Connecting a physiological model to a cognitive architecture presents an attractive option to better simulate a wide range of human behavior. This connection should facilitate both the effects of physiology on cognition (e.g. hunger and decision-making), and the effects of cognition on physiology (e.g. autonomic responses to memory featuring particularly aversive stimuli). To add physiology to a cognitive architecture, it should be represented as a separate module or substrate. We present ACT-R φ (ACT-R Phi), a connection of the physiology simulation system HumMod (Hester et al, 2011) and the cognitive architecture ACT-R (Anderson, 2007) using an newly created ACT-R module. A model of the startle response and its consequent effects on cognition and physiology is presented to demonstrate an example use of the new substrate. This extended version of ACT-R allows a user to computationally realize theories involving cognition, physiology, and their interaction. This architecture has potential applications to training simulations.