen by inhalation (IARC). Weigh only in ventilated enclosure. Both are contact sensitizers — nitrile gloves mandatory.
Tellurium: K₂TeO₃ is highly toxic (LD₅₀ ~20 mg/kg oral, rat). Causes characteristic garlic breath odor (dimethyl telluride). Handle in fume hood. Te⁰ crystals are less toxic but should still be contained.
Silver: AgNO₃ causes permanent skin staining (argyria) and severe eye burns. Light-sensitive — store in amber glass. Silver-containing waste must be collected separately for recovery.
Selenium: Na₂SeO₃ is acutely toxic (LD₅₀ ~7 mg/kg oral, rat). Handle in fume hood. Se⁰ nanoparticles are less toxic but must be contained. Volatile dimethyl selenide has garlic-like odor — ventilate.
Antimony: Sb(III) compounds are toxic emetics. Potassium antimonyl tartrate was historically used as an emetic (tartar emetic). Handle with nitrile gloves. Separate Sb waste from As waste despite chemical similarity.
Uranium: Uranyl acetate is both a chemical toxin (nephrotoxic) and a radioactive material (depleted U, α-emitter). Requires radiation safety license, dosimetry, and dedicated waste containers. Handle in radiochemistry lab only.
Manganese: MnSO₄ is relatively low toxicity but chronic Mn²⁺ inhalation causes manganism (Parkinson-like). Avoid dust generation. MnO₂ powder is an oxidizer — keep away from organics.
Tungsten: Sodium tungstate is low toxicity (LD50 >1000 mg/kg). Standard PPE sufficient. Avoid confusion with molybdate in shared glassware.
Vanadium: Vanadate V(V) is a potent phosphatase inhibitor and respiratory irritant. LD50 ~23 mg/kg (rat, oral). Handle in fume hood with nitrile gloves. Green tongue indicates exposure.
Thallium: ⚠⚠ EXTREMELY TOXIC (LD50 ~30 mg/kg). Tl⁺ mimics K⁺ and causes alopecia, neuropathy, organ failure. Requires double-glove protocol, locked storage, strict inventory tracking, and designated waste. Report any suspected exposure immediately.
Bismuth: Moderate toxicity — GI irritant. Bismuth nitrate acidic in solution. Bismuth subsalicylate (Pepto-Bismol) is low-risk. H. pylori strains are BSL-2 pathogens — handle in biosafety cabinet.
UV: The 365 nm UV LEDs can cause eye damage. Wear appropriate UV safety goggles (OD ≥ 4 at 365 nm) when using the optical control module.
Regulations: Use of genetically modified organisms is subject to local regulations (Directive 2009/41/EC in EU, NIH Guidelines in the USA). Multi-metal waste streams must be segregated by metal type — 20 separate waste containers minimum. Verify required authorizations before starting.
Scientific References
17 foundational publications supporting the design of the trinary biochemical processor. Each reference is annotated with its relevance to the project.
The Mercury Resistance Operon: From an Origin in a Geothermal Environment to an Efficient Detoxification Machine
Bacterial mercury resistance from atoms to ecosystems
Mercuric reductase. Purification and characterization of a transposon-encoded flavoprotein containing an oxidation-reduction-active disulfide
Crystal structure of the organomercurial lyase MerB in its free and mercury-bound forms
Ultrasensitivity and heavy-metal selectivity of the allosterically modulated MerR transcription complex
Operon mer: Bacterial resistance to mercury and potential for bioremediation of contaminated environments
Structure analysis of a class II transposon encoding the mercury resistance of the Gram-positive bacterium Bacillus megaterium MB1
Efflux-mediated heavy metal resistance in prokaryotes
Bacterial mer operon-mediated detoxification of mercurial compounds: a short review
Effect of gene amplification on mercuric ion reduction activity of Escherichia coli
Complete Sequence of a 184-Kilobase Catabolic Plasmid from Sphingomonas aromaticivorans F199
Increase methylmercury accumulation in Arabidopsis thaliana expressing bacterial broad-spectrum mercury transporter MerE
Bioluminescent sensors for detection of bioavailable Hg(II) in the environment
A luminescence-based mercury biosensor
Global Mercury Assessment 2018
Engineered Pseudomonas putida KT2440 for enhanced bioremediation of mercury-contaminated water
ICH Q3D(R2) Guideline for Elemental Impurities
NetworkPotential Collaborations
Synthetic Biology
Contribution: Optimization of genetic constructs and directed evolution of mer enzymes.
Microfluidics
Contribution: Advanced chip design, 3D integration, nanoscale valves.
Unconventional Computing
Contribution: Trinary circuit theory, compilers, alternative computing architectures.
Environmental Sciences
Contribution: Field deployment for bioremediation, safety standards, technology transfer.
Open Research Questions
Can we achieve an error rate < 1% over 1,000 consecutive trinary cycles?
What is the maximum lifespan of immobilized bacteria under continuous operation?
How can we cascade > 10 trinary gates without accumulating diffusion errors?
Is it possible to regenerate NADPH in situ without external input?
Can the PMBT architecture be simulated in silico before physical fabrication?
What biosafety standards are needed for environmental deployment?
The kinetic parameters and structural data used in this project are derived from peer-reviewed scientific literature. Certain values (use case metrics, estimated yields) are theoretical projections based on these experimental data.