Agent-Based Modeling Figure 3. A self-limited inflammatory response (LPS(0) = 350 units). Temporal profiles of essential components that constitute the agent based model resolved within 24 hr. doi:10.1371/journal.pone.0009249.g003 inflammatory (P) and anti-inflammatory (A) mediators. The response was exaggerated under conditions of the second endotoxin stimulation due to the priming of various inflammation-specific intracellular signaling molecules which further propagated the inflammatory reaction to nearby cells/agents. The effect of this lethal potentiation scenario was demonstrated in Figure 7. Additionally, if the second dosage was administered when the inflammatory mediators are diminishing, then the effect is less prominent due to both the lack of cytokines and the receptor desensitization which occurs due to pre-existing infection. Modulation in the dynamics of NF-kB signaling module. Another mode of perturbation of the underlying dynamics of the probed system was related to the presence of a ‘‘prior’’ insult that coupled with the LPS stimulus. It accounted for an increased production of pro-inflammatory mediators as shown in Figure 8. Such a sustained pro-inflammatory signaling was possible to deregulate the NF-kB signaling module and led to a persistent NF-kB activity [49]. The elevated NF-kB activity implied that the nuclear concentration of NF-kB cannot be further constrained by its primary inhibitor, IkBa and eventually settled to a steady state far away from their equilibrium (homeostasis). We simulated this scenario by pre-conditioning the system with low-dose of TNF-a. Since TNF-a is a potent inflammatory instigator that stimulates IKK activity it can perturb the behavior of the system towards an unbalanced immune response. Clinically, such an increased rate in the production of pro-inflammatory mediators might be the outcome of a surgical trauma followed by bacterial infection, a so called two hit scenario [50]. We have demonstrated the ability of our model to simulate the trajectory of an unconstrained inflammatory response. Further, the potential of the proposed model was also demonstrated through its capability to respond to an intervention strategy that intended to modulate the dynamics in favor of a balanced immune response. In Figure 9 the effectiveness of a molecule that inhibited IKK activity (IKK-inhibitor) was simulated. From a biological standpoint, these molecules diffuse into the cytoplasm and bind to IKK triggering its deactivation. This process directly competed with the activation of the NF-kB complex through IKK and therefore attenuation in the pro-inflammatory response was observed. As such, despite the implications of high LPS concentration, the dynamics were reversed towards homeostasis. Qualitatively, this result agreed with experimental data that documented the potential of IKK inhibitors in treating inflam- matory disorders [51]. Our model exhibited a bistable behavior which implied the co- existence of two steady states. Physiologically, such dynamics would reflect either a successful inflammatory resolution or the progression of a systemic inflammatory response syndrome. Such bistability is an essential characteristic of the non-linear dynamics of inflammation as suggested from various animal studies [36]. In an attempt to simulate the bistable behavior, a ‘‘switch’’ in the agent rules was employed. A switch was defined as a conditional procedure under which the output could diverge into different states based on a current set of inputs. In our simulation the switch was the production rate of TNF-a with regard to the energetic state of the macrophage. As the current energy value become lower than a certain threshold, the production of TNF-a via the transcription factor NF-kB was amplified, activating the switch. The rationale behind this rule was predicated upon the hypothesis that the activation of NF-kB, followed by the production of (P) response ultimately decrease the expression of genes that are PLoS ONE | www.plosone.org 6 February 2010 | Volume 5 | Issue 2 | e9249