Simulation of Biological Systems
Simulation of Biological Systems
using Real-Time Object-Oriented Modeling
Ken Webb, Senior Software Designer
ObjecTime Ltd., Kanata
- 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
- 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?
- What is an active object?
- Enzymes within cytoplasm and other cellular spaces
- Membrane proteins
- Are lipid bilayers active objects?
- 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
- 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?