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Cellular Automata Modeling of Complex Biochemical Systems

  • Reference work entry
Encyclopedia of Complexity and Systems Science

Definition of the Subject

Cellular automata are discrete, agent-based models that can be used for the simulation of complex systems [1]. They are composed of:

  • A grid of cells.

  • A set of ingredients called agents that can occupy the cells.

  • A set of local rules governing the behaviors of the agents.

  • Specified initial conditions.

Once these components are defined, a simulation can be carried out. During the simulation the system evolves via a series of discrete time-steps, or iterations, in which the rules are applied to all of the ingredients of the system and the configuration of the system is regularly updated. A striking feature of the cellular automata (CA) models is that they treat not only the ingredients, or agents, of the model as discrete entities, as do the traditional models of physics and chemistry, but in the CA models time (iterations) and space (the cells) are also regarded as discrete, in contrast to the continuous forms assumed for these variables in the traditional,...

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Abbreviations

Agents:

Ingredients under study occupying the cells in the grid.

Asynchronous:

Each cell in turn, at random responds to a rule.

Cells:

Sections of the grid in which the agents exist.

Gravity:

The relative relationship of two agents within the frame of a grid with opposite bound edges.

Grid:

The frame containing the cells and the agents.

Movement:

The simulation of agent movement between cells accomplished by the disappearance of an agent in a cell and the appearance of that agent in an adjacent cell.

Neighborhood:

The cells immediately touching a given cell in the grid.

Rules:

Statements of actions to be taken by an agent under certain conditions. They may take the form of a probability of such an action.

Synchronous:

All cells in a grid exercise a simultaneous response to a rule.

Bibliography

Primary Literature

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Author information

Authors and Affiliations

  1. Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, USA

    Lemont B. Kier

  2. Wright State University, Dayton, USA

    Paul G. Seybold

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  1. Lemont B. Kier
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Editor information

Editors and Affiliations

  1. RAMTECH LIMITED, 122 Escalle Lane, Larkspur, CA, 94939, USA

    Robert A. Meyers Ph. D. (Editor-in-Chief) (Editor-in-Chief)

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Kier, L.B., Seybold, P.G. (2009). Cellular Automata Modeling of Complex Biochemical Systems. In: Meyers, R. (eds) Encyclopedia of Complexity and Systems Science. Springer, New York, NY. https://doi.org/10.1007/978-0-387-30440-3_56

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