BDI-modelling of complex intracellular dynamics

Abstract

A BDI-based continuous-time modelling approach for intracellular dynamics is presented. It is shown how temporalised BDI-models make it possible to model intracellular biochemical processes as decision processes. By abstracting from some of the details of the biochemical pathways, the model achieves understanding in nearly intuitive terms, without losing veracity: classical intentional state properties such as Beliefs, Desires and Intentions, are founded in reality through precise biochemical relations. In an extensive example, the complex regulation of Escherichia coli vis-à-vis lactose, glucose and oxygen is simulated as a discrete-state, continuous-time temporal decision manager. Thus a bridge is introduced between two different scientific areas: the area of BDI-modelling and the area of intracellular dynamics.

Patterns in World Dynamics Indicating Agency

“…A specification of dynamic properties in LEADSTO format has as advantages that it is executable and that (besides in textual or formal format), it can often easily be depicted graphically (as in Figure 7). The LEADSTO format has shown its value especially when temporal relations for basic mechanisms in the (continuous) physical world are modelled and simulated; for example, in cooperation with cell biologists, the bacterium E. coli and its intracellular chemistry have been modelled as an agent in LEADSTO (Jonker, Snoep, Treur, Westerhoff, and Wijngaards, 2008). The textual specification in LEADSTO format of the example depicted in Figure 7 is as follows:…”

Learning to Believe by Feeling: An Agent Model for an Emergent Effect of Feelings on Beliefs

“…This language has been proven successful to obtain agent models in a number of contexts, varying from biochemical processes that make up the dynamics of cell behaviour (cf. [16]) to neurological and cognitive processes (e.g., [4], [5] and [6]). Within LEADSTO the dynamic property or temporal relation a → →D b denotes that when a state property a occurs, then after a certain time delay (which for each relation instance can be specified as any positive real number D), state property b will occur.…”

Representation for reciprocal agent–environment interaction

“…A specification of dynamic properties in leads to format has as advantages that it is executable and that it can often easily be depicted graphically. The leads to format has shown its value especially when temporal or causal relations in the (continuous) physical world are modelled and simulated in an abstract, non-discrete manner; for example, the intracellular chemistry of Escherichia coli (Jonker, Snoep, Treur, Westerhoff, & Wijngaards, 2008).…”