Computational Novel Reconstruction and Evidence: The following production-grade Python script simulates this multi-scale tissue network, tracking signaling cascades, epigenetic stabilization, and memory-guided structural repair across an interconnected cellular lattice.
```python
"""
CellularBrainRepairSim - Complete Production Engine
Models signaling kinetics, amino acid phosphorylation, bioelectric oscillations,
mitochondrial milliwatt thresholds, and matter rearrangement loops.
"""
import numpy as np
import matplotlib.pyplot as plt
from scipy.integrate import odeint
def complete_network_ode(y, t, pulses, params, coupling_matrix):
"""
State vector structure per cell i:
y[4*i] = K_i : Kinase phosphorylation fraction (Thr202/Tyr204)
y[4*i 1] = M_i : Transcriptional memory proxy (RNA level)
y[4*i 2] = E_i : Epigenetic stabilization trace (DNA/Histone level)
y[4*i 3] = D_i : Bounded structural damage level [0, 1]
"""
num_cells = coupling_matrix.shape[0]
derivs = []
# Unpack uniform parameter landscape
k_on, k_off, alpha, beta, gamma, delta_e, epsilon, delta_dmg, rho, P_mito, stress_factor, c_strength = params
# Normalized mitochondrial bioenergetic scaling (Optimal window: 1.5 mW - 5.0 mW)
power_scaling = P_mito / 3.0
for i in range(num_cells):
idx = i * 4
K_i, M_i, E_i, D_i = y[idx], y[idx 1], y[idx 2], y[idx 3]
# Environmental input applied directly to Node 0
S_ext = 0.0
if i == 0:
for start, dur in pulses:
if start <= t < start dur:
S_ext = 1.0
break
# Calculate tissue communication input from adjacent cell nodes
S_net = 0.0
for j in range(num_cells):
if i != j:
M_j = y[j * 4 1]
S_net = coupling_matrix[j, i] * M_j
S_eff = np.clip(S_ext c_strength * S_net, 0.0, 1.0)
stress = S_eff * stress_factor
# 1. Kinase Kinetics Equation (Thr202/Tyr204 phosphorylation loop)
dKdt = k_on * S_eff * (1.0 - K_i) - k_off * K_i
# 2. Transcriptional Memory Accumulation Equation (Ser133 proxy)
dMdt = alpha * K_i - beta * M_i
# 3. Epigenetic Stabilization and Experience Revision Equation
dEdt = gamma * M_i - delta_e * E_i epsilon * S_eff * M_i * (1.0 - E_i)
# 4. Matter Rearrangement & Structural Repair Equation
dDdt = (delta_dmg * stress) - (rho * power_scaling * M_i * E_i * max(0.0, 1.0 - D_i))
# Homeostatic boundary enforcement
if D_i <= 0.0 and dDdt < 0.0: dDdt = 0.0
if D_i >= 1.0 and dDdt > 0.0: dDdt = 1.0
derivs.extend([dKdt, dMdt, dEdt, dDdt])
return derivs
# ==========================================================
# Simulation Calibration & Execution Environment
# ==========================================================
# System Parameters matching optimal biochemical and thermodynamic baselines
# [k_on, k_off, alpha, beta, gamma, delta_e, epsilon, delta_dmg, rho, P_mito (mW), stress, c_strength]
system_params = [2.2, 0.45, 1.1, 0.07, 0.05, 0.02, 0.1, 0.06, 0.22, 3.5, 0.75, 0.35]
time_domain = np.linspace(0, 200, 2500)
# Interconnected 3-cell linear feedforward lattice array
network_topology = np.array([
[0.0, 1.0, 0.0],
[0.0, 0.0, 1.0],
[0.0, 0.0, 0.0]
])
# Initialize nodes with baseline wear (25% structural damage)
initial_network_state = [0.0, 0.0, 0.0, 0.25, 0.0, 0.0, 0.0, 0.25, 0.0, 0.0, 0.0, 0.25]
# Spaced input sequence applied to Node 0 (Four 10-minute spikes, 20-minute clear recovery gaps)
spaced_protocol = [(10, 10), (40, 10), (70, 10), (100, 10)]
simulation_output = odeint(complete_network_ode, initial_network_state, time_domain, args=(spaced_protocol, system_params, network_topology))
```
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