Agent-Based Modeling Figure 9. Exploring the effect of an intervention (anti-inflammatory) strategy that inhibits IKK activity. Such scenario is simulated by administering LPS(t = 0 hr) = 750 and IKK inhibitors, IKK inhibitors (t = 0 hr) = 400 (green line). doi:10.1371/journal.pone.0009249.g009 represents a ‘‘tick’’ or a discrete time point. Each procedure governs the behavior of a specific class of agent; it contains instructions on how an agent should move, whether to bind to a receptor or ‘‘bounce’’ off of the cell membrane, etc. The instructions are conditional (rule) based (if-then) and may involve multiple agents, such as when two molecules bind together, both molecules’ parameters change due to the binding, for instance, they now move in the same pattern. Moreover, the instructions are derived from literature regarding relevant mechanisms for LPS activation [35,43,63], intricate signaling cascades [64,65,66,67,68,69], cyto- kine network [40,41,70] and cell (Th) differentiation [28,31]. The specific rules that determine the behavior of the relevant agents are presented in Table 1. The movement of LPS molecules is characterized by a random walk routine, namely, each molecule heads to a random direction and moves several steps forward. When one LPS molecule comes in contact with its signaling receptor on the surface of the macrophage, it will have a chance to bind to it. Once bound a molecule will no longer be moving freely; it will move in Table 2. List of agents. Cell types Stimulus, mediator Receptors Intracellular signaling molecules Cellular component doi:10.1371/journal.pone.0009249.t002 Macrophage, Th-0, Th-1, Th-2 LPS, IL-12, IL-4, TNF-a TLR4, IL-12R, IL-4R, TNFR IKK, NF-kB, IkBa Plasma membrane, nucleus accordance with its counterpart. Such process triggers the pro- duction of the proximal inflammation-specific mediator, TNF-a causing a decrease in receptor’s sensitivity. Receptor sensitivity determines the probability by which one LPS molecule will bind to its endotoxin receptor. Bound LPS molecules are degraded shortly, freeing up the receptor. Molecules of TNF-a also move randomly where they can diffuse into the cell (move past the cell membrane agents) and bind to their appropriate receptors either from the cytoplasm or from outside of the membrane. The activated receptor will trigger downstream a signal transduction cascade that stimulates IKK activity. Activated IKKs move randomly inside the cytosol while they are not capable in moving past the cell membrane agents or enter the nucleus region. They activate the NF-kB complex by dissociating the bound between NF-kB and its inhibitor, IkBa. This is achieved through the phosphorylation of the inhibitory protein IkBa where dissociated IkBa is therefore ubiquitinated and degraded by the proteasome. Activated NF-kB then moves into the nucleus region initiating the transcriptional machinery program which up-regulates the transcription of IkBa, of pro-inflammatory cytokines (P) followed by a decrease in the energetic state of the macrophage. Activated IkBas are capable of moving into the nucleus, binding to activated NF-kB molecules, and deactivate them, as they retrieve nuclear concentrations of NF-kB by forming an inactive complex in the cytoplasmic region. The pro-inflammatory (P) agents are limited by cell membranes and their presence excites the production of anti-inflammatory cytokines (A) and the migration of undifferentiated T-helper cells (Th0) which are not present under conditions of no infec7tious challenge. However, the secretion of pro-inflammatory (P) mole- cules by macrophages during the progression of the inflammatory PLoS ONE | www.plosone.org 11 February 2010 | Volume 5 | Issue 2 | e9249