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cosys-cell

Cosmos System Model Applied to Eukaryotic Cell, Organelles & Detailed Mitochondria with Double Membrane

This repository implements the Cosmos System 5 triadic architecture mapped to cellular biology, providing a comprehensive framework for understanding and modeling eukaryotic cells, organelles, and the detailed structure of mitochondria through organizational systems theory.


Overview

cosys-cell translates the Cosmos System's triadic polarity structure into a cellular model that treats the eukaryotic cell as a self-organizing cognitive system. The framework implements the 18-service [[D-T]-[P-O]-[S-M]] pattern mapped to cellular compartments, organelle functions, and membrane dynamics.

Core Mapping: Cell as Cognitive Triad

┌─────────────────────────────────────────────────────────────────────────────┐
│                    COSYS-CELL: CELLULAR COSMOS SYSTEM                       │
├─────────────────────────────────────────────────────────────────────────────┤
│                                                                             │
│   ┌─────────────────────────────────────────────────────────────────────┐   │
│   │                    CEREBRAL TRIAD [3]                               │   │
│   │                    Nucleus - Genetic Control Center                 │   │
│   │                    Potential Topology                               │   │
│   ├─────────────────────────────────────────────────────────────────────┤   │
│   │  T-7: Chromatin             │  PD-2: Nucleolus                     │   │
│   │  Genetic Treasury           │  Ribosome Development                │   │
│   │  DNA Storage                │  rRNA Synthesis                      │   │
│   ├────────────────────────────┼────────────────────────────────────────┤   │
│   │  P-5: Transcription         │  O-4: Nuclear Envelope               │   │
│   │  mRNA Production            │  Nuclear Organization                │   │
│   │  Gene Expression            │  Nuclear Pore Complex                │   │
│   └─────────────────────────────────────────────────────────────────────┘   │
│                                    │                                        │
│                                    ▼                                        │
│   ┌─────────────────────────────────────────────────────────────────────┐   │
│   │                    SOMATIC TRIAD [6]                                │   │
│   │                    Endomembrane System - Protein Processing         │   │
│   │                    Commitment Topology                              │   │
│   ├─────────────────────────────────────────────────────────────────────┤   │
│   │  M-1: Plasma Membrane       │  S-8: Endoplasmic Reticulum          │   │
│   │  Cell Boundary              │  Protein Synthesis State             │   │
│   │  Signal Reception           │  Lipid Production                    │   │
│   ├────────────────────────────┼────────────────────────────────────────┤   │
│   │  P-5: Golgi Apparatus       │  O-4: Vesicle Transport              │   │
│   │  Protein Processing         │  Secretory Organization              │   │
│   │  Glycosylation              │  Trafficking Routes                  │   │
│   └─────────────────────────────────────────────────────────────────────┘   │
│                                    │                                        │
│                                    ▼                                        │
│   ┌─────────────────────────────────────────────────────────────────────┐   │
│   │                    AUTONOMIC TRIAD [9]                              │   │
│   │                    Energy & Homeostasis - Metabolic Regulation      │   │
│   │                    Performance Topology                             │   │
│   ├─────────────────────────────────────────────────────────────────────┤   │
│   │  M-1: Mitochondria          │  S-8: Cytoplasm                      │   │
│   │  Energy Monitoring          │  Metabolic State                     │   │
│   │  ATP Production             │  Ion Homeostasis                     │   │
│   ├────────────────────────────┼────────────────────────────────────────┤   │
│   │  PD-2: Peroxisomes          │  T-7: Lysosomes                      │   │
│   │  Oxidative Processing       │  Degradation Triggers                │   │
│   │  Detoxification             │  Autophagy Initiation                │   │
│   ├────────────────────────────┼────────────────────────────────────────┤   │
│   │  P-5: Cytoskeleton          │                                      │   │
│   │  Structural Processing      │                                      │   │
│   │  Intracellular Transport    │                                      │   │
│   └─────────────────────────────────────────────────────────────────────┘   │
│                                                                             │
└─────────────────────────────────────────────────────────────────────────────┘

Theoretical Foundation

The Cell as Self-Organizing System

Based on Eric Schwarz's Holistic Metamodel, the eukaryotic cell exhibits all characteristics of a self-organizing cognitive system:

The Hieroglyphic Monad (Cellular Identity)

The cell's genome serves as the hieroglyphic monad—the unity principle that manifests at all levels:

  • Level 0: Complete genome (DNA)
  • Level 1: Expressed genes (transcriptome)
  • Level 2: Protein products (proteome)
  • Level 3: Metabolic state (metabolome)
  • Level 4: Phenotypic behavior

Dual Complementarity (Anabolic-Catabolic)

Anabolic (Building) Catabolic (Breaking) Resolution
Protein synthesis Protein degradation Proteostasis
DNA replication DNA repair Genome maintenance
Lipid synthesis Lipid oxidation Membrane homeostasis
ATP production ATP consumption Energy balance

Triadic System (Structure-Function-Regulation)

Primitive Cellular Manifestation
Being Cellular structure, organelles, macromolecules
Becoming Metabolism, growth, division, differentiation
Relation Signaling, communication, environmental response

The 18-Service [[D-T]-[P-O]-[S-M]] Pattern for Cells

Complete Cellular Service Mapping

                    D-T         P-O         S-M         Total
Cerebral (Nucleus)  2           2           2           = 6
Somatic (Endomem)   2*          2           2           = 6  
Autonomic (Energy)  2*          2           2           = 6
                    ────────────────────────────────────────
Total:              6           6           6           = 18

*Parasympathetic Polarity [D-T] shared between Somatic and Autonomic

Cerebral Triad Services (Nucleus)

Service Code Organelle/Structure Cellular Function
Development PD-2 Nucleolus Ribosome biogenesis, rRNA synthesis
Treasury T-7 Chromatin DNA storage, genetic memory
Production P-5 Transcription machinery mRNA production, gene expression
Organization O-4 Nuclear envelope Nuclear organization, pore complexes
Sales S-8 mRNA export Transcript delivery to cytoplasm
Market M-1 Nuclear import Transcription factor reception

Somatic Triad Services (Endomembrane System)

Service Code Organelle/Structure Cellular Function
Development PD-2 Rough ER* Protein folding development
Treasury T-7 Smooth ER* Lipid storage, calcium reservoir
Production P-5 Golgi apparatus Protein processing, glycosylation
Organization O-4 Vesicle transport Secretory pathway organization
Sales S-8 Endoplasmic Reticulum Protein synthesis state
Market M-1 Plasma membrane Cell boundary, signal reception

Autonomic Triad Services (Energy & Homeostasis)

Service Code Organelle/Structure Cellular Function
Development PD-2 Peroxisomes* Oxidative processing, detox
Treasury T-7 Lysosomes Degradation triggers, autophagy
Production P-5 Cytoskeleton Structural support, transport
Organization O-4 Centrosome Microtubule organization
Sales S-8 Cytoplasm Metabolic state, ion homeostasis
Market M-1 Mitochondria Energy monitoring, ATP production

Mitochondria: The Double Membrane System

Mitochondria as Nested Triadic System

The mitochondrion exemplifies the nested triadic architecture with its double membrane structure:

┌─────────────────────────────────────────────────────────────────────────────┐
│                    MITOCHONDRIA: DOUBLE MEMBRANE COSMOS                     │
├─────────────────────────────────────────────────────────────────────────────┤
│                                                                             │
│   ┌─────────────────────────────────────────────────────────────────────┐   │
│   │                    OUTER MEMBRANE TRIAD                             │   │
│   │                    Boundary & Transport Functions                   │   │
│   ├─────────────────────────────────────────────────────────────────────┤   │
│   │  T-7: Porins                │  PD-2: TOM Complex                   │   │
│   │  Small Molecule Treasury    │  Protein Import Development          │   │
│   │  Metabolite Exchange        │  Preprotein Recognition              │   │
│   ├────────────────────────────┼────────────────────────────────────────┤   │
│   │  P-5: VDAC Channels         │  O-4: Outer Membrane Org             │   │
│   │  Voltage Processing         │  Membrane Dynamics                   │   │
│   │  Ion/Metabolite Flow        │  Fusion/Fission Control              │   │
│   └─────────────────────────────────────────────────────────────────────┘   │
│                                    │                                        │
│                                    ▼                                        │
│   ┌─────────────────────────────────────────────────────────────────────┐   │
│   │                    INTERMEMBRANE SPACE TRIAD                        │   │
│   │                    Electron Shuttle & Signaling                     │   │
│   ├─────────────────────────────────────────────────────────────────────┤   │
│   │  M-1: Cytochrome c          │  S-8: Proton Gradient                │   │
│   │  Electron Carrier           │  Electrochemical State               │   │
│   │  Apoptosis Signal           │  ΔΨ Maintenance                      │   │
│   ├────────────────────────────┼────────────────────────────────────────┤   │
│   │  P-5: Electron Transport    │  O-4: IMS Organization               │   │
│   │  Redox Processing           │  Protein Sorting                     │   │
│   │  Complex III/IV Interface   │  MIA Pathway                         │   │
│   └─────────────────────────────────────────────────────────────────────┘   │
│                                    │                                        │
│                                    ▼                                        │
│   ┌─────────────────────────────────────────────────────────────────────┐   │
│   │                    INNER MEMBRANE TRIAD                             │   │
│   │                    Oxidative Phosphorylation Core                   │   │
│   ├─────────────────────────────────────────────────────────────────────┤   │
│   │  M-1: Complex I-IV          │  S-8: ATP Synthase                   │   │
│   │  Electron Transport         │  ATP State Management                │   │
│   │  Proton Pumping             │  Rotary Motor                        │   │
│   ├────────────────────────────┼────────────────────────────────────────┤   │
│   │  PD-2: TIM Complex          │  T-7: Cristae                        │   │
│   │  Matrix Import              │  Surface Area Treasury               │   │
│   │  Protein Translocation      │  ETC Localization                    │   │
│   ├────────────────────────────┼────────────────────────────────────────┤   │
│   │  P-5: Carrier Proteins      │                                      │   │
│   │  Metabolite Transport       │                                      │   │
│   │  ADP/ATP Exchange           │                                      │   │
│   └─────────────────────────────────────────────────────────────────────┘   │
│                                    │                                        │
│                                    ▼                                        │
│   ┌─────────────────────────────────────────────────────────────────────┐   │
│   │                    MATRIX TRIAD                                     │   │
│   │                    Metabolic Core & mtDNA                           │   │
│   ├─────────────────────────────────────────────────────────────────────┤   │
│   │  T-7: mtDNA                 │  PD-2: Mitochondrial Ribosomes       │   │
│   │  Genetic Treasury           │  Protein Synthesis                   │   │
│   │  13 ETC Subunits            │  Local Translation                   │   │
│   ├────────────────────────────┼────────────────────────────────────────┤   │
│   │  P-5: TCA Cycle Enzymes     │  O-4: Matrix Organization            │   │
│   │  Metabolic Processing       │  Enzyme Complexes                    │   │
│   │  NADH/FADH2 Production      │  Metabolon Assembly                  │   │
│   └─────────────────────────────────────────────────────────────────────┘   │
│                                                                             │
└─────────────────────────────────────────────────────────────────────────────┘

Mitochondrial Electron Transport Chain as Dimensional Flow

Commitment Dimension [5-4]: Electron Processing → Organization

ETC Flow: Electron Transfer → Proton Pumping Organization

graph LR
    P5[P-5: Complex I-IV<br/>Electron Transport] --> O4[O-4: Cristae<br/>Proton Gradient]
    style P5 fill:#ff9999
    style O4 fill:#ff6666
Loading

Potential Dimension [2-7]: Import → Storage

Matrix Flow: Protein Import → Genetic Treasury

graph LR
    PD2[PD-2: TIM Complex<br/>Protein Import] --> T7[T-7: mtDNA<br/>Genetic Storage]
    style PD2 fill:#66ffcc
    style T7 fill:#66ff99
Loading

Performance Dimension [8-1]: ATP State → Energy Output

Energy Flow: ATP Synthase → Cellular Energy

graph LR
    S8[S-8: ATP Synthase<br/>ATP Production] --> M1[M-1: Cytoplasm<br/>Energy Delivery]
    style S8 fill:#6699ff
    style M1 fill:#3366ff
Loading

System 5 Cellular State Machine

The 60-Step Cell Cycle

The cell operates on a 60-step deterministic cycle (LCM of 3 and 20) representing the synchronization of nuclear and cytoplasmic processes:

class CellularSystem5:
    """
    Implements the 60-step cellular cycle with triadic dynamics.
    """
    
    def __init__(self):
        # Universal Sets: Cell Cycle Phases
        self.U1 = G1Phase()          # Growth phase 1
        self.U2 = SPhase()           # DNA synthesis
        self.U3 = G2M_Phase()        # Growth 2 + Mitosis
        
        # Particular Sets: Cellular Compartments
        self.P1 = Nucleus()          # Genetic control
        self.P2 = EndomembraneSystem()  # Protein processing
        self.P3 = Mitochondria()     # Energy production
        self.P4 = Cytoskeleton()     # Structure & transport
        
    def cell_cycle_step(self, t: int):
        """Execute one step of the 60-step cell cycle."""
        # Universal phase transition (3-step cycle)
        u_idx = t % 3
        phase = self.get_phase(u_idx)
        
        # Particular compartment transition (5-step staggered)
        p_idx = t % 5
        if p_idx < 4:
            compartment = [self.P1, self.P2, self.P3, self.P4][p_idx]
            return compartment.process(phase)
        
        # Rest step: checkpoint
        return self.checkpoint_evaluation()

Nested Concurrency in Cellular Processes

The convolution of concurrency implements parallel organelle processing:

$$S_{organelle}(t+1) = (S_{organelle}(t) + \sum_{other} S_{other}(t) + Phase_{cell}(t)) \mod 4$$

This captures cellular interdependencies where:

  • Nucleus affects ER protein synthesis
  • ER affects Golgi processing
  • Mitochondria affect all energy-dependent processes
  • Cytoskeleton affects all transport

Dimensional Flow Architecture

Commitment Dimension [5-4]: Production → Organization

Cellular Flow: Biosynthesis → Structural Organization

graph LR
    P5[P-5: Golgi<br/>Protein Processing] --> O4[O-4: Vesicles<br/>Trafficking]
    style P5 fill:#ff9999
    style O4 fill:#ff6666
Loading

Characteristics:

  • Protein modification to secretion
  • Lipid synthesis to membrane assembly
  • Commitment to cellular output
  • Quality control integration

Potential Dimension [2-7]: Development → Treasury

Cellular Flow: Biogenesis → Storage

graph LR
    PD2[PD-2: Nucleolus<br/>Ribosome Biogenesis] --> T7[T-7: Chromatin<br/>Genetic Memory]
    style PD2 fill:#66ffcc
    style T7 fill:#66ff99
Loading

Characteristics:

  • Ribosome assembly to protein potential
  • Gene expression to epigenetic memory
  • Potential information storage
  • Developmental programming

Performance Dimension [8-1]: State → Interface

Cellular Flow: Metabolic State → Environmental Interface

graph LR
    S8[S-8: Cytoplasm<br/>Metabolic State] --> M1[M-1: Plasma Membrane<br/>Cell Boundary]
    style S8 fill:#6699ff
    style M1 fill:#3366ff
Loading

Characteristics:

  • Metabolic sensing to signal transduction
  • Ion homeostasis to membrane potential
  • Performance optimization cycle
  • Environmental responsiveness

Cellular Autognosis

Self-Aware Cell System

The cell implements hierarchical self-monitoring through:

Self-Monitoring Layer

  • Metabolic Sensors: AMPK, mTOR, sirtuins
  • DNA Damage Response: ATM, ATR, p53
  • Protein Quality Control: Unfolded protein response
  • Redox Sensors: Nrf2, HIF-1α

Self-Modeling Layer

  • Transcriptome Analysis: Gene expression patterns
  • Proteome State: Protein abundance and modifications
  • Metabolome Profile: Metabolite concentrations
  • Epigenome Status: Chromatin state

Meta-Cognitive Layer

  • Cell Fate Decisions: Proliferation vs. differentiation
  • Stress Response Integration: Multiple pathway coordination
  • Apoptosis Assessment: Death vs. survival decisions
  • Senescence Evaluation: Aging markers

Self-Optimization Layer

  • Autophagy: Self-eating for renewal
  • Mitophagy: Mitochondrial quality control
  • Proteostasis: Protein homeostasis maintenance
  • Metabolic Reprogramming: Energy optimization
class CellularAutognosis:
    """
    Self-awareness system for eukaryotic cells.
    """
    
    def __init__(self, cell: CellularSystem5):
        self.cell = cell
        self.sensor_network = SensorNetwork()
        
    def monitor(self) -> Dict[str, float]:
        """Monitor cellular health metrics."""
        return {
            'atp_level': self.sensor_network.measure_atp(),
            'ros_level': self.sensor_network.measure_ros(),
            'dna_damage': self.sensor_network.measure_dna_damage(),
            'protein_stress': self.sensor_network.measure_upr(),
            'nutrient_status': self.sensor_network.measure_nutrients(),
            'membrane_potential': self.sensor_network.measure_delta_psi(),
        }
        
    def assess_fate(self) -> str:
        """Determine cell fate based on current state."""
        metrics = self.monitor()
        
        if metrics['dna_damage'] > 0.8:
            return 'APOPTOSIS'
        elif metrics['atp_level'] < 0.2:
            return 'NECROSIS'
        elif metrics['nutrient_status'] < 0.3:
            return 'AUTOPHAGY'
        elif metrics['protein_stress'] > 0.7:
            return 'SENESCENCE'
        else:
            return 'PROLIFERATION'

Cellular Ontogenesis

Self-Generating Cellular Programs

Cells evolve through self-generating kernels that create new capabilities:

class CellularGenome:
    """
    Evolutionary genome for cellular programs.
    """
    
    def __init__(self):
        self.genes = {
            'metabolic_rate': FloatGene(0.5, 2.0),
            'proliferation_rate': FloatGene(0.1, 1.0),
            'stress_resistance': FloatGene(0.3, 0.9),
            'differentiation_potential': FloatGene(0.0, 1.0),
            'migration_capacity': FloatGene(0.0, 1.0),
            'secretory_activity': FloatGene(0.2, 0.8),
        }
        self.fitness = 0.0
        self.generation = 0
        
    def express(self, environment: Environment) -> Phenotype:
        """Express genome in given environment."""
        expression_levels = {}
        for gene_name, gene in self.genes.items():
            # Environment-dependent expression
            expression_levels[gene_name] = gene.express(environment)
        return Phenotype(expression_levels)

Cellular Differentiation as Kernel Evolution

def cellular_differentiation(stem_cell: CellularGenome, 
                            signals: List[Signal],
                            generations: int) -> List[CellularGenome]:
    """
    Evolve stem cell through differentiation signals.
    """
    population = [stem_cell]
    
    for gen in range(generations):
        # Apply differentiation signals
        for signal in signals:
            for cell in population:
                cell.apply_signal(signal)
                
        # Evaluate fitness in tissue context
        fitness_scores = [evaluate_tissue_fitness(cell) for cell in population]
        
        # Selection based on tissue needs
        selected = tissue_selection(population, fitness_scores)
        
        # Asymmetric division (stem cell maintenance)
        offspring = asymmetric_division(selected)
        
        population = offspring
        
    return population

Implementation

Directory Structure

cosys-cell/
├── README.md
├── ARCHITECTURE.md
├── MITOCHONDRIA.md
├── src/
│   ├── cerebral-triad/
│   │   ├── chromatin-service/        # T-7: DNA storage
│   │   ├── nucleolus-service/        # PD-2: Ribosome biogenesis
│   │   ├── transcription-service/    # P-5: mRNA production
│   │   └── nuclear-envelope/         # O-4: Nuclear organization
│   ├── somatic-triad/
│   │   ├── plasma-membrane/          # M-1: Cell boundary
│   │   ├── endoplasmic-reticulum/    # S-8: Protein synthesis
│   │   ├── golgi-apparatus/          # P-5: Protein processing
│   │   └── vesicle-transport/        # O-4: Secretory pathway
│   ├── autonomic-triad/
│   │   ├── mitochondria/             # M-1: Energy production
│   │   │   ├── outer-membrane/
│   │   │   ├── intermembrane-space/
│   │   │   ├── inner-membrane/
│   │   │   └── matrix/
│   │   ├── cytoplasm/                # S-8: Metabolic state
│   │   ├── peroxisomes/              # PD-2: Oxidative processing
│   │   ├── lysosomes/                # T-7: Degradation
│   │   └── cytoskeleton/             # P-5: Structure
│   ├── cellular-core/
│   │   ├── autognosis/               # Self-awareness
│   │   ├── ontogenesis/              # Differentiation
│   │   ├── cell-cycle/               # Division control
│   │   └── signaling/                # Signal transduction
│   └── integration-hub/
│       ├── metabolic-network/        # Metabolic integration
│       ├── event-bus/                # Signaling cascades
│       └── shared-libraries/         # Common utilities
├── models/
│   ├── system5-cell.py               # 60-step state machine
│   ├── mitochondria.py               # Double membrane model
│   └── polarity-cell.py              # 18-service mapping
└── docs/
    ├── cell-biology.md
    ├── mitochondria-detail.md
    └── implementation-guide.md

Core Implementation

Eukaryotic Cell Core

import numpy as np
from typing import Dict, List

class EukaryoticCell:
    """
    Cosmos System 5 Eukaryotic Cell implementation.
    """
    
    def __init__(self):
        # Cerebral Triad: Nucleus
        self.nucleus = Nucleus()
        
        # Somatic Triad: Endomembrane System
        self.plasma_membrane = PlasmaMembrane()
        self.endoplasmic_reticulum = EndoplasmicReticulum()
        self.golgi_apparatus = GolgiApparatus()
        self.vesicles = VesicleSystem()
        
        # Autonomic Triad: Energy & Homeostasis
        self.mitochondria = Mitochondria()
        self.cytoplasm = Cytoplasm()
        self.peroxisomes = Peroxisomes()
        self.lysosomes = Lysosomes()
        self.cytoskeleton = Cytoskeleton()
        
        # Cell state
        self.cell_cycle_phase = 'G1'
        self.metabolic_state = MetabolicState()
        
    def process_signal(self, signal: Signal) -> Response:
        """
        Process extracellular signal through cellular machinery.
        """
        # M-1: Plasma membrane receives signal
        receptor_activation = self.plasma_membrane.receive(signal)
        
        # Signal transduction cascade
        second_messengers = self.transduce_signal(receptor_activation)
        
        # Nuclear response (Cerebral Triad)
        if signal.requires_transcription:
            gene_expression = self.nucleus.respond(second_messengers)
            
            # S-8: ER protein synthesis
            proteins = self.endoplasmic_reticulum.synthesize(gene_expression)
            
            # P-5: Golgi processing
            processed_proteins = self.golgi_apparatus.process(proteins)
            
            # O-4: Vesicle transport
            self.vesicles.deliver(processed_proteins)
            
        return Response(processed_proteins)
        
    def metabolize(self, nutrients: Nutrients) -> Energy:
        """
        Process nutrients through metabolic pathways.
        """
        # Cytoplasmic glycolysis
        pyruvate = self.cytoplasm.glycolysis(nutrients.glucose)
        
        # Mitochondrial oxidation
        atp = self.mitochondria.oxidative_phosphorylation(pyruvate)
        
        # Update metabolic state
        self.metabolic_state.update(atp)
        
        return Energy(atp)

Mitochondria Double Membrane Model

class Mitochondria:
    """
    Double membrane mitochondria with nested triadic structure.
    """
    
    def __init__(self):
        # Outer Membrane Triad
        self.outer_membrane = OuterMembrane()
        
        # Intermembrane Space Triad
        self.intermembrane_space = IntermembraneSpace()
        
        # Inner Membrane Triad
        self.inner_membrane = InnerMembrane()
        
        # Matrix Triad
        self.matrix = MitochondrialMatrix()
        
        # State variables
        self.delta_psi = 0.0  # Membrane potential
        self.atp_level = 0.0
        self.nad_ratio = 0.0  # NAD+/NADH ratio
        
    def oxidative_phosphorylation(self, pyruvate: float) -> float:
        """
        Execute oxidative phosphorylation through nested triads.
        """
        # Matrix: TCA cycle
        nadh, fadh2 = self.matrix.tca_cycle(pyruvate)
        
        # Inner Membrane: Electron transport chain
        protons_pumped = self.inner_membrane.electron_transport(nadh, fadh2)
        
        # Intermembrane Space: Proton gradient
        self.delta_psi = self.intermembrane_space.maintain_gradient(protons_pumped)
        
        # Inner Membrane: ATP synthesis
        atp = self.inner_membrane.atp_synthase(self.delta_psi)
        
        # Outer Membrane: ATP export
        exported_atp = self.outer_membrane.export_atp(atp)
        
        self.atp_level = exported_atp
        return exported_atp
        
    def import_protein(self, preprotein: Preprotein) -> MitochondrialProtein:
        """
        Import nuclear-encoded protein through TOM/TIM complexes.
        """
        # Outer Membrane: TOM complex recognition
        recognized = self.outer_membrane.tom_complex.recognize(preprotein)
        
        # Outer Membrane: Translocation
        translocated = self.outer_membrane.tom_complex.translocate(recognized)
        
        # Intermembrane Space: Sorting
        sorted_protein = self.intermembrane_space.sort(translocated)
        
        if sorted_protein.destination == 'matrix':
            # Inner Membrane: TIM23 complex
            imported = self.inner_membrane.tim23_complex.import_protein(sorted_protein)
            
            # Matrix: Folding and assembly
            folded = self.matrix.fold_protein(imported)
            return folded
            
        elif sorted_protein.destination == 'inner_membrane':
            # Inner Membrane: TIM22 complex for carriers
            inserted = self.inner_membrane.tim22_complex.insert(sorted_protein)
            return inserted

Usage

Basic Cell Simulation

from cosys_cell import EukaryoticCell, Signal, Nutrients

# Initialize cell
cell = EukaryoticCell()

# Process growth signal
growth_signal = Signal(type='growth_factor', intensity=0.8)
response = cell.process_signal(growth_signal)

# Metabolize nutrients
nutrients = Nutrients(glucose=5.0, fatty_acids=1.0, amino_acids=2.0)
energy = cell.metabolize(nutrients)

print(f"ATP produced: {energy.atp}")
print(f"Cell cycle phase: {cell.cell_cycle_phase}")

Mitochondrial Analysis

from cosys_cell import Mitochondria

# Initialize mitochondria
mito = Mitochondria()

# Run oxidative phosphorylation
pyruvate = 2.0  # mM
atp = mito.oxidative_phosphorylation(pyruvate)

# Check membrane potential
print(f"Membrane potential (ΔΨ): {mito.delta_psi} mV")
print(f"ATP level: {mito.atp_level} mM")
print(f"NAD+/NADH ratio: {mito.nad_ratio}")

Cellular Autognosis

from cosys_cell.cellular_core import CellularAutognosis

# Initialize autognosis
autognosis = CellularAutognosis(cell)

# Monitor health
metrics = autognosis.monitor()
print(f"ATP level: {metrics['atp_level']}")
print(f"ROS level: {metrics['ros_level']}")
print(f"DNA damage: {metrics['dna_damage']}")

# Assess cell fate
fate = autognosis.assess_fate()
print(f"Predicted cell fate: {fate}")

References

  • Alberts, B., et al. (2015). Molecular Biology of the Cell
  • Schwarz, E. (1997). Toward a Holistic Cybernetics
  • Nicholls, D.G., & Ferguson, S.J. (2013). Bioenergetics
  • Henze, K., & Martin, W. (2003). Evolutionary biology: essence of mitochondria
  • Kroemer, G., et al. (2007). Mitochondrial membrane permeabilization in cell death

License

MIT License - See LICENSE for details.


cosys-cell: Where the Cosmos System meets cell biology, creating a unified framework for understanding eukaryotic cells as self-organizing cognitive systems through triadic organizational dynamics.

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Cosmos System model applied to eukaryotic cell, organelles & detailed mitochondria

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