Modelling cytoskeleton morphogenesis with SBTools

Markus Schwehm
University of Tübingen, Institute of Medical biometry, Germa

Manuel Poppe
University of Tübingen, Computer Science Department, Germany

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     Last modified: March 31, 2006

Abstract
For the modelling of complex biological systems no single homogeneous modelling approach can be successful. Instead the integration of different modelling techniques is necessary in order to model phenomena on very different space and time scales. SBTools implements and integrates stochastic and deterministic modelling approaches in Java within the Eclipse platform.
Properties of the SBT modelling tools: The basic modelling unit is the "Entity" which is an object with discrete and/or continuous internal state. The entities are grouped into several suites. Entities have a position in a global space and can change the position dynamically. Entities have a dynamic list of ties to other entities. State transitions of entities can trigger delayed events in connected entities. All events are executed in correct time sequence by a discrete event simulation engine. Deterministic modelling techniques (PDEs) are integrated effectively into the discrete event model.
We apply SBTools to the modelling of cytoskeleton morphogenesis. The model integrates a deterministic reaction-diffusion system for the GTP metabolism with a stochastic particle system for the microtubule network. GTP molecules can move from the deterministic model to the particle system to build microtubule segments and back. The microtubuli grow in the direction of largest GTP concentration while consuming GTP and thus inhibiting other microtubuli to grow into the same region. The model allows to observe emergent morphological patterns.