Variational compilation of native gates for efficient trapped-ion Hamiltonian simulation

Quantum simulation on noisy intermediate-scale quantum (NISQ) hardware is limited by short coherence time and gate errors. We present a universal variational compilation optimization method (VCOM) that directly leverages the native gate set of trapped-ion processors, namely single-qubit rotations and global Ising-type XX interactions, to construct shallow circuits for simulating molecular Hamiltonians. Specifically, VCOM employs a hybrid optimization strategy combining genetic algorithms with gradient-based refinement to compile Pauli string evolution operators e^-iPt, thereby substantially reducing circuit depth and multi-qubit gate overhead in Hamiltonian simulation. Applied to hydrogen chains, the compiled circuits achieve fidelities comparable to standard decompositions while reducing the proportion of two-qubit operations to only 1.9%-4.6% of the total native gates, a significant improvement over the standard second-order Trotter-Suzuki product formula. Under experimentally motivated laser-intensity and phase-noise models, the proposed scheme maintains high fidelity and exhibits significantly slower degradation than direct native gate decompositions of conventional circuits. These results establish native-gate-based variational compilation as a scalable and practical approach for digital quantum simulation on trapped-ion platforms, with potential extensions to strongly correlated systems and non-equilibrium dynamics.