Simulation of Biological Systems

Simulation of Biological Systems
using Real-Time Object-Oriented Modeling


Ken Webb, Senior Software Designer

ObjecTime Ltd., Kanata




Ken Webb

(613) 591-7057


  • Why I am trying to model biological systems
  • Professional interest in highly complex systems
  • Possible analogies with complex telecommunication systems
  • The purpose of this presentation is to exchange information
  • I will do a 30 minute presentation
  • Followed by 30 minute discussion, and questions in both directions


  • ObjecTime Developer is a tool for visually modeling, programming and executing real-time event-driven systems.
  • I’ve recently been using it as a tool to produce a prototype simulation of some aspects of a cell and the nervous system.

Overview of My Prototype Model

  • Major things that my prototype partially models:
  • Enzyme reactions, especially Glycolysis and TCA pathways
  • Neuron circuits, including action potentials, post synaptic potential, membrane proteins, dendrites, cell body, axons, etc.
  • O2/CO2 cycle, including circulatory system, plants, atmosphere
  • Amino acid structure of proteins
  • Size:
  • 100,000+ objects at run-time including 300 neurons
  • 300 actor classes (enzymes, proteins, various containers & spaces)
  • 100 C++ data classes (small molecules)

Some Modeling Issues

  • What are the active objects - enzymes, other proteins, ribosomes, lipid bilayers, others?
  • What are some other the architecturally significant entities and patterns?
  • What does the cell control architecture look like?
  • How to model trillions of components?
  • How to model communication within and between cells?
  • Wrestling with the modeling of emergent levels?

Active Objects

  • What is an active object?
  • Enzymes within cytoplasm and other cellular spaces
  • Membrane proteins
  • Are lipid bilayers active objects?
  • Ribosomes
  • What other active objects are there?

Architecturally Significant Entities 1

  • Hierarchically-organized containment structures
  • Cell, NervousSystem, Membrane, Organelles, etc.

Architecturally Significant Entities 2

  • Spaces and space passageways
  • Ex: protein and vesicle traffic outward from the nucleus

Cell Control Architecture

  • Telecommunication devices such as telephone and data switches are built with two architectures:

1) a high-speed data path architecture

2) a less-optimized control/network management architecture

  • Example from a real telecommunication switch
  • Analogies with biological cells

Modeling Trillions of Components

  • Small molecules as C++ classes with internal counters
  • Allows up to 4 billion instances of glucose, oxygen, etc. within each cellular space
  • I assume that each small molecule is identical, and has the same state, as every other small molecule of the same type
  • Enzymes and other active object instances represent all objects of that type within a given cellular space, using a counter
  • I also assume that active objects of the same type are all identical
  • Cells, Organelles
  • Mitochondria are modeled as replicated actors
  • Each can have its own individual state

Modeling Cell Communication

  • Circulatory System example


  • Emergence of enzyme/protein behavior from amino acid polymer structures
  • Emergence of metabolic pathways from enzyme/protein collective behaviors
  • Emergence of neural circuit behavior from collections of neurons and synapses

What’s Next

  • Attach Java applets to observe the running model
  • simulated microscope views
  • simulated laboratory graphs of substrate levels
  • other views?
  • Capture statistics in a database
  • Continue developing Nervous System/Cell model
  • Add missing details

Some of My Many Questions

  • Am I building a reasonable extendible architecture?
  • Have I chosen the right active objects?
  • What significant architectural entities am I not aware of?
  • What would be some interesting things to model from a biologist’s perspective?
  • Is there any potential value of this type of modeling to the biological community? Educational? Research?
  • Are Neurons and Erythrocytes representative of the range of cell types? What would be several other good cell types to test the model against?
  • How many types of neurons are there? How divergent are they?
  • Where can I find the kinetic constants (Vmax, Km) for major enzymes?
  • Are the mechanoreceptors in the skin part of the neuron, or are they separate cells?
  • What are the discrete compartments of the brain?
  • What mechanism guarantees that connected neurons have compatible neurotransmitters?