Quantum simulation seeks to efficiently solve quantum many-body problems using programmable quantum devices, and quantum optical systems of atoms and ions provide one of the most promising way to implement quantum simulators in the laboratory. In this talk, we highlight recent advancements in both analog and digital quantum simulations, covering topics from condensed matter physics to high-energy physics. We begin with a brief overview of atomic platforms and the engineering of many-body Hamiltonians. Next, we provide examples of recent research that includes programming and verifying quantum simulators through Hamiltonian learning, investigating large-scale entanglement, and simulating lattice gauge theories. We conclude with a forward-looking perspective on quantum simulators as programmable quantum sensors.