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Figure 1 | Immunome Research

Figure 1

From: Model refinement through high-performance computing: an agent-based HIV example

Figure 1

Agent interactions Viral agents can move from one neighbourhood to the next, (providing there is sufficient space for them, which is checked using a dedicated function). Upon arrival in a new neighbourhood, these agents can perform a single operation only: infection of a CD4 agent. First step is the selection of CD4 target. Possibility of infection is then assessed, (e.g. if CD4 agent is activated). Infection, if it takes place, is implemented as transfer of viral genome information into the CD4 agent and destruction of viral agent. CD4 agents incorporate mobility and can reach new neighbourhoods. As for viral agents, this includes checking, through a dedicated function, that space is available. Upon arrival and if already activated, the agent can activate a CD8 neighbour. Activation follows a process similar to that of infection, detailed above. A possible target is selected, assessed, (in terms of agents bearing “compatible” clonotypes), and then activated when this is possible. If a CD4 agent is infected, it may produce a new viral agent. In the early stages after its own activation, an agent also produces some additional CD4 agents, to enhance immune response. CD8 agent mobility is implemented similarly. In its new neigbourhood, the agent produces new CD8 agents, (if it is currently multiplicating), or targets infected CD4 and APC agents, (if it is activated). Some CD8 agents can enter a state representing memory cells. These agents, (with a greater life span and faster reactivation), interact with all agent types in their neighbourhood, in order to monitor known viral strains, and can be directly reactivated. Final agent type, APC, implements mobility and associated functions needed to query the environment. APC agents interact with viral agents, in the sense that they can ingest them to present viral strain information to other agents. They also interact with CD4 agents, which they can try to activate by presenting viral information. Success of activation is based on affinity between viral epitope and CD4 clonotype.

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