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EVE is a simulation framework that is able to model predictive internal models around of complex environments. EVE operates under the “[[central dogma]],” the assumption that all biochemical pathways proceed through the following steps: [[DNA]] => [[RNA]] => [[protein]]. Furthermore, the biochemical networks evolve in an asynchronous and stochastic manner. These two assumptions allow for the simulation of temporal dynamics of cascades of biochemical interactions/transformations.
Building upon previous attempts to simulate cellular behavior, such as [[circadian rhythms]], EVE, according to its makers, “integrates many features that improve the biochemical, evolutionary, and ecological realism of our simulations, features that are crucial for simulating microbial regulatory networks in the context of interactions with the environment.”<ref>{{Cite web|url=http://www.princeton.edu/main/news/archive/S21/30/22I85/index.xml?section=science|title=Thinking ahead: Bacteria anticipate coming changes in their environment}}</ref> The program takes into account all the molecular species and their interactions, including but limited to RNA, mRNA, and proteins. Each component is represented by a so-called node, which contains simulates biological parameters, such as basal expression, degradation, and regulatory strength. The program links these network of nodes together and simulates the interactions between the individual nodes.
Each response pathway is modeled to have a high energetic cost. The artificial organism takes in energy in form of “food” from the surroundings, while each interaction pathway expends high levels of energy. This setup generates a selection pressure that favors energy minimization.
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