NanoCERN Specs

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NanoCERN Instrument Specifications: The “Physics-First” Healing Reactor

Version: 1.0
Date: 2026-01-16
Status: SPECIFICATION
Reference: Physics Framework | NanoCERN CLI

1. System Overview

The NanoCERN Instrument is the physical instantiation of the Physics-First Healing Framework. It is a closed-loop feedback system designed to measure the Healing State Vector ($S_H$) in real-time and apply corrective Control Fields ($u(t)$) to steer biological tissue out of the “Scar Attractor” and into the “Regeneration Attractor”.

It combines:
1. Hardware: A specialized bioreactor with integrated sensor/actuator arrays.
2. Software: The nanocern_cli engine running as the real-time controller.

1.1 The Loop

  1. Sense: Hardware measures raw signals $\to$ Compute $S_H(t)$.
  2. Reason: nanocern_cli checks $S_H$ against atoms/HEAL-*.ku constraints.
  3. Act: If constraint violated, Controller computes $\Delta u(t)$.
  4. Drive: Hardware generates field $\vec{E}(t), \vec{B}(t)$.

2. Sensor Inventory (The $S_H$ Measurement Array)

To measure the 10 variables of $S_H$, the instrument requires the following specific sensors.

$S_H$ Index Variable Sensor Hardware Spec Resolution / Range
1 $\Phi_m$ (Membrane Potential) Optical Mapping System (Voltage-sensitive dyes) OR High-Density Micro-Electrode Array (MEA) $10 \mu m$ spatial, $1 mV$ precision
2 $\sigma_{dc}$ (Conductivity) Electrical Impedance Tomography (EIT) Array (4-point probe configuration) $0.1 S/m$ precision, $10 Hz$ sampling
3 $\Delta \mu$ (Chem. Gradient) Ion-Selective Field Effect Transistors (ISFETs) array ($Ca^{2+}, K^+, pH$) $0.1 pH$ unit, $1 mM$ conc.
4 $\kappa_{an}$ (Stiffness) Ultrasound Elastography Transducer (Shear wave imaging) $1 kPa$ stiffness resolution
5 $T_{noise}$ (Thermal Noise) Micro-Calorimeter Array (Thermopile or IR Microbolometer) $1 mK$ thermal resolution
6 $\epsilon_r$ (Permittivity) Dielectric Spectroscopy Probe (10 Hz – 10 MHz sweep) $\Delta \epsilon < 100$
7 $\vec{J}_{ion}$ (Current Density) Vibrating Probe Electrode (measures local voltage gradients in medium) $1 \mu A/cm^2$ sensitivity
8 $\Gamma_{bound}$ (Continuity) EIT Boundary Algorithm (Calculated from Variable 2 array) Edge detection < $1mm$
9 $\rho_{S}$ (Entropy Rate) Computed Metric (Derived from $J_{ion} \cdot \nabla \Phi$ and Heat flux) N/A (Computational)
10 $\Psi_{mech}$ (Tension) Traction Force Microscopy (TFM) substrate (fluorescent beads) $10 Pa$ traction stress

3. Actuator Inventory (The Field Generators)

The “drug” is the field. The hardware must generate precise electromagnetic and mechanical waveforms.

Band Frequency Actuator Hardware Purpose
DC $0 Hz$ Ag/AgCl Non-Polarizing Electrodes (Fluid bridged) Iontophoresis, Morphogen gradient setup ($\Delta \mu$)
ELF $10 – 1000 Hz$ Helmholtz Coils (3-axis orthogonal) Induce $\vec{E}$ via Faraday ($dB/dt$). Modulate $\Phi_m$ without contact.
RF $10 – 50 MHz$ Capacitive Plates (Insulated) Dielectric heating, Tissue warming ($T_{noise}$ control).
Mech $0.1 – 10 Hz$ Piezoelectric Stretchers (Uniaxial/Biaxial) Apply strain $\varepsilon$ to modulate $\Psi_{mech}$ and $\kappa_{an}$.

4. The “NanoCERN” Bioreactor Chassis

The physical housing for the experiment.

4.1 Specifications

  • Chamber Volume: $5 mL – 50 mL$ (Variable geometry).
  • Temperature Control: PID loop ($37.0^\circ C \pm 0.1^\circ C$).
  • Atmosphere: $5\% CO_2$ incubator compatibility.
  • Optical Access: Glass bottom for inverted microscopy (TFM/Optical Mapping).
  • Shielding: Faraday Cage (Copper mesh) to exclude external $50/60 Hz$ noise.

4.2 Controller Interface (The “Brain”)

  • ADC (Input): 16-channel, 24-bit, 100 kS/s (for EIT and MEA).
  • DAC (Output): 4-channel, 16-bit, 1 MS/s (Arbitrary Waveform Generator for fields).
  • Protocol: USB 3.0 or Ethernet to Host PC running nanocern_cli.

5. Software Integration Plan

How nanocern_cli controls the hardware.

  1. Driver Layer: A Python wrapper (nanocern.hardware) talks to the ADC/DAC.
  2. State Estimator:
    • Reads raw voltages from ADC.
    • Inverts EIT matrix to get $\sigma(x,y)$.
    • Outputs $S_H(t)$ vector.
  3. The Reasoner:
    • nanocern check atoms/HEAL-001.ku --state $S_H
    • If False (Scar detected):
      • Lookup correction in KU.
      • Example: “Increase ELF Field frequency to 150Hz”.
  4. Feedback Loop:
    • DAC updates voltage out.
    • Wait $\Delta t$.
    • Repeat.

6. Bill of Materials (BoM) – Phase 1 Prototype

Item Component Estimated Cost Status
1 Controller Red Pitaya STEMlab or NI DAQ $500 – $2000
2 Electrodes Sintered Ag/AgCl pellets $50
3 Amplifiers Instrumentation Amps (AD620/INA128) $20
4 Coils Custom wound copper wire (200 turns) $30
5 Chassis 3D Printed PETG + Copper Mesh $50
6 Compute Laptop with nanocern_cli N/A

7. Safety Limits (Hardcoded in Firmware)

  • Max Current: $100 \mu A$ (Hardware fuse).
  • Max Voltage: $10 V$ (Compliance limit).
  • Max Temp: $39^\circ C$ (Cutoff).

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