Research and development of hypersonic air-breathing vehicles capable of sustained operation in flight have received renewed interest by the international scientific community in the past decade. The series of HyShot flight experiments performed by the Centre for Hypersonics at the University of Queensland, Australia, in the early 2000s demonstrated successful flight operation of a scramjet engine for a time period of 6 to 10 seconds at Mach 7.5 and led to the HyCAUSE joint project between the United States Defense Advanced Research Projects Agency (DARPA) and the Australian Defence, Science and Technology Organisation (DSTO), also focused on scramjet operation (at Mach 10). These two pioneering programs culminated in the on-going Hypersonic International Flight Research Experimentation Program (HIFiRE), a collaborative effort among the United States Air Force Research Laboratory (AFRL), NASA, and the Australian DSTO. NASA’s X-43 aircraft and the on-going Boeing X-51 WaveRider (a collaborative effort with the AFRL, DARPA, NASA, and Pratt & Whitney) are also among the suite of recent experimental programs on hypersonic scramjet-based propulsion. The HIFiRE program (see Jackson et al. 2011, for an overview) comprises a set of eight flight tests, the second of which (HIFiRE-2) was intended to demonstrate transition from dual-mode to scram-mode operation over a flight Mach range from 6 to 8 at nearly constant dynamic pressure, achieving a combustion efficiency of at least 70% in the scram-mode. The flight test, successfully flown in May 2012, was supported by a campaign of ground tests (Hass et al. 2009; Cabell et al. 2011) performed in the HIFiRE Direct Connect Rig (HDCR) at the NASA Langley Arc-Heated Scramjet Test Facility (AHSFT). Additionally, computational fluid dynamics (CFD) simulations of the HDCR using Reynolds-Averaged Navier Stokes (RANS) solvers were performed to complement the ground tests in the design and development of the flowpath for the flight experiment (Storch et al. 2011; Bynum & Baurle 2011). Besides the aforementioned mode transition (ie, operation at variable Mach number from dual to scramjet operation), other key elements that set the HIFiRE scramjet apart from its predecessors are the use of a hydrocarbon fuel (versus the hydrogen fuel used in HyShot and HyCAUSE programs), a multi-staged fuel injection system, and the presence of a cavity-based flame-holder located in between the two injection stages. While low-fidelity, RANS simulations are a powerful engineering tool valuable in the design phases of these experimentation programs, higher-fidelity simulation techniques are required to discern the physical phenomena dominating at the different turbulence scales present in the flow (Fulton et al. 2012). Turbulent mixing, which plays a central role in supersonic combustion, and the unsteadiness due to large-scale turbulent motions, which can lead to flow instabilities inside the engine, are two such phenomena for which higher-fidelity simulations provide superior predicting capabilities than RANS. With today’s computational power, direct numerical simulation (DNS) techniques that