The SEparator for CApture Reactions (SECAR) is a next-generation recoil mass separator system at the National Superconducting Cyclotron Laboratory (NSCL) and Facility for Rare Isotope Beams (FRIB) at Michigan State University. SECAR was designed for precise and direct measurements of reaction rates relevant to the explosive synthesis of elements in astrophysical sites such as X-ray bursts and novae. Once SECAR is operational, it will be utilized for precise measurements of low energy (p,$\gamma$) and (p,$\alpha$) reactions in inverse kinematics with beams of proton-rich radioactive nuclei of masses up to A = 65. The work discussed in this thesis was dedicated to the commissioning of the beamline, including diagnostic devices, to characterizing the system, and defining operational approaches that ensure reliable, reproducible, and optimal performance. To maximize the performance of the device, careful beam alignment to the central ion optical axis needs to be achieved, which can be difficult to attain through manual tuning in a quantitative and reproducible way. Additionally, the ion optical settings need to be verified and optimized to ensure adequate mass separation. In this thesis, the first development of an online Bayesian optimization with a Gaussian process model to tune a nuclear astrophysics recoil separator and improve its ion optical properties is reported. The method is shown to improve recoil separator performance, increase objectivity and reproducibility, and reduce setup and tuning time significantly. It is now used routinely for all separator tuning. As precise knowledge of the beam energy is critical when measuring narrow resonances, the energy calibration of the first bending dipole pair was performed to provide independent incoming beam energy determinations in the SECAR system. This was achieved through the measurement of the $\gamma$-ray yields of the \textsuperscript{27}Al(p,$\gamma$)\textsuperscript{28}Si resonances at $E_p$ = 992 and 1800 keV/u with a BGO (Bismuth Germanate) array at the SECAR target chamber. Two measurements were obtained for each resonance, one with a H\textsuperscript{+} beam and one with a H$^+_2$, to cover a larger rigidity range. By fitting the observed $\gamma$-ray yields with a thick target yield curve, a dipole calibration factor of $k$ = 3.6501$\times$10\textsuperscript{-3} $\pm$ 6.2$\times$10\textsuperscript{-6} (0.17\%) T/$\sqrt{keV amu}$ was obtained. To achieve higher accuracy when extrapolating to higher energies, the energy calibration was also performed taking into account relativistic effects.This commissioning work paves the way for SECAR to achieve its scientific goals of improving our understanding of stellar explosions. By providing accurate thermonuclear reaction rates, astrophysical models will in turn provide better understanding of explosions such as novae and X-ray bursts.
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