Agent-Based Modeling Figure 1. Interacting components/agents involved in the propagation of LPS signaling on macrophages. Yellow triangles reflect the extracellular signal (LPS) and white circles represent the plasma membrane. Red polygons refer to the endotoxin (LPS) receptor and blue polygons refer to the TNF-a receptor. Light green polygons correspond to IL-4 receptors and dark green polygons reflect the presence of kinase (IKK). Blue+orange squares represent the inactive (bound) NF-kB with its inhibitor, IkBa while the grey area refers to the nucleus. doi:10.1371/journal.pone.0009249.g001 LPS from its signaling receptor (R), a signal transduction cascade is triggered that up-regulates the transcription of TNF-a. Since pro- inflammatory cytokines might be responsible for perpetuating and amplifying the inflammatory reaction through the critical node (IKK) [36], such interaction is simulated via the positive interaction between TNF-a, and the kinase activity (IKK). Consequently, the presence of pro-inflammatory mediators (P) promoted the migration of mature T helper cells [37] where Th0 cells become Th1, while the production of anti-inflammatory mediators (A) incited formation of Th2 cells which further potentiate the anti-inflammatory response (A) [28]. Since the anti-inflammatory arm of the host defense system restores homeostasis, the anti-inflammatory component of the model, including anti-inflammatory mediator agents (A), was assumed to exert its counter-regulatory properties by stimulating the degra- dation rate of the early potent pro-inflammatory mediator TNF-a, coupled with the active populations of T helper cells. In particular, the Th2 agents continuously produced anti-inflammatory media- tors to ensure that the population of (A) agents was sufficient to attenuate TNF-a production in macrophages. Since circulating pro-inflammatory (P) agents have the ability to turn Th0 into Th1, instead of Th2, the population of Th2 cells is primarily affected by the concentration of (P) agents. Therefore, the resolution of the inflammatory response is highly dependent on the balance between pro- and anti-inflammatory mediators that are addition- ally regulated by the energetic state of macrophages. To establish the link between the inflammatory response and the cellular energetic state, we assumed that upon activation of a pre-defined threshold the essential energetic response was assumed to subsequently modulate the degradation rate of TNF-a [38]. The production rate of the inflammatory mediator TNF-a increased when the energetic state was lowered during the progression of the inflammatory reaction by NF-kB. Meanwhile, the presence of anti- inflammatory mediators leads to a decrease in the proximal inflammatory mediator, TNF-a. All the interacting components that constitute the agent based model of inflammation were shown in Figure 2. Qualitative Assessment of the Model A self-limited inflammatory response to the endotoxin stimulus corresponds to resolved dynamic profiles for all the elements constituting the model. The objective was to produce the dynamic profiles of a successful inflammatory resolution as shown in Figure 3 that qualitatively agreed with the previously models using a deterministic approach [33,34]. While the inflammatory stimulus, namely LPS agents were successfully cleared within 1 h, the activation of anti-inflammatory cytokines expedited the attenuation of the early pro-inflammatory cytokine TNF-a with subsequent termination of the pro-inflammatory signaling cascade. The correctness of the model was evaluated based on its ability to qualitatively predict the uncontrolled responses as below. Implications of increased insult. High concentrations of LPS, corresponding to an increase in the strength of the inflammatory insult, can be responsible for the amplification of the host immune response [39]. This event is followed by a dysregulation in host defense intrinsic dynamics leading to an unconstrained inflammatory response even after the circulating levels of LPS have been cleared. The model predicted the situation where the initial levels of LPS are increased in Figure 4. We observed that when the concentration of the inflammatory PLoS ONE | www.plosone.org 4 February 2010 | Volume 5 | Issue 2 | e9249