The CKSD Simulator

The CKSD Simulator has been developed as a tool to investigate the interplay of

Conformation, Kinetics, Structure, and Dynamics

A simple specification language facilitates the communication of the network models to the simulation engine. The specification comprises three parts: the definition of microcomponents, the definition of macrocomponents, and the prescription for setting the initial configuration of the 3D-simulation space.

All molecular species participating in the simulated biochemical network are assigned to either the macro- or the microcomponent category. The microcomponents represent small metabolites and ions, while macrocomponents represent macromolecules, mainly proteins.

Microcomponents are treated as fixed, i.e., individual microcomponents of the same type are indistinguishable. Therefore it is sufficient to represent the number of each type of microcomponent per elementary cell in the simulation space. The different types of microcomponents are characterized by different properties, such as mass, effective diameter, or charge. The microcomponents constitute the milieu in which macrocomponents are embedded. Each elementary cell of the simulation space can accommodate one macrocomponent and the local microcomponent milieu.

Macrocomponents are characterized by their individual states and therefore each macromolecule is represented individually during simulation. A macrocomponent corresponds to a compound finite state automaton, patterned as a dodecahedron with each one of its twelve surfaces representing a subunit of the macromolecule. Each such subunit is a finite state automaton whose states represent the physical and chemical states of the subunit.

The state of a subunit may exhibit the following three effects:

1. It can affect the state of a neighboring subunit either within the same macrocomponent or within a macrocomponent in the immediate vicinity.
2. The state of a subunit determines the affinity of the corresponding dodecahedron surface towards other dodecahedrons, i.e., other macrocomponents.
3. Any subunit state may be endowed with a catalytic property that transforms microcomponents at the location of that subunit.

All macrocomponents of a given type possess the same state-to-state transition behavior. The two factors that influence the state transition of a subunit are the states of the neighboring subunits and the microcomponents present at the location of the subunit. Thus the interactions among macro- and microcomponents are circular: microcomponents influence the states of macrocomponents, while the macrocomponents in turn catalyze transformations among microcomponents.

A variety of virtual devices provide the interface between a simulated model and the user. Passive devices are employed to observe the time development of a simulation. Active devices make it possible to intervene to modify the state of the simulation, e.g., by injecting a desired molecular species into a specific location in the simulation space.

The figure on the right shows a snapshot of one of the Tcl/Tk graphical user interfaces which have been implemented for some of the virtual devices. Close up: 60k.

A more detailed description will appear here at some point, but for now I have to refer to the publications.

© K.-P. Zauner, 1999. Located at: http://www.cs.wayne.edu/~kjz/