Jenga-Krotov algorithm: Efficient compilation of multiqubit gates for exchange-only qubits

Exchange-only (EO) qubits, implemented in triple-quantum-dot systems, offer a compelling platform for scalable semiconductor-based quantum computing by enabling universal control through purely exchange interactions. While high-fidelity single- and two-qubit gates have been demonstrated, the synthesis of efficient multiqubit operations—such as the Toffoli gate—remains a key bottleneck. Conventional gate decompositions into elementary operations lead to prohibitively long and error-prone pulse sequences, limiting practical deployment. In this work, we introduce a gradient-based optimization algorithm, Jenga-Krotov (JK), tailored to discover compact, high-fidelity EO gate sequences. Applying JK to the Toffoli gate, we reduce the number of required exchange unitaries from 216 (in direct decomposition) to 92, and compress the time steps required from 162 to 50, all while maintaining target fidelity. Under realistic noise, the accumulated gate error from our optimized sequence is an order of magnitude lower than that of conventional approaches. We have also applied the JK algorithm to other multiqubit gates and algorithm. For the Fredkin gate, it reduces the number of time steps from 200 to 104 and the number of exchange unitaries from 276 to 172. For the quantum Fourier transform, it compresses the sequence from 180 to 80 time steps and from 237 to 202 exchange unitaries. These results demonstrate that the JK algorithm is a general and scalable strategy for multiqubit gate synthesis in EO architectures, potentially facilitating realization of multiqubit algorithms on semiconductor platforms.