1. X.-H. Dan, Z.-R. Long, T.-Y. Qiu, J. P. Menzel, Q. Shi, and V. S. Batista, Nonadiabatic H-atom scattering channels on Ge (111) elucidated by the hierarchical equations of motion,  J. Chem. Phys. 164, 024115 (2026)

2. T.-C. Li, H.-Y. Zhang, and Q. Shi, Theoretical study of ultrafast electron transfer in arabidopsis thaliana cryptochrome: A comparative study of mode specific contributions and perturbative methods, Chin. J. Chem. Phys. 39, 51-60 (2026)

3. Y.-J. Chen, S.-C. Zhang, and Q. Shi, Simulation of one and two qubit superconducting quantum gates in the presence of non-Markovian noise, Phys. Rev. B 113, 094302 (2026)

4. T.-C. Li, P. Venkatesh, Q. Shi, and A. Montoya-Castillo. For molecular polaritons, disorder and phonon timescales control the activation of dark states in the thermodynamic limit, arXiv:2603.06868 (2026)

5.  H.-Y. Zhang, X.-Y. Liu, X.-H. Dan, and Q. Shi, Simulation of homogeneous electrochemical proton-coupled electron transfer using the hybrid-bath hierarchical equations of motion, J. Chem. Phys. 164, 224110 (2026)

1. W.-Z. Guan, Y.-Y. Liu, and Q. Shi, Simulation of Quantum Diffusion on a One-Dimensional Periodic Potential, J. Phys. Chem. C. 129.2, 1149-1156 (2025)

2. T.-C. Li, C.-H. Huang, S.-M. Bai, and Q. Shi, Theoretical Methods Based on Linear Response Theory to Simulate Dynamics and Absorption Spectra of Molecular Polaritons, J. Chem. Phys. 162.9, 094105 (2025)

3.  C.-H. Huang, S.-M. Bai, and Q. Shi, A Theoretical Model for Linear and Nonlinear Spectroscopy of Plexcitons, J. Chem. Theory Comput. 21.7, 3612-3524 (2025)

4. S.-C. Zhang and Q. Shi, Time-evolving matrix product operator method in a nondiagonal basis set based on the derivative of the path-integral expression, Phys. Rev. A 111, 062210 (2025)

5. S.-C. Zhang, Z.-Y. Liu, P. Bao, and Q. Shi, A multiset matrix product state approach to hierarchical equations of motion and its application to vibrational relaxation on metal surfaces, J. Chem. Phys. 163, 094102 (2025)

6. Y.-L. Ding, C.-H. Huang, Y.-J. Chen, S.-M. Bai, and Q. Shi, Simulation of the Pump–Probe Spectra and Bright State Dynamics of Molecular Polaritons, J. Phys. Chem. Lett. (2025)

1. S.-C. Zhang, Y. Chen and Q. Shi, Simulating the operation of a quantum computer in a dissipative environment, J. Chem. Phys. 160, 054101 (2024)

2. T.-C. Li, Y.-M. Yan and Q. Shi, Is there a finite mobility for the one vibrational mode Holstein model? Implications from real time simulations, J. Chem. Phys. 160, 111102 (2024)

3. W.-Z. Guan, P. Bao, J.-W. Peng, Z.-G. Lan, and Q. Shi, mpsqd: A matrix product state based Python package to simulate closed and open system quantum dynamics, J. Chem. Phys. 161, 122501 (2024)

4. X.-Y. Liu, X.-H. Dan, and Q. Shi, Theoretical study of proton-coupled electron transfer reaction in metal-hydride complexes, Chin. J. Chem. Phys. 37.2, 199 (2024).

5. C.-H. Huang, S.-M. Bai, and Q. Shi, Simulation of the Pump–Probe Spectra and Excitation Energy Relaxation of the B850 Band of the LH2 Complex in Purple Bacteria, J. Phys. Chem. B, 128.31, 7467-7475 (2024)

6. S.-M. Bai, S.-C. Zhang, C.-H. Huang, and Q. Shi, Hierarchical Equations of Motion for Quantum Chemical Dynamics: Recent Methodology Developments and Applications, Acc. Chem. Res. 57, 21, 3151–3160 (2024)

1. X.-H. Dan, M. Xu, J. T. Stockburger, J. Ankerhold and Q. Shi, Efficient low-temperature simulations for fermionic reservoirs with the hierarchical equations of motion method: Application to the Anderson impurity model, Phys. Rev. B, 107,195429 (2023)

2.  X.-H. Dan and Q. Shi, Theoretical study of nonadiabatic hydrogen atom scattering dynamics on metal surfaces using the hierarchical equations of motion method, J. Chem. Phys. 159, 044101 (2023)

1. T.-C. Li, Y.-M. Yan and Q. Shi, A low-temperature quantum Fokker-Planck equation that improves the numerical stability of the hierarchical equations of motion for the Brownian oscillator spectral density, J. Chem. Phys. 156, 064107 (2022)

2. X.-H. Dan, M. Xu, Y.-M. Yan and Q. Shi, Generalized master equation for charge transport in a molecular junction: Exact memory kernels and their high order expansion, J. Chem. Phys. 156, 134114 (2022)

3. T. Xing, T.-C. Li, Y.-M. Yan and Q. Shi, Mixed quantum classical reaction rates based on the phase space formulation of the hierarchical equations of motion, Chin. J. Chem. Phys. 35.5, 727 (2022)

4. T. Xing, T.-C. Li, Y.-M. Yan, S.-M. Bai and Q. Shi, Application of the imaginary time hierarchical equations of motion method to calculate real time correlation functions, J. Chem. Phys. 156, 244102 (2022)

5. M. Xu, Y.-M. Yan, Q. Shi, J. Ankerhold and J. T. Stockburger, Taming Quantum Noise for Efficient Low Temperature Simulations of Open Quantum Systems, Phys. Rev. Lett. 129, 230601 (2022)

1. Y.-M. Yan, M. Xu, T.-C. Li and Q. Shi, Efficient propagation of the hierarchical equations of motion using the Tucker and hierarchical Tucker tensors, J. Chem. Phys. 154(19): 194104 (2021)

2. Y.-Y. Liu, Y.-M. Yan, T. Xing and Q. Shi, Understanding the Large Kinetic Isotope Effect of Hydrogen Tunneling in Condensed Phases by Using Double-Well Model Systems, J. Phys. Chem. B, 125.22, 5959–5970 (2021)

3. P. Bao, Christian P. Hettich, Q. Shi and J.-L. Gao, Block-Localized Excitation for Excimer Complex and Diabatic Coupling, J. Chem. Theory Comput. 17, 1, 240–254 (2021)

1. Y.-M. Yan, T. Xing and Q. Shi, A new method to improve the numerical stability of the hierarchical equations of motion for discrete harmonic oscillator modes, J. Chem. Phys. 153(20), 204109 (2020)

2. Y.-M. Yan, Y.-Y. Liu, T. Xing and Q. Shi, Theoretical study of excitation energy transfer and nonlinear spectroscopy of photosynthetic light‐harvesting complexes using the nonperturbative reduced dynamics method, WIREs Comput Mol Sci e1498 (2020)

1. Y.-M. Yan, M. Xu, Y.-Y. Liu and Q. Shi, Theoretical study of charge carrier transport in organic molecular crystals using the Nakajima-Zwanzig-Mori generalized master equation, J. Chem. Phys. 150(23), 234101 (2019)

2. Y. Xu, P. Bao, K. Song and Q. Shi, Theoretical study of proton coupled electron transfer reaction in the light state of the AppA BLUF photoreceptor, J. Comput. Chem. 40(9), 1005-1014 (2019)

3. M. Xu, Y.-Y. Liu, K. Song and Q. Shi, A non-perturbative approach to simulate heterogeneous electron transfer dynamics: Effective mode treatment of the continuum electronic states, J. Chem. Phys. 150(4), 044109 (2019)

1. Y.-Y. Liu, Y.-M. Yan, M. Xu, K. Song and Q. Shi, Exact generator and its high order expansions in time-convolutionless generalized master equation: Applications to spin-boson model and excitation energy transfer, Chin. J. Chem. Phys. 31(4), 575 (2018)

2. Q. Shi, Y. Xu, Y.-Y. Yan and M. Xu, Efficient propagation of the hierarchical equations of motion using the matrix product state method, J. Chem. Phys. 148(17), 174102 (2018)

3. M. Xu, Y.-M. Yan, Y.-Y. Liu and Q. Shi, Convergence of high order memory kernels in the Nakajima-Zwanzig generalized master equation and rate constants: Case study of the spin-boson model, J. Chem. Phys. 148(16), 164101 (2018)

4. X. Leng, Y.-M. Yan, R.-D. Zhu, K. Song, Y.-X. Weng and Q. Shi, Simulation of the two-dimensional electronic spectroscopy and energy transfer dynamics of light-harvesting complex ii at ambient temperature. J. Phys. Chem. B 122(17), 4642-4652 (2018)

5. Y. Xu, K. Song and Q. Shi, Mixed quantum-classical simulation of the hydride transfer reaction catalyzed by dihydrofolate reductase based on a mapped system-harmonic bath model, J. Chem. Phys. 148(10), 102322 (2018)

6. Y.-M. Yan, L.-Z. Song and Q. Shi, Understanding the free energy barrier and multiple timescale dynamics of charge separation in organic photovoltaic cells, J. Chem. Phys. 148(8), 084109 (2018)

7. R.-H. Zheng, W.-M. Wei, M. Xu and Q. Shi, Sum-frequency vibrational spectroscopy of limonene chiral liquids due to the nonadiabatic effect, Phys. Chem. Chem. Phys. 20(10), 7053-7058 (2018)

1. W.-W. Zhao, K. Song, Y. Chen, H. Wang, Z. Liu, Q. Shi, J.-B. Huang and Y. Wang, Aggregation of a cationic gemini surfactant with a chelating molecule and effects from calcium ions, Langmuir, 33(44), 12719-12728 (2017)

2. W.-Q. Li, L.-L. Zhu, Q. Shi, J.-J. Ren, Q. Peng and Z.-G. Shuai, Excitonic coupling effect on the nonradiative decay rate in molecular aggregates: Formalism and application, Chem. Phys. Lett. 683, 507-514 (2017)

3. K. Song and Q. Shi, Theoretical study of photoinduced proton coupled electron transfer reaction using the non-perturbative hierarchical equations of motion method, J. Chem. Phys. 146(18), 184108 (2017)

4. L.-Z. Song and Q. Shi, Hierarchical equations of motion method applied to nonequilibrium heat transport in model molecular junctions: Transient heat current and high-order moments of the current operator, Phys. Rev. B 95(6), 064308 (2017)

5. M. Xu, L.-Z. Song, K. Song and Q. Shi, Convergence of high order perturbative expansions in open system quantum dynamics, J. Chem. Phys. 146(6), 064102 (2017)

6. X. Leng, S. Yue, Y.-X. Weng, K. Song and Q. Shi, Effects of finite laser pulse width on two-dimensional electronic spectroscopy, Chem. Phys. Lett. 667, 79-86 (2017)