Advanced Bio-Computing

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.

-1
Toxic
0
Intermediate
+1
Detoxified
Hg
Mercury
mer operon
As
Arsenic
ars operon
Cu
Copper
cop operon
Cd
Cadmium
cad operon
Zn
Zinc
czc/znt operon
Cr
Chromium
chr operon
Pb
Lead
pbr operon
Co
Cobalt
cnr operon
Te
Tellurium
ter operon
Ni
Nickel
ncc operon
Ag
Silver
sil operon
Se
Selenium
ser operon
Sb
Antimony
ars operon
U
Uranium
mtr operon
Mn
Manganese
mnx operon
W
Tungsten
tup/wtp operon
V
Vanadium
van operon
Mo
Molybdenum
mod operon
Tl
Thallium
tll operon
Bi
Bismuth
bir operon
Encoding System

Biochemical Trinary Logic

Each compatible metal provides three distinct chemical states encoding -1, 0 and +1.

mer operon (merA, merB, merR)

Three distinct chemical states of mercury encode the logical values. The mer operon provides complete enzymatic machinery for reversible mercury transformations.

-1
Toxic

MeHg (Methylmercury)

Highly toxic organic form of mercury. Represents the most negative state in our trinary logic.

0
Intermediate

Hg²⁺ (Ionic Mercury)

Inorganic ionic form, intermediate product of demethylation by MerB. Neutral state of the logic.

+1
Detoxified

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⁺

MeHg
(-1)
MerB
Hg²⁺
(0)
MerA
Hg⁰
(+1)

Tableau Comparatif

Vue synthétique des 20 métaux, opérons, mécanismes et états trits

MétalOpéronMécanisme−10+1
HgMercury
merRéductionMeHg (Methylmercury)Hg²⁺ (Ionic Mercury)Hg⁰ (Elemental Mercury)
AsArsenic
arsRéductionOrgano-As (MMA/DMA)As(III) (Arsenite)As(V) effluxed (Arsenate)
CuCopper
copRéductionCu⁺ (Cuprous, free)Cu²⁺ (Cupric)Cu effluxed (Sequestered)
CdCadmium
cadRéductionCd²⁺ (Free cytoplasmic)Cd-MT (Sequestered)Cd²⁺ effluxed (Expelled)
ZnZinc
czc/zntRéductionZn²⁺ (Free cytoplasmic)Zn-MT (Metallothionein-bound)Zn²⁺ effluxed
CrChromium
chrRéductionCrO₄²⁻ — Cr(VI)Cr(III) solubleCr(OH)₃ precipitate
PbLead
pbrRéductionPb²⁺ (Free cytoplasmic)Pb-phosphate (intracellular)Pb₃(PO₄)₂ effluxed
CoCobalt
cnrRéductionCo²⁺ (Free cytoplasmic)Co-chaperone complexCo²⁺ effluxed
TeTellurium
ter/tehPrécipitationTeO₃²⁻ — TelluriteTeO₄²⁻ — TellurateTe⁰ (Black crystals)
NiNickel
ncc/cnrRéductionNi²⁺ (Free cytoplasmic)Ni-HypAB (chaperone-bound)Ni²⁺ effluxed
AgSilver
silRéductionAg⁺ (Free ionic)Ag-SilE (periplasmic chaperone)Ag⁺ effluxed / Ag⁰ NPs
SeSelenium
selenite reductasePrécipitationSeO₃²⁻ (Selenite)Se⁰ nanoparticles (red)Se²⁻ / Org-Se (selenocysteine)
SbAntimony
ars (Sb-specific)RéductionSb(III) / SbO⁺ (Antimonite)Sb(V) (Antimonate)Sb(III) effluxed
UUranium
Cytochrome-basedPrécipitationUO₂²⁺ (Uranyl, soluble)U(V) (transient)UO₂ (Uraninite, insoluble)
MnManganese
mnt/mnxPrécipitationMn²⁺ (excess free ionic)Mn²⁺ (regulated homeostasis)MnO₂ (Birnessite, insoluble)
WTungsten
tup/wtpPrécipitationWO₄²⁻ (Tungstate excess)W-MPT (Tungstopterin)WS₂↓ (Tungstenite)
VVanadium
van/vnaPrécipitationVO₄³⁻ (Vanadate V(V))VO²⁺ (Vanadyl V(IV))V₂O₃↓ (Vanadium oxide ppt)
MoMolybdenum
modPrécipitationMoO₄²⁻ (Molybdate excess)Mo-PPT (Molybdopterin)MoS₂↓ (Molybdenite)
TlThallium
tllPrécipitationTl⁺ (Thallous Tl(I))Tl-MnOx (Sorbed)Tl₂O₃↓ (Tl(III) oxide)
BiBismuth
birEffluxBi³⁺ (Bismuth ion)Bi-thiol (Chelated)Bi₂S₃↓ (Bismuthinite)
Réduction(11)
Efflux(1)
Précipitation(8)

Pipeline de Traitement Trinary

Architecture générale du processeur biochimique — de l'entrée du métal au trit encodé

1🧪ImportTransport membranaireMerT, ArsB, CopA, ModABC...
2⚗️TransformationRéaction enzymatiqueRéduction / Oxydation / Efflux
3📡DétectionBiosenseur opéron-spécifiqueMerR-GFP, ArsR-mCherry...
4🔢EncodageClassification 3 états−1 (toxique) · 0 (inter.) · +1 (détox.)
5🧮CalculLogique ternaire ALUT-AND, T-OR, T-NAND, MUX...
log₂(3) ≈ 1.585 bits
Capacité par trit
3²⁰ ≈ 3.49 × 10⁹
Espace d'état (20 trits)
+58.5% par élément
Avantage vs binaire
~12 cycles/h (sfGFP)
Fréquence max
Trinary Logic

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

Primitives

f(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.

T-AND
B = -1
B = 0
B = +1
A = -1
-1
-1
-1
A = 0
-1
0
0
A = +1
-1
0
+1
16
Total Gates
operations
12
Binary Ops
3×3 tables
4
Unary Ops
3×1 tables
3^20
State Space
≈ 3.49 × 10⁹
Design

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.

Schematic

Functional Chip Schematic

CTRLREGCLK
CTRLALUOP
MUXREGSELECT
REGALUDATA
ALUBUSRESULT
SENSMUXDETECT
BUSFPGAOUTPUT
FPGAMEMSTORE
MEMQSIGPROGRAM
PWRALUATP
OPTCTRL
ECCALUCHECK
THERMREG
SIGCONDSENSADC
CLKSYNCQSIGSYNC
COFACTPWRNAD+
SCAFFOLDALUPROX
20
Modules
17
Data Buses
20
Metal Channels
16
Logic Gates
12
Pipeline Stages
~10⁹/mL
Cell Density
Biochemistry

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

1
Glycolysis

Glucose → 2 Pyruvate + 2 ATP + 2 NADH

Primary carbon catabolism

2
TCA Cycle

Acetyl-CoA → 2 CO₂ + 3 NADH + FADH₂ + GTP

Complete oxidation & reducing equivalents

3
Pentose Phosphate

G6P → Ribulose-5P + 2 NADPH + CO₂

NADPH supply for reductases (MerA, ArsC, ChrR)

4
Oxidative Phosphorylation

NADH + O₂ → NAD⁺ + H₂O + ~2.5 ATP

ATP regeneration (∸36 ATP/glucose)

Pipeline

Complete Operational Pipeline

💧
PHASE 1

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).

Duration:~2 min
💧
P1
📡
P2
📶
P3
🔀
P4
📦
P5
P6
⚙️
P7
P8
📊
P9
🖥️
P10
💾
P11
♻️
P12
Total cycle time:~42 min(limited by biosensor maturation & CRISPR write)
Modules

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.

Implementation

Real Design Components

From concept to realization: the bacterial strains, enzymes, microfluidic systems, and biosensors needed to build a functional prototype.

Bio

Candidate Bacterial Strains

Primary chassis (GRAS, BSL-1)

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.

Tolerance:50–100 µM Hg²⁺ / multi-metal engineered
merA*merB*merR*arsRDABC*copA*cueO*cadA*chrR*
Multi-metal donor (pMOL28 + pMOL30)

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.

Tolerance:> 100 µM for Hg, Zn, Co, Ni, Pb, Cr
merRTPABDEarsRDABCcopSRABCDcadA/cadCczcCBADRSchrBAFcnrCBAYXHpbrRABCD
Extracellular U(VI) reduction & bio-electronic interface

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.

Tolerance:~500 µM U(VI) (native)
pilAomcSomcZppcAomcBmacA
Dissimilatory metal reducer (U, Cr, Mn, Se)

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.

Tolerance:Multi-metal: U, Cr(VI), Se(VI), Mn(IV)
mtrCABomcAcymAchrR*SO_0009 (Se reductase)
Nickel resistance source (ncc operon)

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.

Tolerance:> 20 mM Ni²⁺
nccCBAnccYXHcnr-homolog
Silver resistance source (sil operon)

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.

Tolerance:> 1 mM Ag⁺
silCFBAGPsilRSsilE
Selenate respirer (Se channel)

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.

Tolerance:10–50 mM SeO₄²⁻ (respiratory)
serABCserDynfEFGH (Se reduction)
Mn(II) oxidizer (Mn channel)

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.

Tolerance:Up to 10 mM Mn²⁺
mnxDEFGmntRmntABCmnxG (MCO)
Radiation-resistant metal reducer (U, Cr)

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.

Tolerance:Survives 5 kGy γ-radiation + 500 µM Cr(VI)
PprI (IrrE)dr1159 (ChrR-homolog)pprArecAssbMn-antioxidant complex
Photosynthetic arsenite methylator

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.

Tolerance:10 mM As(III) with ArsM methylation
arsMarsRarsCarsHpufLM (photosystem)nifHDK
Acidophilic metal leacher (Cu, Zn, Co)

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.

Tolerance:Growth at pH 1.5–3.0, 800 mM Fe²⁺
rus (rusticyanin)iro (iron oxidase)tetH (tetrathionate hydrolase)copA*czcD*
Sulfate reducer / metal precipitator

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.

Tolerance:> 200 µM U(VI), 500 µM Cr(VI)
dsrABCD (dissimilatory sulfite reductase)hmc (high-MW cytochrome)fdhABUO₂²⁺ reductase (c₃-type cyt)
Chromate/selenate reducer (broad-spectrum)

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.

Tolerance:2 mM Cr(VI), 10 mM SeO₄²⁻
chrR*nemA (N-ethylmaleimide reductase)yieF (ChrR-homolog)nfsA/nfsBgrxA (glutaredoxin)
Hyperthermophilic tungstoenzyme host

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.

Tolerance:> 500 µM WO₄²⁻ (native)
aor (W-AOR)tupABCwtpABCmoaA (Mo-PPT synth.)narGHI (W-nitrate reductase)
Vanadate-respiring anaerobe

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.

Tolerance:6 g/L vanadate V(V)
vanA (vanadate reductase)vbp (V-binding protein)narGHI (nitrate reductase)hydrogenase
Mo-cofactor biosynthesis specialist

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.

Tolerance:10 mM MoO₄²⁻ (homeostatic)
modABCmodE (Mo sensor)moaABCDE (Moco synth.)sorAB (sulfite oxidase)xdhABC (xanthine DH)
Thallium-tolerant Mn-oxidizer

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.

Tolerance:~50 µM Tl(I) (Mn-oxidation mediated)
mnxGmnxEFsodA (Mn-SOD)katE (catalase)copA (Cu export)
Bismuth efflux model (RND pumps)

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.

Tolerance:~128 µg/mL Bi-subsalicylate
HP0605 (tolC)HP0606 (acrB)HP0607 (acrA)nixA (Ni importer)hpn (Ni metallothionein)
Thermophilic W-cofactor specialist

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.

Tolerance:5 mM WO₄²⁻ (thermophilic)
tupABCaor (W-AOR)wtp operontth_RS09230 (W-dependent DMSO reductase)
V-nitrogenase & Mo-cofactor donor

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.

Tolerance:200 µM VO₄³⁻ / 10 mM MoO₄²⁻
vnfDGK (V-nitrogenase)vnfHmodABCnifDK (Mo-nitrogenase)FeMoco biosynthesis
Arsenic methylation / DtxR regulator model

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.

Tolerance:10 mM As(V) / 5 mM As(III)
arsRBCarsM (As methyltransferase)dtxR (Fe/Mn regulator)mntH (Mn import)
Plasmid-cured multi-metal reference

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.

Tolerance:Reduced (reference baseline)
Δ-pMOL28 (chr/mer lost)Δ-pMOL30 (czc/pbr lost)chromosomal zntAcopS/copR
Chromate reduction & multi-drug efflux

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.

Tolerance:5 mM CrO₄²⁻ / 1 mM Cd²⁺
chrR (chromate reductase)mexAB-oprM (RND efflux)czr operonPA2065 (Cd efflux)
Dissimilatory selenate/arsenate respiration

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.

Tolerance:10 mM SeO₄²⁻ / 20 mM AsO₄³⁻
arrAB (arsenate reductase)srdBCA (selenate reductase)napABnrfA
Uranium & heavy metal biosorption (S-layer)

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.

Tolerance:5 mM U(VI) (biosorption)
slfB (S-layer protein)U-binding S-layer domainsmerA (plasmid-borne)pbrR-like
Cadmium/Lead/Arsenic P-type ATPase donor

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.

Tolerance:5 mM Cd²⁺ / 1 mM Pb²⁺
cadA (Cd/Pb ATPase)cadC (Cd sensor)arsRBC (pI258)blaZ (β-lactamase)
Molybdenum cofactor (Moco) biosynthesis

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.

Tolerance:50 mM MoO₄²⁻ (Mop sequestration)
mop (Mo storage)modABCxdhABC (xanthine DH)dorA (DMSO reductase)
Sulfate reducer for CdS/Bi₂S₃ nanoparticle biogenesis

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.

Tolerance:30 mM sulfate / 500 µM Cd²⁺
dsr operon (sulfite reductase)sat (sulfate adenylyltransferase)apr (APS reductase)fhc (formate DH)
Recombinant protein expression chassis

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.

Tolerance:Varies (expression-dependent)
T7 RNAP (DE3)lon⁻ ompT⁻ (protease-deficient)pET system compatibleBL21-Gold (Hte)
S-layer metal biosorption platform

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.

Tolerance:500 µM Cd²⁺ / 200 µM U(VI)
rsaA (S-layer, 98 kDa)rsaA-6xHis fusionsheavy metal binding peptidesparacrystalline lattice
Enzymes

Key Enzymes by Operon

MerA — Mercuric Reductase

EC 1.16.1.1
Catalyzed Reaction
Hg²⁺ + NADPH + H⁺ → Hg⁰ + NADP⁺ + 2H⁺
k_cat
~8.6 s⁻¹
K_m
~9 µM (Hg²⁺)
Structure
Homodimer, ~120 kDa
Cofactors
NADPHFADActive Cys residues

Disulfide 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

MerPHg
Periplasm

First capture of extracellular Hg²⁺, transfer to MerT via thiol binding.

MerTHg
Inner membrane

Specific channel transporting Hg²⁺ from periplasm to cytoplasm.

MerC/MerEHg
Inner membrane

MerC: alternative Hg²⁺ entry. MerE: specialized in CH₃Hg⁺ and phenylmercury import.

ArsB/ArsAAs
Inner membrane

ArsB antiporter (H⁺-driven) + ArsA ATPase for enhanced arsenite expulsion. Primary detoxification route.

ArsDAs
Cytoplasm

Transfers As(III) to ArsA with high efficiency, increasing pump affinity by ~3× and reducing Km.

CopZCu
Cytoplasm

CXXC-motif metallochaperone shuttling Cu⁺ to CopA P-type ATPase. Prevents free Cu⁺ toxicity.

CusABCCu
Inner + Outer membrane

RND-type transenvelope complex exporting Cu⁺/Ag⁺ directly to extracellular space. Bypasses periplasm.

CadA/CadCCd
Inner membrane / Cytoplasm

CadA: P-type ATPase for Cd²⁺ efflux. CadC: sensor that de-represses cadA upon Cd²⁺ detection.

CzcCBAZn
Inner + Outer membrane

Tripartite RND efflux system providing high-level Zn²⁺/Cd²⁺/Co²⁺ resistance via proton-driven transenvelope export.

CzcDZn
Inner membrane

CDF-family antiporter providing basal Zn²⁺ efflux. His-rich cytoplasmic loop buffers Zn²⁺ before export.

ChrACr
Inner membrane

CHR superfamily chromate-specific antiporter. Only known CrO₄²⁻-specific efflux pump, driven by proton motive force.

PbrA/PbrDPb
Inner membrane / Cytoplasm

PbrD sequesters Pb²⁺ intracellularly and delivers it to PbrA P-type ATPase for ATP-driven efflux.

CnrCBACo
Inner + Outer membrane

RND-type tripartite system from C. metallidurans. Primary Co²⁺/Ni²⁺ export route via proton antiport.

RcnACo
Inner membrane

NiCoT-family transporter providing secondary Co²⁺/Ni²⁺ efflux. Regulated by RcnR repressor.

TerCTe
Inner membrane

Integral membrane protein conferring tellurite resistance. May facilitate TeO₃²⁻ export or intracellular reduction to Te⁰.

NccCBANi
Inner + Outer membrane

RND-type tripartite efflux system from A. xylosoxidans. Optimized for Ni²⁺ export with Co²⁺ as secondary substrate.

SilPAg
Inner membrane

Silver-specific P-type ATPase pumping Ag⁺ to periplasm. Receives Ag⁺ from SilF periplasmic chaperone.

SilCBAAg
Inner + Outer membrane

RND complex ejecting periplasmic Ag⁺ to extracellular space. Works in tandem with SilP for full Ag⁺ detoxification.

SilF/SilEAg
Periplasm

SilE: Ag⁺-binding protein (His-rich) capturing free Ag⁺. SilF: metallochaperone shuttling Ag⁺ from SilE to SilCBA/SilP.

SerABCSe
Periplasm

Molybdoenzyme complex reducing SeO₄²⁻ to SeO₃²⁻. First step of selenium detoxification pathway in T. selenatis.

YdfNSe
Cytoplasm

Thioredoxin-dependent reductase converting SeO₃²⁻ to Se⁰ red nanoparticles. Visual readout of Se trinary state.

ArsB (Sb)Sb
Inner membrane

Cross-reactive ArsB antiporter exporting Sb(III) via H⁺ antiport. Same transporter as arsenite efflux with similar affinity.

MtrCABU
Outer membrane

Transmembrane electron conduit (MtrC-MtrA-MtrB) enabling extracellular UO₂²⁺ reduction by Shewanella. Decaheme cytochromes relay electrons.

OmcA/OmcSU
Outer membrane / pili

Decaheme cytochromes on cell surface (Shewanella OmcA) or conductive pili (Geobacter OmcS). Direct contact with UO₂²⁺ for reduction.

MntABCMn
Inner membrane

High-affinity Mn²⁺ import controlled by MntR. MntC binds periplasmic Mn²⁺, MntB is the permease, MntA hydrolyzes ATP.

MntHMn
Inner membrane

NRAMP-family H⁺-coupled Mn²⁺ importer. Secondary import route complementing MntABC. Also imports Fe²⁺.

PprI/IrrEU
Cytoplasm

Master switch protein from D. radiodurans that activates DNA repair, ROS detoxification, and metal resistance genes simultaneously. Enhances processor reliability under radiation stress.

DsrABCd
Cytoplasm

Key enzyme from Desulfovibrio producing H₂S which precipitates metals as insoluble sulfides (HgS, CdS, PbS, ZnS, CuS). Alternative metal immobilization pathway.

Rus (Rusticyanin)Cu
Periplasm

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.

NemA/YieFCr
Cytoplasm

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.

TupABCW
Inner membrane

ABC-type tungstate importer. TupA periplasmic binding protein (Kd ~0.5 nM) discriminates WO₄²⁻ from MoO₄²⁻. TupB permease + TupC ATPase. Primary W acquisition system.

WtpABCW
Inner membrane

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.

VBP (secreted)V
Extracellular

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.

ModBCMo
Inner membrane

Inner membrane components of the ModABC molybdate transporter. ModB provides the transmembrane channel; ModC hydrolyzes ATP. Expression repressed by ModE when Mo is sufficient.

HP0605/TolCBi
Outer membrane

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.

KdpFABCTl
Inner membrane

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.

KefB/KefCTl
Inner membrane

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.

CopACu
Inner membrane

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.

ModAMo
Periplasm

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.

NikABCDENi
Inner membrane

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.

UreENi
Cytoplasm

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.

PitAV
Inner membrane

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.

BirAB (AcrAB)Bi
Inner membrane

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.

ZnuABCZn
Inner membrane

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/PbrCPb
Inner membrane / Periplasm

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.

TehABTe
Inner membrane

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.

ArsP (ACR3)Sb
Inner membrane

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.

CorACo
Inner membrane

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⁺].

µFluidics

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)

Volume: 0.5–5 µL · Material: PDMS/glass

Isolated micro-chambers containing bacterial populations immobilized in an alginate matrix. Each chamber maintains a stable trinary state.

Diffusion Channels (Bus)

Cross-section: 50–200 µm · Flow rate: 0.1–10 µL/min

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

Volume: 10–50 µL · Multi-input

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

UV LED 365 nm · pH-stat · Syringe pump

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)

Christmas-tree network · 8–16 output concentrations · Logarithmic or linear

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)

PDMS multilayer · 400 addressable valves · 15 psi actuation

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

Peltier elements · Range: 4–45°C · ±0.1°C precision

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

16-channel · PMT + CCD · 350–750 nm spectral range

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

20 output channels · PTFE tubing · Class III containment

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

NADPH/ATP recycling · Glucose-6P dehydrogenase · Creatine kinase

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

Acoustic (40 kHz) + chemical · Throughput: 10⁶ cells/min

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)

T-junction + flow-focusing · 50 pL – 5 nL droplets · 10 kHz generation rate

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

Residence time: 5–120 min · Volume: 50–500 µL · Serpentine geometry

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

20-channel · Au/Pt/C screen-printed electrodes · ±1 nA sensitivity

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

32 reservoirs · 50 µL each · Evaporation-sealed

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

NdFeB micro-magnets · 500 mT gradient · Capture efficiency: >98%

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

40-channel solenoid array · 0–30 psi · 5 ms switching

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

170 µm borosilicate coverslip · 20× NA 0.75 objective compatible · Multi-spectral

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

Control Module
µController + UV LED + pH-stat
PDMS Chip
Inputs
Toxic (-1)
Ionic (0)
Detoxified (+1)
Registers
3 chambers
alginate + bacteria
ALU
Multi-Enzyme ALU
20 operons
Sensors
GFP / AAS
Trit readout
Detection

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.

20+1
Biosensor Channels
20 metal + 1 MUX
12
Readout Technologies
orthogonal methods
400–720 nm
Spectral Range
13 fluorophores
10
Cofactors Tracked
critical metabolites
12
Cross-talk Pairs
mitigated interactions
<30 s
Cycle Readout
SWASV full scan
Select Channel
CH 1HgActivator (MerR-family)

MerR-GFP / AAS / GC-ICP-MS

LOD: 0.01 nM Hg²⁺15–30 min0.01 nM – 100 µM
Reportersuperfolder GFP (sfGFP)
PromoterPmerT (divergent from merR)
RegulatorMerR homodimer
Signal TypeTriple orthogonal
FluorophoresfGFP
Excitation485 nm
Emission509 nm
Trit State Readout — 3 Logical States
−1
MeHg (CH₃Hg⁺)
Signal: GC-ICP-MS m/z 202

Methylmercury detected by gas chromatography hyphenated ICP-MS. MerB demethylation activity confirmed.

0
Hg²⁺ (ionic)
Signal: sfGFP fluorescence (509 nm)

MerR activates PmerT → sfGFP expression proportional to ionic mercury. Linear 3-log range.

+1
Hg⁰ (metallic)
Signal: Cold-vapor AAS (253.7 nm)

MerA reductase product Hg⁰ quantified by cold-vapor atomic absorption at the mercury resonance line.

Cross-talk

Minimal — MerR is exquisitely Hg-specific. Au(I) and Cd²⁺ show <0.1% cross-reactivity.

Secondary Readout

Electrochemical anodic stripping at −0.4 V (Hg/Au film)

Method

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.

Readout Technology Matrix — 12 Orthogonal Methods
💡
Fluorescence
13 channels
Hg, As, Cu, Cd, Zn, Cr, Pb, Co, Ni, Sb, W, V, Mo

Genetically encoded fluorescent reporters (GFP/mCherry/YFP/CFP/BFP/etc.) under metal-responsive promoters. 13 orthogonal fluorophores spanning 440–720 nm.

Bioluminescence
3 channels
Mn, Bi, (Te secondary)

luxCDABE operon from Vibrio. Autonomous light emission — no external excitation. Ideal for in-field deployment and miniaturized readout.

🎨
Colorimetric
6 channels
Se, Te, Mn, U, Tl, Cr

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.

Electrochemical
20 channels
All metals (SWASV multiplexer)

Screen-printed electrode array with SWASV. Provides quantitative backup for all 20 channels. <30 s scan time. nM sensitivity.

🔮
Plasmonic (SPR)
2 channels
Ag, Cu

Biogenic metal nanoparticle surface plasmon resonance. Ag⁰ NPs at ~420 nm, Cu⁰ NPs at ~570 nm. Self-reporting nanoparticle biosynthesis.

🔬
Raman Spectroscopy
2 channels
Se, Te

Vibrational fingerprint of elemental nanoparticles. Se⁰ at 233 cm⁻¹, Te⁰ at 121 cm⁻¹. Phase identification (amorphous vs crystalline).

🧲
EPR Spectroscopy
2 channels
V, U

Electron paramagnetic resonance for paramagnetic metal species. V(IV) 8-line pattern (⁵¹V I=7/2), U(V) intermediate detection.

🔥
Atomic Absorption
4 channels
Hg, As, Sb, Tl

AAS/AFS with hydride generation (As, Sb) or cold vapor (Hg). Element-specific confirmation at resonance wavelengths.

⚛️
Mass Spectrometry
5 channels
Hg, Co, Ni, Mo, Bi

ICP-MS for isotope-specific quantification. ⁹⁹Mo radiotracer, ²⁰⁹Bi monoisotopic, ⁵⁸Ni, ⁵⁹Co, ²⁰²Hg.

☢️
X-ray Methods
3 channels
U, Te, Tl

XRD for crystal structure (UO₂ fluorite), XRF for element ID (Te Kα), XPS for surface chemistry (Tl-MnO₂).

📡
Impedance (EIS)
8 channels
Cu, Zn, Cd, Pb, Co, Ni, Ag, Mn

Electrochemical impedance spectroscopy. Charge-transfer resistance shifts on metal-protein binding. Label-free, real-time kinetics. 10 Hz–100 kHz sweep.

🧬
qPCR / RT-qPCR
20 channels
All metals (transcript level)

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 sweep
ElectrodesScreen-printed carbon electrode array (SPCE)
Scan Rate50 mV/s
Resolution12-bit ADC (4096 levels per channel)
InterfaceSPI → FPGA → USB
SWASV Stripping Potentials (vs. Ag/AgCl)
Hg: -0.40 V
As: -0.10 V
Cu: +0.05 V
Cd: -0.65 V
Zn: -0.98 V
Cr: -0.20 V
Pb: -0.35 V
Co: -0.30 V
Te: -0.55 V
Ni: -0.50 V
Ag: +0.25 V
Se: -0.45 V
Sb: -0.15 V
U: -0.80 V
Mn: -1.10 V
W: -0.60 V
V: -0.70 V
Mo: -0.75 V
Tl: -0.48 V
Bi: -0.22 V

Integrated 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.

Signal Transduction Cascades — 13 Regulatory Families
MerR Family
Passive
HgCuZnPb

Activator — metal binding triggers DNA underwinding at promoter spacer (19→17 bp effective), switching RNAP from closed to open complex. Sub-second conformational switch.

MerRCueRZntRPbrR
Cofactors: None
ArsR/SmtB Family
Passive
As/SbCdZn

Repressor — metal binding at α3N or α5 site induces dissociation from operator DNA, allowing RNAP access. Derepression kinetics: t½ ~2–5 min.

ArsRCadCSmtB
Cofactors: None
Two-Component (TCS)
1 ATP/cycle
AgCuBi

Sensor kinase autophosphorylates His upon periplasmic metal detection → phosphotransfer to RR Asp → RR~P activates target promoter. ATP-dependent signal amplification.

SilRSCusRSBisRS
Cofactors: ATP, Mg²⁺
ECF Sigma Factors
Passive
CoNi

Anti-sigma (Y) sequesters sigma (H). Periplasmic sensor (X) binds metal → conformational change releases H → H recruits RNAP to σ-dependent promoter.

CnrYXHNccYXH
Cofactors: None
DtxR/MntR Family
Passive
Mn

Metal-activated repressor. Binuclear Mn²⁺ binding (sites A+C) stabilizes DNA-binding conformation → represses import. Simultaneously derepresses efflux for dual-mode regulation.

MntR
Cofactors: None
ModE Family
Passive
Mo

Molybdate-binding TF. Mo-ModE dimer represses modABC importer AND activates moaABCDE for Moco biosynthesis. Dual-function self-regulating sensor.

ModE
Cofactors: Moco (product)
ChrB/ChrS Sensors
Passive
Cr

Membrane-associated chromate sensor. ChrB senses external CrO₄²⁻ concentration and positively regulates chrA efflux expression. ChrS provides secondary chromate sensing for signal amplification.

ChrBChrS
Cofactors: None
TerB/TerD Sensors
Passive
Te

The 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.

TerBTerDTerZ
Cofactors: None
Oxyanion Transporters
Passive
VW

Vanadate 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.

PitAVBP
Cofactors: None
Chalcogen Reductases
NADPH
Se

Selenium sensing via selenate reductase activity. SerABC-mediated reduction produces Se⁰ nanoparticles as a direct visual signal. SelR cysteine-selenocysteine switch regulates selenoprotein expression.

SelRSerABC
Cofactors: Moco (SerA)
K⁺ Mimicry System
1 ATP/cycle
Tl

Tl⁺ 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.

KdpDEKefB
Cofactors: ATP, GSH
MtrCAB/PpcA Pathway
Electron donor (lactate/H₂)
U

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).

PpcACymAOmcA
Cofactors: Heme, Menaquinone
Biosensor Cofactor Requirements — 10 Essential Metabolites
NADPHCRITICAL
~50 nmol/min/mg
Reductase electron donor
MerA (Hg)ChrR (Cr)ArsC (As)SerABC (Se)
Regen: G6PDH / ICDH / MaeB
NADHCRITICAL
~200 nmol/min/mg
ETC & dehydrogenase cofactor
NDH-2LuxCDABE (Mn/Bi biolum.)
Regen: TCA cycle (MDH, αKGDH)
FAD/FMNCRITICAL
~2 nmol/min/mg
Flavin prosthetic groups
MerA (FAD)ChrR (FMN)MtrCAB (FAD)
Regen: RibABCDE pathway
GSHCRITICAL
~5 mM pool
Thiol buffer & metal chelation
As(III)-GSHCd-GSH effluxSb-GSH
Regen: GshA/GshB (γ-GCS + GS)
ATPCRITICAL
~3 mM steady-state
P-type ATPase & kinase energy
CadA (Cd/Pb)ZntA (Zn)CopA (Cu)SilP (Ag)
Regen: F₁F₀-ATPase / SLP
SAM
~0.5 nmol/min/mg
Methyl donor
ArsM (As→TMA)MerB (organomercury)
Regen: MetK (MAT)
Thioredoxin
~10 µM pool
Disulfide reduction
ArsC (Trx class)Oxidative stress
Regen: TrxB reductase
Fe-S ClustersCRITICAL
~15 min/cluster
Electron transfer prosthetics
Ferredoxin (W, V)Hydrogenase
Regen: ISC/SUF pathway
Moco
~30 min assembly
Molybdenum cofactor
ModABC (Mo)DMSORNarGHI
Regen: MoaABCDE + MobA
Cobalamin (B12)
~60 min de novo
Radical SAM cofactor
MerB (2°)MetH
Regen: CobA-T pathway
Cross-Reactivity Matrix — 12 Critical Pairs
Zn²⁺ / Cd²⁺HIGH

ZntR and CadC both bind divalent d¹⁰ ions. CadC has ~100× Cd selectivity via α5 site geometry.

Mitigation: Kinetic gating: Cd response at 5 min, Zn at 15 min. Differential promoter strengths.
Cu⁺ / Ag⁺HIGH

CueR binds both monovalent d¹⁰ ions via Cys-Cys coordination. SilRS provides Ag-specific bypass.

Mitigation: SilRS reporter for Ag; CueR gated by SilRS negative signal.
As(III) / Sb(III)MEDIUM

ArsR Cys32/34/37 triad binds both metalloids identically.

Mitigation: ArsM methylation produces volatile TMA(III) from As only. Headspace GC-MS discriminator.
Co²⁺ / Ni²⁺MEDIUM

CnrYXH and NccYXH are paralogs with overlapping metal specificity above 100 µM.

Mitigation: ECF sigma promoter swap: PcnrC (Co) vs PnccC (Ni). >50× discrimination at <100 µM.
Hg²⁺ / Cu²⁺LOW

MerR is exquisitely Hg-selective (Kd ~10⁻³⁸ M). Cu >1 mM may weakly activate.

Mitigation: CueR reporter subtracts Cu signal. MerR threshold well below Cu interference range.
Pb²⁺ / Cd²⁺LOW

PbrR has ~200× Pb selectivity via Cys-His-Glu coordination. CadA transports both.

Mitigation: Reporter-level: PbrR-GFP vs CadC-mCherry. Efflux cross-talk managed by concentration.
Mn²⁺ / Fe²⁺LOW

MntR has ~1000× Mn selectivity via binuclear site A geometry.

Mitigation: Iron-limited media + Fur keeps Fe²⁺ below MntR activation threshold.
V(V) / Cr(VI)LOW

Both oxyanions similar to phosphate/sulfate.

Mitigation: ChrB sensor is Cr-specific; V uses NarGHI reduction with distinct reporter.
Se / TeMEDIUM

Both Group 16 chalcogens. Selenate/tellurate reductases (SerABC) show ~10% cross-activity toward TeO₄²⁻.

Mitigation: Se⁰ produces red NPs (233 cm⁻¹ Raman), Te⁰ produces black NPs (121 cm⁻¹). Spectral discrimination resolves overlap.
W(VI) / Mo(VI)HIGH

WO₄²⁻ and MoO₄²⁻ are near-identical oxyanions. ModA binds both with similar Kd (~20 nM). ModE repressor cannot distinguish.

Mitigation: TupA has >1000× selectivity for W over Mo. Use TupABC pathway for W channel; ModABC for Mo only. Sequential media with tungstate-depleted Mo loading.
Tl⁺ / K⁺HIGH

Tl⁺ mimics K⁺ (ionic radii: 1.49 vs 1.38 Å). KdpFABC imports both. All K⁺ channels are Tl⁺-permeable.

Mitigation: DPAdSV with Bi-film electrode provides Tl-specific electrochemical readout. K⁺-free minimal media eliminates background. δ-MnO₂ colorimetric readout specific to Tl⁺ sorption.
Sb(III) / Bi(III)LOW

Both Group 15 heavy pnictogens but different coordination chemistry. Sb(III) prefers sulfur ligation, Bi(III) prefers oxygen/nitrogen.

Mitigation: ArsR is Sb-specific (Cys coordination). BisRS two-component system is Bi-specific (periplasmic His-kinase). Orthogonal detection pathways with no cross-reactivity at regulatory level.

Complete Operational Pipeline

1
Injection

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).

2
Storage & Encoding

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.

3
Routing

Pneumatic valves direct flows to the ALU chamber according to the desired instruction (T-AND, T-OR, T-NOT).

4
Computation

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.

5
Readout

Biosensors (GFP fluorescence, electrochemistry, AAS) determine the resulting trinary state and transmit to the controller.

6
Control Loop

The microcontroller adjusts pH, UV, and NADPH flow for the next cycle. The processor is ready for a new operation.

Applications

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.

🌍

Environmental Bioremediation

Intelligent soil and water decontamination

The trinary processor drives autonomous, programmable bioremediation: PMBT bacterial colonies detect, compute the optimal strategy, and decontaminate without human intervention.

Problem

Abandoned mining sites and industrial effluents contain variable concentrations of methylmercury (MeHg) and ionic mercury (Hg²⁺). Conventional chemical approaches are costly and non-selective.

Trinary Solution

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.

Advantage

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.

> 98%
Hg²⁺ Removal
~30 min
Cycle Time
~$0.1/L
Est. Cost
Continuous
Autonomy
Technical

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
  1. 1PCR amplification of merA, merB and merR genes from C. metallidurans CH34
  2. 2Cloning into the pBBR1MCS-5 broad-host-range shuttle vector (Ptrc inducible promoter)
  3. 3Transformation of P. putida KT2440 by electroporation (2.5 kV, 25 µF)
  4. 4Selection on LB medium + gentamicin (30 µg/mL) + HgCl₂ (10 µM)
  5. 5Verification by Sanger sequencing and MerA activity assay (NADPH absorbance at 340 nm)
  6. 6Construction of the MerR-sfGFP reporter for trinary readout
  7. 7Submission of genetic constructs (merA-sfGFP, merB-mCherry, merR-YFP) to the iGEM registry in standardized BioBricks™ format
  8. 8Parallel cloning of ars (arsenic), cop (copper) and cad (cadmium) operons for multi-metal extension

KineticsMathematical Model

Michaelis-Menten for MerA (Hg)

v_MerA = V_max,A · [Hg²⁺] / (K_m,A + [Hg²⁺])
V_max,A
~516 nmol/min/mg (kcat ~8.6 s⁻¹)
Fox & Walsh, 1982
K_m,A (Hg²⁺)
~9 µM
Barkay et al., 2003
K_m,A (NADPH)
~15 µM
Fox & Walsh, 1982

Michaelis-Menten for MerB (Hg)

v_MerB = V_max,B · [CH₃Hg⁺] / (K_m,B + [CH₃Hg⁺])
V_max,B
~1.2 µmol/min/mg
Lafrance-Vanasse et al., 2009
K_m,B
~0.5 µM
Lafrance-Vanasse et al., 2009

ArsC Reductase (As)

v_ArsC = V_max · [As(V)] / (K_m + [As(V)])
kcat
~0.02 s⁻¹
Messens et al., 2002
K_m (As(V))
~2 mM
Messens et al., 2002
Cofactor
Thioredoxin/Glutaredoxin
Martin et al., 2001

CueO Multicopper Oxidase (Cu)

v_CueO = V_max · [Cu⁺] / (K_m + [Cu⁺])
kcat
~5.7 s⁻¹ (with Cu⁺ substrate)
Singh et al., 2011
K_m (Cu⁺)
~80 µM
Grass & Rensing, 2001
Cofactor
4 Cu atoms (T1/T2/T3 centers), O₂
Roberts et al., 2002

ChrR Chromate Reductase (Cr)

v_ChrR = V_max · [CrO₄²⁻] / (K_m + [CrO₄²⁻])
kcat
~0.12 s⁻¹
Ackerley et al., 2004
K_m (Cr(VI))
~50 µM
Park et al., 2000
Cofactor
NADH, FMN
Ackerley et al., 2004

Generalized Regulator Activation (Hill)

f_act = [Mⁿ⁺]ʰ / (K_dʰ + [Mⁿ⁺]ʰ)
MerR K_d
~1 nM (Hg²⁺)
Ralston & O'Halloran, 1990
CueR K_d
~10⁻²¹ M (Cu⁺)
Changela et al., 2003
ArsR K_d
~1 µM (As(III))
Xu et al., 1998
n (Hill)
~1.5–2.0 (regulator-dependent)
cooperativity estimates

CadA P-type ATPase Efflux (Cd)

v_CadA = V_max · [Cd²⁺]_cyt / (K_m + [Cd²⁺]_cyt) · [ATP] / (K_ATP + [ATP])
kcat
~8 ions/s
Nucifora et al., 1989
K_m (Cd²⁺)
~0.3 µM
Tsai et al., 2002
K_ATP
~0.1 mM
Tsai et al., 2002
Substrate specificity
Cd²⁺ >> Pb²⁺ > Zn²⁺
Rensing et al., 1998

MnxG Mn(II) Oxidase (Mn)

v_MnxG = V_max · [Mn²⁺] / (K_m + [Mn²⁺]) · [O₂] / (K_O₂ + [O₂])
kcat
~1.5 s⁻¹
Soldatova et al., 2017
K_m (Mn²⁺)
~20 µM
Dick et al., 2008
K_O₂
~50 µM (ambient O₂ sufficient)
Butterfield et al., 2013
Product
MnO₂ birnessite nanoparticles (brown precipitate)
Bargar et al., 2005

SerABC Selenate Reductase (Se)

v_SerABC = V_max · [SeO₄²⁻] / (K_m + [SeO₄²⁻])
kcat
~12 s⁻¹
Schröder et al., 1997
K_m (SeO₄²⁻)
~16 µM
Schröder et al., 1997
Cofactor
Molybdopterin (Mo-MGD), [4Fe-4S] clusters, cyt b
Maher & Macy, 2002
Product
SeO₃²⁻ → Se⁰ red nanoparticles (two-step)
Lenz & Lens, 2009

MtrCAB Electron Conduit — U(VI) Reduction

v_UO₂ = k_ET · [c-heme_red] · [UO₂²⁺] / (K_m + [UO₂²⁺])
k_ET (OmcA)
~0.8 s⁻¹ per heme
Shi et al., 2007
K_m (UO₂²⁺)
~50 µM
Marshall et al., 2006
Heme count
10 c-type hemes per MtrC + 10 per OmcA = 20 electron relays
Richardson et al., 2012
Product
UO₂(s) uraninite nanoparticles (XRD-confirmed)
Lovley et al., 1991

RND Efflux Pump Kinetics (CzcCBA / CnrCBA / SilCBA)

v_RND = V_max · [M²⁺]_peri / (K_m + [M²⁺]_peri) · Δp / Δp_max
CzcCBA kcat
~100 Zn²⁺ ions/s
Nies, 2003
CnrCBA kcat
~80 Co²⁺ ions/s
Tibazarwa et al., 2000
SilCBA kcat
~60 Ag⁺ ions/s
Silver, 2003
Δp (PMF)
~150–180 mV (proton motive force)
Goldberg et al., 1999
Stoichiometry
2 H⁺ per metal ion (antiport)
Nies & Silver, 1995

Biosensor Response Curve (Generic Reporter)

F(t) = F_max · [Mⁿ⁺]ʰ / (EC₅₀ʰ + [Mⁿ⁺]ʰ) · (1 − e^(−t/τ))
MerR-GFP EC₅₀
~5 nM Hg²⁺ (τ ≈ 30 min)
Virta et al., 1995
ArsR-mCherry EC₅₀
~50 nM As(III) (τ ≈ 45 min)
Stocker et al., 2003
CueR-YFP EC₅₀
~1 nM Cu⁺ (τ ≈ 20 min)
Changela et al., 2003
Dynamic range
3–5 decades (typ. 10 nM to 100 µM)
van der Meer & Belkin, 2010
h (Hill coeff.)
1.2–2.5 (varies by regulator)
empirical fits

Coupled Multi-Metal ODE System

d[Mⁿ⁺]/dt = v_import − v_efflux − v_transform
v_import
Operon-specific uptake (MerT, ArsB reverse, CopA import, etc.)
per-metal transport kinetics
v_efflux
P-type ATPase / RND pump (CadA, ZntA, CopA, CnrCBA, SilCBA)
metal-specific
v_transform
Reductase/oxidase/methyltransferase (MerA, ArsC, ChrR, CueO, MnxG)
enzymatic conversion
d[cofactors]/dt
NADPH, thioredoxin, ATP consumed and regenerated
metabolic coupling

Cross-Talk Inhibition Matrix

v_eff,i = v_i · ∏(j≠i) (1 − α_ij · [Mⁿ⁺_j] / K_inhib,ij)
α_Hg→Cu
~0.15 (Hg²⁺ competes with Cu⁺ at CopA)
Rensing & Grass, 2003
α_As→Sb
~0.85 (ArsR binds both As(III) and Sb(III))
Ordóñez et al., 2008
α_Zn→Cd
~0.40 (CzcCBA accepts both Zn²⁺ and Cd²⁺)
Nies, 2003
α_Co→Ni
~0.60 (CnrCBA/NccCBA cross-react)
Tibazarwa et al., 2000
Mitigation
Temporal multiplexing (process metals sequentially) or spatial isolation
design strategy

Thermodynamique de réduction — ΔG°' standard

ΔG°' = −nFΔE°' = −nF(E°'_accepteur − E°'_donneur)
Hg²⁺/Hg⁰ E°'
+0.85 V ; ΔG°' = −164 kJ/mol (n=2)
Bard et al., 1985
Cr(VI)/Cr(III) E°'
+1.33 V ; ΔG°' = −385 kJ/mol (n=3)
Lide, CRC Handbook
U(VI)/U(IV) E°'
+0.086 V ; ΔG°' = −16.6 kJ/mol (n=2)
Lovley et al., 1991
Se(VI)/Se(0) E°'
+0.75 V ; ΔG°' = −434 kJ/mol (n=6)
Schröder et al., 1997
Te(IV)/Te(0) E°'
+0.59 V ; ΔG°' = −228 kJ/mol (n=4)
Baesman et al., 2007
F (Faraday)
96 485 C/mol
constante fondamentale

Équation de Nernst — Potentiel redox in vivo

E = E°' + (RT/nF) · ln([ox]/[red])
R (constante gaz)
8.314 J/(mol·K)
constante fondamentale
T (température)
310 K (37°C) typique
conditions physiologiques
RT/F à 37°C
26.7 mV (facteur thermique)
calculé
Exemple Hg
E = 0.85 + 0.0134·ln([Hg²⁺]/[Hg⁰]) V
n=2
Exemple U
E = 0.086 + 0.0134·ln([UO₂²⁺]/[UO₂]) V
n=2

Entropie de Shannon — Capacité informationnelle trinary

H₃ = −Σ p_i · log₃(p_i) ; C = N · log₂(3) bits
H₃ (max)
1 trit = log₂(3) ≈ 1.585 bits (équiprobable)
théorie de l'information
1 tryte (3 trits)
log₂(27) ≈ 4.755 bits
calculé
20 métaux (20 trits)
3²⁰ = 3 486 784 401 états ≈ 31.7 bits
calculé
Avantage vs binaire
+58.5% de densité informationnelle par élément
log₂(3)/1 = 1.585
Redondance (code correcteur)
Hamming ternaire : d_min = 3 avec 7 trits → corrige 1 erreur
Golay ternaire

Stœchiométrie — Bilan massique par cycle de calcul

Σ(réactifs) = Σ(produits) ; n_NADPH = n_e− / 2
MerA (1 cycle Hg)
1 Hg²⁺ + 1 NADPH → 1 Hg⁰ + 1 NADP⁺ + H⁺
Fox & Walsh, 1982
ChrR (1 cycle Cr)
1 CrO₄²⁻ + 3 NADH → 1 Cr³⁺ + 3 NAD⁺ (6e⁻)
Ackerley et al., 2004
ArsC (1 cycle As)
1 As(V) + 2 Trx_red → 1 As(III) + 2 Trx_ox (2e⁻)
Messens et al., 2002
MnxG (1 cycle Mn)
2 Mn²⁺ + O₂ + 2H₂O → 2 MnO₂ + 4H⁺ (4e⁻)
Soldatova et al., 2017
Coût énergétique total
~2–10 ATP par commutation de trit (pompe-dépendant)
estimation système

Cinétique de commutation — Temps de transition inter-états

t_switch = t_enzyme + t_diffusion + t_readout ≈ K_m/(V_max·[E]) + L²/(2D) + τ_GFP
t_enzyme (MerA)
~0.12 s (1/kcat = 1/8.6 s⁻¹)
Fox & Walsh, 1982
t_diffusion (Hg²⁺)
~50 s (L=100µm, D=10⁻⁹ m²/s)
Einstein-Smoluchowski
t_readout (GFP)
~1200 s (maturation 20 min)
Virta et al., 1995
Fréquence max
~3 cycles/heure (limité par biosenseur)
estimation système
Optimisation
sfGFP rapide (τ≈4 min) → ~12 cycles/heure
Pédelacq et al., 2006

CircuitsAdvanced Logic Circuits

Trinary Half-Adder

Adds two trits A and B, producing a sum S and a carry C.

S = (A + B) mod 3 C = floor((A + B) / 3)

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.

Complexity: 2 ALU chambers + 6 biosensors

Trinary Multiplexer (TMUX)

Selects one input from three (I₋₁, I₀, I₊₁) based on the selector value S.

Y = I_S (output = input indexed by 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.

Complexity: 3 valves + 1 sensor + optical circuit

Trinary Comparator

Compares two trits A and B: output = -1 if A<B, 0 if A=B, +1 if A>B.

Y = sign(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).

Complexity: 1 chamber + 3 biosensors

Trinary Flip-Flop (Memory)

Stores one trit stably and maintains it between clock cycles.

Q(t+1) = D if CLK=1, else Q(t)

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.

Complexity: 1 isolated chamber + valve + UV LED

Trinary T-XOR

Balanced trinary exclusive OR: detects the difference between two trits.

Y = (A − B) mod 3

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.

Complexity: 2 ALU chambers + 3 biosensors + feedback module

Universal T-NAND Cascade

Functionally complete gate: any trinary function can be built from T-NAND alone.

T-NAND(A,B) = T-NOT(T-AND(A,B)) = −min(A,B)

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.

Complexity: 2 ALU chambers per gate unit

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).

Y = X_s where s = 9·S₂ + 3·S₁ + S₀ (selector decodes 0–19, 7 unused)

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.

Complexity: 20 input channels + 20 valves + 3-trit decoder

T-SHIFT (Trinary Shift)

Shifts a trit value by one position: +1 or -1.

Y = clamp(A + d, -1, +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.

Complexity: 1 chamber + 2 directional valves + syringe pump

T-ROTATE (Cyclic Rotation)

Cyclic rotation of trinary states: -1 → 0 → +1 → -1.

Y = (A + 1) mod 3 − 1

Implementation: Cascade of two MerB (demethylation) and MerA (reduction) chambers with calibrated residence times. An optical bypass (CRISPRi) allows reversing the rotation direction.

Complexity: 2 sequential chambers + optogenetic bypass
Materials

BOM & Fabrication Techniques

Complete Bill of Materials and detailed fabrication protocols for building a functional trinary processor prototype.

BOMBill of Materials

🧬

Biology & Microbiology

8 components
Cupriavidus metallidurans CH341 strain

Donor strain for mer operon

Source of merA, merB, merR, merT, merP, merC, merE genes

~$80
DSMZ (DSM 2839) / ATCC 43123
Pseudomonas putida KT24401 strain

GRAS host chassis

Biosafety level 1, well-documented genetic tools

~$80
ATCC 47054 / DSMZ
Plasmid pBBR1MCS-51 stock

Broad-host-range shuttle vector

GentR, stable replication, compatible with P. putida

~$75
Addgene #87093 or equivalent
sfGFP / mCherry / YFP3 plasmids

Fluorescent reporter genes

Fused to mer promoters for trinary readout

~$65/each
Addgene
LB Medium (Luria-Bertani)500 g powder

Tryptone 10g/L, yeast extract 5g/L, NaCl 10g/L

Culture and selection

~$45
Sigma-Aldrich / Fisher
M9 Minimal Medium500 mL 5×

M9 salts + 0.4% glucose

Culture under controlled conditions

~$35
Sigma-Aldrich M6030
Gentamicin sulfate1 g

Selection antibiotic (30 µg/mL)

Selection of pBBR1MCS-5 transformants

~$30
Sigma-Aldrich G1264
LIVE/DEAD BacLight Kit1 kit

Syto9 + Propidium iodide

Viability verification after immobilization

~$350
Invitrogen L7012

Estimated Cost Summary

🧬 Biology & Microbiology$760960
⚗️ Chemical Reagents$525600
⚗️ Multi-Metal Reagents (As/Cu/Cd)$455530
⚗️ Extended Metal Reagents (Zn/Cr/Pb/Co/Te/Ni/Ag)$335420
⚗️ Se/Sb/U/Mn Reagents$270350
⚗️ W/V/Mo/Tl/Bi Reagents$345445
🦠 Multi-Metal Bacterial Strains$1,6951,920
🔬 Microfluidics & Fabrication$9751,350
Equipment & Electronics$1,5503,800
🧪 Molecular Biology$750900
🛡️ Safety & Consumables$205250
📄 Paper Microfluidics (µPAD)$350880
Estimated Total Prototype Cost
$8,215 – $12,405
Excluding basic lab equipment (fume hood, incubator, microscope, centrifuge, autoclave)

FabricationFabrication Techniques

Soft Lithography

Master technique for fabricating the SU-8 master mold and PDMS chips.

1
Mask design

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.

2
Wafer preparation

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.

3
SU-8 spin-coating

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.

4
UV exposure

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.

5
Development

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.

6
Mold silanization

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.

Literature

Scientific References

17 foundational publications supporting the design of the trinary biochemical processor. Each reference is annotated with its relevance to the project.

1
Boyd, E.S. & Barkay, T. (2012)

The Mercury Resistance Operon: From an Origin in a Geothermal Environment to an Efficient Detoxification Machine

Frontiers in Microbiology, 3, 349 · DOI
Relevance: Phylogenetic analysis demonstrating the thermophilic origin of the merA gene, fundamental for strain selection in the processor.
mer operonevolutiongeothermal
2
Barkay, T., Miller, S.M. & Summers, A.O. (2003)

Bacterial mercury resistance from atoms to ecosystems

FEMS Microbiology Reviews, 27(2-3), 355–384 · DOI
Relevance: Key review covering the molecular mechanisms of MerA and MerB, and the kinetic constants used in our model.
reviewMerAMerBecosystems
3
Fox, B. & Walsh, C.T. (1982)

Mercuric reductase. Purification and characterization of a transposon-encoded flavoprotein containing an oxidation-reduction-active disulfide

Journal of Biological Chemistry, 257(5), 2498–2503 · DOI
Relevance: Primary source of MerA V_max and K_m parameters used in the processor kinetic model.
MerAkineticsNADPHflavoprotein
4
Lafrance-Vanasse, J., Bhatt, M., Bhatt, A., et al. (2009)

Crystal structure of the organomercurial lyase MerB in its free and mercury-bound forms

Journal of Biological Chemistry, 284(2), 938–944 · DOI
Relevance: Crystal structure of MerB at 1.8 Å resolution. Source of structural and mechanistic data for ALU chamber design.
MerBcrystallographymechanism
5
Ralston, D.M. & O'Halloran, T.V. (1990)

Ultrasensitivity and heavy-metal selectivity of the allosterically modulated MerR transcription complex

Proceedings of the National Academy of Sciences, 87(10), 3846–3850 · DOI
Relevance: Demonstration of nanomolar MerR sensitivity — basis of the trinary readout system via genetic biosensor.
MerRbiosensorallosteryultrasensitive
6
Nascimento, A.M.A. & Chartone-Souza, E. (2003)

Operon mer: Bacterial resistance to mercury and potential for bioremediation of contaminated environments

Genetics and Molecular Research, 2(1), 92–101
Relevance: Review of bioremediation applications — justification for the primary use case of the trinary processor.
bioremediationmer operonenvironment
7
Huang, C.C., Narita, M., Yamagata, T., et al. (1999)

Structure analysis of a class II transposon encoding the mercury resistance of the Gram-positive bacterium Bacillus megaterium MB1

Gene, 239(2), 361–366 · DOI
Relevance: Characterization of the mer operon in Gram-positive bacteria — exploitable genetic diversity for processor variants.
BacillustransposonGram-positive
8
Nies, D.H. (2003)

Efflux-mediated heavy metal resistance in prokaryotes

FEMS Microbiology Reviews, 27(2-3), 313–339 · DOI
Relevance: Heavy metal efflux mechanisms (Hg, As, Cu, Cd) — relevant for transport proteins and multi-metal detection.
effluxheavy metalspumpsmulti-metal
9
Mathema, V.B., Thakuri, B.C. & Sillanpää, M. (2011)

Bacterial mer operon-mediated detoxification of mercurial compounds: a short review

Archives of Microbiology, 193(12), 837–844 · DOI
Relevance: Summary of detoxification pathways — source for the 6-step operational pipeline.
short reviewdetoxificationmer operon
10
Philippidis, G.P., Malmberg, L.H., Hu, W.S. & Schottel, J.L. (1991)

Effect of gene amplification on mercuric ion reduction activity of Escherichia coli

Applied and Environmental Microbiology, 57(12), 3558–3564 · DOI
Relevance: Demonstration that merA overexpression proportionally increases reductase activity — key for ALU calibration.
amplificationE. colioverexpression
11
Romine, M.F., Stillwell, L.C., Wong, K.-K., et al. (1999)

Complete Sequence of a 184-Kilobase Catabolic Plasmid from Sphingomonas aromaticivorans F199

Journal of Bacteriology, 181(5), 1585–1602 · DOI
Relevance: Reference for mer gene-carrying plasmids — basis for the cloning vector system.
plasmidSphingomonassequencing
12
Sone, Y., Nakamura, R., Pan-Hou, H., et al. (2013)

Increase methylmercury accumulation in Arabidopsis thaliana expressing bacterial broad-spectrum mercury transporter MerE

AMB Express, 3(1), 52 · DOI
Relevance: Functional characterization of MerE — organomercurial transporter integrated into our design.
MerEtransportorganomercurials
13
Selifonova, O., Burlage, R. & Barkay, T. (1993)

Bioluminescent sensors for detection of bioavailable Hg(II) in the environment

Applied and Environmental Microbiology, 59(9), 3083–3090 · DOI
Relevance: First merR-lux bioluminescent biosensors for bioavailable Hg detection — foundation of the trinary biosensor concept.
biosensorbioluminescencemerR-luxbioavailable Hg
14
Virta, M., Lampinen, J. & Karp, M. (1995)

A luminescence-based mercury biosensor

Analytical Chemistry, 67(3), 667–669 · DOI
Relevance: Quantitative merR-luciferase biosensor with sub-nanomolar sensitivity — validation of fluorescent reporter readout.
biosensorluminescencemerRanalytical
15
UNEP (United Nations Environment Programme) (2019)

Global Mercury Assessment 2018

UN Environment Programme, Chemicals and Health Branch
Relevance: Global mercury assessment: 37% of emissions originate from artisanal and small-scale gold mining (ASGM). Basis for mining surveillance and Minamata compliance use cases.
MinamataASGMglobal emissionspolicy
16
Wang, D., Huang, S., Liu, P., et al. (2022)

Engineered Pseudomonas putida KT2440 for enhanced bioremediation of mercury-contaminated water

ACS Synthetic Biology, 11(4), 1496–1507 · DOI
Relevance: Engineered P. putida KT2440 strain with mer operon: > 98% Hg²⁺ removal. Experimental validation of bioremediation and water treatment use case.
P. putidaKT2440engineeringbioremediation>98% removal
17
ICH Expert Working Group (2014)

ICH Q3D(R2) Guideline for Elemental Impurities

International Council for Harmonisation of Technical Requirements for Pharmaceuticals
Relevance: International standard setting mercury limits in pharmaceuticals: < 3 µg/g oral, < 0.3 µg/g parenteral — basis for the pharmaceutical quality control use case.
ICHQ3Dmercurypharmaceuticallimits

NetworkPotential Collaborations

Synthetic Biology

Partners: iGEM laboratories, MIT, Imperial College, ETH Zürich

Contribution: Optimization of genetic constructs and directed evolution of mer enzymes.

Microfluidics

Partners: Micro/nanofabrication groups (Stanford, EPFL, Institut Curie)

Contribution: Advanced chip design, 3D integration, nanoscale valves.

Unconventional Computing

Partners: Ternary computing community, DNA computing, neuromorphic computing

Contribution: Trinary circuit theory, compilers, alternative computing architectures.

Environmental Sciences

Partners: UNEP, Minamata Convention, environmental NGOs

Contribution: Field deployment for bioremediation, safety standards, technology transfer.

Open Research Questions

Reliability

Can we achieve an error rate < 1% over 1,000 consecutive trinary cycles?

Stability

What is the maximum lifespan of immobilized bacteria under continuous operation?

Scalability

How can we cascade > 10 trinary gates without accumulating diffusion errors?

Energy

Is it possible to regenerate NADPH in situ without external input?

Modeling

Can the PMBT architecture be simulated in silico before physical fabrication?

Regulation

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.