Publications



Stay tuned for our group's future research activities!


You can find Joonho's updated list of publications on his Google scholar page.  (* denotes equal contribution)



Preprints

(4) J. Chen, J. Lee, W. Dou

“How to correct Ehrenfest nonadiabatic dynamics in open quantum systems: Ehrenfest plus random force (E+σ) dynamics”.

arXiv:2407.11672
(3) T. Jiang, J. Zhang, M. Baumgarten, M.-F. Chen, H. Q. Dinh, A. Ganeshram, N. Maskara, A. Ni, J. Lee

“Walking through Hilbert Space with Quantum Computers”.

arXiv:2407.11672
(2) P.J. Robinson, J. Lee, A. Mahajan, D.R. Reichman

“Ab Initio Polaron Wave Functions”.

arXiv:2405.08700
(1) A. Mahajan, P.J. Robinson, J. Lee, D.R. Reichman

“Structure and dynamics of electron-phonon coupled systems using neural quantum states”.

arXiv:2405.08701



Published

(13) P.J. Robinson*, A. Rettig*, H. Q. Dinh*, M.-F. Chen*, J. Lee

“Condensed-Phase Quantum Chemistry”.

Wiley Interdiscip. Rev. Comput. Mol. Sci, 2025; 15:e70005 arXiv:2403.13207
(12) T. Jiang, B. O'Gorman, A. Mahajan, J. Lee

“Unbiasing Fermionic Auxiliary-Field Quantum Monte Carlo with Matrix Product State Trial Wavefunctions”.

Phys. Rev. Research 7, 013038 (2025) arXiv:2405.05440
(11) T. Jiang, M. Baumgarten, P.-F. Loos, A. Mahajan, A. Scemama, S. F. Ung, J. Zhang, F. D. Malone, J. Lee

“Improved Modularity and New Features in ipie: Towards Even Larger AFQMC Calculations on CPUs and GPUs at Zero and Finite Temperatures”.

J. Chem. Phys. 161, 162502 (2024) arXiv:2406.16238
(10) C. Zhao, J. Lee, W. Dou

“Stochastic Resolution of Identity to CC2 for Large Systems: Ground State and Triplet Excitation Energy Calculations”.

J. Phys. Chem. A 2024
(9) F. Ivander, L.P. Lindoy, and J. Lee

“Unified Framework for Open Quantum Dynamics with Memory”.

Nature Communications (2024) 15:8087 arXiv:2312.13233
(8) C. Zhao, Q. Ou, J. Lee, W. Dou

“Stochastic Resolution of Identity to CC2 for Large Systems: Excited State Properties”.

J. Chem. Theory Comput. 2024, 20, 12, 5188-5195
(7) K. Wan, W. J. Huggins, J. Lee, R. Babbush

“Matchgate Shadows for Fermionic Quantum Simulation”.

Communications in Mathematical Physics 404, 629–700 (2023)
(6) N. C. Rubin, D. W. Berry, A. Kononov, F. D. Malone, T. Khattar, A. White, J. Lee, H. Neven, R. Babbush, A. D. Baczewski

“Quantum computation of stopping power for inertial fusion target design”.

PNAS 2024, 121, e2317772121
(5) A. Mahajan, J. S. Kurian, J. Lee, D. R. Reichman, S. Sharma

“Response properties in phaseless auxiliary field quantum Monte Carlo”.

J. Chem. Phys. 159, 184101 (2023) , Editor's Pick.
(4) S. F. Ung, J. Lee, and D. R. Reichman

“Competing Generalized Wigner Crystal States in Moiré Heterostructures”.

Phys. Rev. B 108, 245113
(3) R. Babbush, W. J. Huggins, D. W. Berry, S. F. Ung, A. Zhao, D. R. Reichman, H. Neven, A. D. Baczewski, and J. Lee.

“Quantum simulation of exact electron dynamics can be more efficient than classical mean-field methods”.

Nat. Comm. 2023. 14, 4058.
(2) F. D. Malone, A. Mahajan, J. S. Spencer, and J. Lee.

“ipie: A Python-Based Auxiliary-Field Quantum Monte Carlo Program with Flexibility and Efficiency on CPUs and GPUs”.

J. Chem. Theory Comput. 2023, 19, 109–121.
(1) W. J. Huggins*, B. A. O’Gorman, N. C. Rubin, D. R. Reichman, R. Babbush, and J. Lee*.

“Unbiasing fermionic quantum Monte Carlo with a quantum computer”.

Nature, 2022, 603, 416–420. arXiv, 2022. eprint: 2207.13776.



Before Harvard/Google

(70) N. C. Rubin, D. W. Berry, F. D. Malone, A. F. White, T. Khattar, A. E. Deprince III, S. Sicolo, K¨uhn, M. Kaicher, J. Lee, et al.

“Fault-tolerant quantum simulation of materials using Bloch orbitals”.

PRX Quantum 4, 040303 (2023) arXiv, 2023. eprint: 2302.05531.
(69) A. Rettig, J. Lee, and M. Head-Gordon.

“Even Faster Exact Exchange for Solids via Tensor Hypercontraction”.

arXiv, 2023. eprint: 2304.05505.
(68) A. Morvan, B. Villalonga, X. Mi, S. Mandr´a, A. Bengtsson, P. V. Klimov, Z. Chen, S. Hong, C. Erickson, I. K. Drozdov, et al.

“Phase transition in Random Circuit Sampling”.

arXiv, 2023. eprint: 2304.11119.
(67) X. Mi, A. A. Michailidis, S. Shabani, K. C. Miao, P. V. Klimov, J. Lloyd, E. Rosenberg, R. Acharya, I. Aleiner, T. I. Andersen, et al.

“Stable Quantum Correlated Many Body States via Engineered Dissipation”.

Science 383, 1332–1337 (2024)
(66) J. C. Hoke, M. Ippoliti, D. Abanin, R. Acharya, M. Ansmann, F. Arute, K. Arya, A. Asfaw, J. Atalaya, J. C. Bardin, et al.

“Quantum information phases in space-time: measurement-induced entanglement and teleportation on a noisy quantum processor”.

arXiv, 2023. eprint: 2303.04792.
(65) T. I. Andersen, Y. D. Lensky, K. Kechedzhi, I. Drozdov, A. Bengtsson, S. Hong, A. Morvan, X. Mi, A. Opremcak, R. Acharya, et al.

“Non-Abelian braiding of graph vertices in a superconducting processor”.

Nature, 2023, 1–6.
(63) A. Mandal, D. Xu, A. Mahajan, J. Lee, M. Delor, and D. R. Reichman.

“Microscopic Theory of Multimode Polariton Dispersion in Multilayered Materials”.

Nano Lett. 2023, 23, 4082–4089
(62) S. Lee, J. Lee, H. Zhai, Y. Tong, A. M. Dalzell, A. Kumar, P. Helms, J. Gray, Z.-H. Cui, W. Liu, et al.

“Evaluating the evidence for exponential quantum advantage in ground-state quantum chemistry”.

Nat. Commun. 2023, 14, 1–7.
(61) T. E. O’Brien, G. Anselmetti, F. Gkritsis, V. E. Elfving, S. Polla, W. J. Huggins, O. Oumarou, K. Kechedzhi, D. Abanin, R. Acharya, et al.

“Purification-based quantum error mitigation of pair-correlated electron simulations”.

arXiv, 2022. eprint: 2210.10799.
(59) K. Wan, W. J. Huggins, J. Lee, and R. Babbush.

“Matchgate Shadows for Fermionic Quantum Simulation”.

arXiv, 2022. eprint: 2207.13723.
(58) T. E. O’Brien, M. Streif, N. C. Rubin, R. Santagati, Y. Su, W. J. Huggins, J. J. Goings, N. Moll, E. Kyoseva, M. Degroote, et al.

“Efficient quantum computation of molecular forces and other energy gradients”.

Phys. Rev. Res. 2022, 4, 043210.
(57) M. S. Chen, J. Lee, H.-Z. Ye, T. C. Berkelbach, D. R. Reichman, and T. E. Markland.

“Data-Efficient Machine Learning Potentials from Transfer Learning of Periodic Correlated Electronic Structure Methods: Liquid Water at AFQMC, CCSD, and CCSD(T) Accuracy”.

J. Chem. Theory Comput. 2023, 2023.
(56) A. Rettig, J. Shee, J. Lee, and M. Head-Gordon.

“Revisiting the Orbital Energy Dependent Regularization of Orbital-Optimized Second-Order Møller-Plesset Theory”.

J. Chem. Theory Comput. 2022, 18, 5382–5392.
(55) J. Lee, A. Rettig, X. Feng, E. Epifanovsky, and M. Head-Gordon.

“Faster Exact Exchange for Solids via occ-RI-K: Application to Combinatorially Optimized Range-Separated Hybrid Functionals for Simple Solids with Pseudopotentials Near the Basis Set Limit”.

J. Chem. Theory Comput. 2022, 18, 7336–7349.
(54) J. Lee, H. Q. Pham, and D. R. Reichman.

“Twenty Years of Auxiliary-Field Quantum Monte Carlo in Quantum Chemistry: An Overview and Assessment on Main Group Chemistry and Bond-Breaking”.

J. Chem. Theory Comput. 2022, 18, (Editor’s Choice, Front Cover Article), 7024–7042.
(52) R. Acharya, I. Aleiner, R. Allen, T. I. Andersen, M. Ansmann, F. Arute, K. Arya, A. Asfaw, J. Atalaya, R. Babbush, et al.

“Suppressing quantum errors by scaling a surface code logical qubit”.

Nature, 2023, 614, 676–681.
(51) A. Morvan, T. I. Andersen, X. Mi, C. Neill, A. Petukhov, K. Kechedzhi, D. A. Abanin, A. Michailidis, R. Acharya, F. Arute, et al.

“Formation of robust bound states of interacting microwave photons”.

Nature, 2022, 612, 240–245.
(50) A. Mahajan, J. Lee, and S. Sharma.

“Selected configuration interaction wave functions in phaseless auxiliary field quantum Monte Carlo”.

J. Chem. Phys. 2022, 156, 174111.
(49) X. Mi, M. Sonner, M. Y. Niu, K. W. Lee, B. Foxen, R. Acharya, I. Aleiner, T. I. Andersen, F. Arute, K. Arya, et al.

“Noise-resilient edge modes on a chain of superconducting qubits”.

Science, 2022, 378, 785–790.
(48) J. J. Goings, A. White, J. Lee, C. S. Tautermann, M. Degroote, C. Gidney, T. Shiozaki, R. Babbush, and N. C. Rubin.

“Reliably assessing the electronic structure of cytochrome P450 on today’s classical computers and tomorrow’s quantum computers”.

Proc. Natl. Acad. Sci. U.S.A. 2022, 119, e2203533119.
(47) J. E. T. Smith, J. Lee, and S. Sharma.

“Near-exact nuclear gradients of complete active space self-consistent field wave functions”.

J. Chem. Phys. 2022, 157, 094104.
(46) W. Dou, J. Lee, J. Zhu, L. Mej´ıa, D. R. Reichman, R. Baer, and E. Rabani.

“Time-Dependent Second-Order Green’s Function Theory for Neutral Excitations”.

J. Chem. Theory Comput. 2022, 18, 5221–5232.
(45) J. E. Arias-Martinez, L. A. Cunha, K. J. Oosterbaan, J. Lee, and M. HeadGordon.

“Accurate core excitation and ionization energies from a state-specific coupled-cluster singles and doubles approach”.

Phys. Chem. Chem. Phys. 2022, 24, 20728–20741.
(44) J. L. Weber, H. Vuong, P. A. Devlaminck, J. Shee, J. Lee, D. R. Reichman, and R. A. Friesner.

“A Localized-Orbital Energy Evaluation for Auxiliary-Field Quantum Monte Carlo”.

J. Chem. Theory Comput. 2022, 18, 3447–3459.
(43) N. C. Rubin, J. Lee, and R. Babbush.

“Compressing Many-Body Fermion Operators under Unitary Constraints”.

J. Chem. Theory Comput. 2022, 18, 1480– 1488.
(42) J. Shee, M. Loipersberger, A. Rettig, J. Lee, and M. Head-Gordon.

“Regularized Second-Order Møller–Plesset Theory: A More Accurate Alternative to Conventional MP2 for Noncovalent Interactions and Transition Metal Thermochemistry for the Same Computational Cost”.

J. Phys. Chem. Lett. 2021, 12, 12084–12097.
(41) T. Stauch, B. Ganoe, J. Wong, J. Lee, A. Rettig, J. Liang, J. Li, E. Epifanovsky, T. Head-Gordon, and M. Head-Gordon.

“Molecular magnetisabilities computed via finite fields: assessing alternatives to MP2 and revisiting magnetic exaltations in aromatic and antiaromatic species”.

Mol. Phys. 2021, 119, e1990426.
(40) J. Lee, X. Feng, L. A. Cunha, J. F. Gonthier, E. Epifanovsky, and M. HeadGordon.

“Approaching the basis set limit in Gaussian-orbital-based periodic calculations with transferability: Performance of pure density functionals for simple semiconductors”.

J. Chem. Phys. 2021, 155, 164102.
(38) X. Mi, M. Ippoliti, C. Quintana, A. Greene, Z. Chen, J. Gross, F. Arute, K. Arya, J. Atalaya, R. Babbush, et al.

“Time-crystalline eigenstate order on a quantum processor”.

Nature, 2022, 601, 531–536.
(37) J. R. McClean, N. C. Rubin, J. Lee, M. P. Harrigan, T. E. O’Brien, R. Babbush, W. J. Huggins, and H.-Y. Huang.

“What the foundations of quantum computer science teach us about chemistry”.

J. Chem. Phys. 2021, 155, 150901.
(36) W. J. Huggins, S. McArdle, T. E. O’Brien, J. Lee, N. C. Rubin, S. Boixo, K. B. Whaley, R. Babbush, and J. R. McClean.

“Virtual Distillation for Quantum Error Mitigation”.

Phys. Rev. X, 2021, 11, 041036.
(35) E. Epifanovsky, A. T. B. Gilbert, X. Feng, J. Lee, Y. Mao, N. Mardirossian, P. Pokhilko, A. F. White, M. P. Coons, A. L. Dempwolff, et al.

“Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package”.

J. Chem. Phys. 2021, 155, 084801.
(34) M. Loipersberger, L. W. Bertels, J. Lee, and M. Head-Gordon.

“Exploring the Limits of Second- and Third-Order Møller–Plesset Perturbation Theories for Noncovalent Interactions: Revisiting MP2.5 and Assessing the Importance of Regularization and Reference Orbitals”.

J. Chem. Theory Comput. 2021, 2021,
(33) J. Lee, D. W. Berry, C. Gidney, W. J. Huggins, J. R. McClean, N. Wiebe, and R. Babbush.

“Even More Efficient Quantum Computations of Chemistry Through Tensor Hypercontraction”.

PRX Quantum, 2021, 2, 030305.
(32) L. A. Cunha, J. Lee, D. Hait, C. W. McCurdy, and M. Head-Gordon.

“Exploring spin symmetry-breaking effects for static field ionization of atoms: Is there an analog to the Coulson–Fischer point in bond dissociation?”

J. Chem. Phys. 2021, 155, 014309.
(31) J. Shee, M. Loipersberger, D. Hait, J. Lee, and M. Head-Gordon.

“Revealing the nature of electron correlation in transition metal complexes with symmetry breaking and chemical intuition”.

J. Chem. Phys. 2021, 154, 194109.
(30) J. Lee, F. D. Malone, M. A. Morales, and D. R. Reichman.

“Spectral Functions from Auxiliary-Field Quantum Monte Carlo without Analytic Continuation: The Extended Koopmans’ Theorem Approach”.

J. Chem. Theory Comput. 2021, 17, 3372–3387.
(29) J. Lee, S. Zhang, and D. R. Reichman.

“Constrained-Path Auxiliary-Field Quantum Monte Carlo for Coupled Electrons and Phonons”.

Phys. Rev. B, 2021, 103, 115123.
(28) J. Lee, M. A. Morales, and F. D. Malone.

“A phaseless auxiliary-field quantum Monte Carlo perspective on the uniform electron gas at finite temperatures: Issues, observations, and benchmark study”.

J. Chem. Phys. 2021, 154, 064109.
(27) L. W. Bertels, J. Lee, and M. Head-Gordon.

“Polishing the Gold Standard: The Role of Orbital Choice in CCSD(T) Vibrational Frequency Prediction”.

J. Chem. Theory Comput. 2021, 17, 742–755.
(26) S. P. Veccham, J. Lee, Y. Mao, P. R. Horn, and M. Head-Gordon.

“A nonperturbative pairwise-additive analysis of charge transfer contributions to intermolecular interaction energies”.

Phys. Chem. Chem. Phys. 2021, 23, 928– 943.
(25) J. Lee and D. R. Reichman.

“Stochastic Resolution-of-the-Identity Auxiliary-Field Quantum Monte Carlo: Scaling Reduction without Overhead”.

J. Chem. Phys. 2020, 153, 044131. (Editor’s Pick).
(24) J. Lee, F. D. Malone, and D. R. Reichman.

“The performance of phaseless auxiliary-field quantum Monte Carlo on the ground state electronic energy of benzene”.

J. Chem. Phys. 2020, 153, 126101.
(23) W. J. Huggins, J. Lee, U. Baek, B. O’Gorman, and K. B. Whaley.

“A nonorthogonal variational quantum eigensolver”.

New J. Phys. 2020, 22, 073009.
(22) P. Kent, A. Annaberdiyev, A. Benali, M. C. Bennett, E. J. Landinez Borda, P. Doak, H. Hao, K. D. Jordan, J. T. Krogel, I. Kylanpaa, et al.

“QMCPACK: Advances in the development, efficiency, and application of auxiliary field and real-space variational and diffusion quantum Monte Carlo”.

J. Chem. Phys. 2020, 152, 174105. (Editor’s Pick).
(21) J. Lee, F. D. Malone, and M. A. Morales.

“Utilizing Essential Symmetry Breaking in Auxiliary-Field Quantum Monte Carlo: Application to the Spin Gaps of the C36 Fullerene and an Iron Porphyrin Model Complex”.

J. Chem. Theory Comput. 2020, 16, 3019–3027.
(20) J. Lee, L. Lin, and M. Head-Gordon.

“Systematically Improvable Tensor Hypercontraction: Interpolative Separable Density-Fitting for Molecules Applied to Exact Exchange, Second- and Third-Order Møller-Plesset Perturbation Theory”.

J. Chem. Theory Comput. 2019, 16, 243–263.
(19) J. Lee, D. W. Small, and M. Head-Gordon.

“Excited states via coupled cluster theory without equation-of-motion methods: Seeking higher roots with application to doubly excited states and double core hole states”.

J. Chem. Phys. 151 2019, 214103.
(18) S. P. Veccham, J. Lee, and M. Head-Gordon.

“Making Many-Body Interactions Nearly Pairwise Additive: The Polarized Many-Body Expansion Approach”.

J. Chem. Phys. 2019, 151, 194101.
(17) M. Loipersberger, J. Lee, Y. Mao, A. K. Das, K. Ikeda, J. Thirman, T. Head-Gordon, and M. Head-Gordon.

“Energy Decomposition Analysis for Interactions of Radicals: Theory and Implementation at the MP2 Level with Application to Hydration of Halogenated Benzene Cations and Complexes between CO – 2 and Pyridine and Imidazole”.

J. Phys. Chem. A, 2019, 123, 9621–9633.
(16) J. Lee, L. W. Bertels, D. W. Small, and M. Head-Gordon.

“Kohn-sham density functional theory with complex, spin-restricted orbitals: Accessing a new class of densities without the symmetry dilemma”.

Phys. Rev. Lett. 2019, 123, 113001. (arXiv:1904.08093).
(15) J. Lee, F. D. Malone, and M. A. Morales.

“An auxiliary-field quantum Monte Carlo perspective on the ground state of the dense uniform electron gas: An investigation with Hartree-Fock trial wavefunctions”.

J. Chem. Phys. 2019, 151, 064122.
(14) L. W. Bertels, J. Lee, and M. Head-Gordon.

“Third-Order Møller-Plesset Perturbation Theory Made Useful? Choice of Orbitals and Scaling Greatly Improves Accuracy for Thermochemistry, Kinetics, and Intermolecular Interactions”.

J. Phys. Chem. Lett. 2019, 10, 4170–4176.
(13) J. Lee and M. Head-Gordon.

“Two single-reference approaches to singlet biradicaloid problems: Complex, restricted orbitals and approximate spin-projection combined with regularized orbital-optimized Møller-Plesset perturbation theory”.

J. Chem. Phys. 2019, 150, 244106.
(12) J. Lee and M. Head-Gordon.

“Distinguishing artificial and essential symmetry breaking in a single determinant: approach and application to the C60, C36, and C20 fullerenes”.

Phys. Chem. Chem. Phys. 2019, 21, 4763–4778. (2019 PCCP HOT Articles) (arXiv:1812.05266).
(11) J. Lee*, W. J. Huggins*, M. Head-Gordon, and K. B. Whaley.

“Generalized Unitary Coupled Cluster Wave functions for Quantum Computation”.

J. Chem. Theory Comput. 2018, 15, 311–324. (arXiv:1810.02327)
(10) J. Lee, D. Lee, A. Kocherzhenko, L. Greenman, D. T. Finley, M. B. Francis, and K. B. Whaley.

“Molecular Mechanics Simulations and Improved Tight-binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment”.

J. Phys. Chem. B, 2018, 122, 12292–12301. (Supplementary Cover Article)(arXiv:1809.02324).
(9) J. Lee, D. W. Small, and M. Head-Gordon.

“Open-Shell Coupled-Cluster ValenceBond Theory Augmented with an Independent Amplitude Approximation for Three-Pair Correlations: Application to a Model Oxygen-Evolving Complex and Single Molecular Magnet”.

J. Chem. Phys. 2018, 149, 244121. (arXiv:1808.06743).
(8) J. Lee and M. Head-Gordon.

“Regularized Orbital-Optimized Second-Order Møller-Plesset Perturbation Theory: A Reliable Fifth-Order Scaling Electron Correlation Model with Orbital Energy Dependent Regularizers”.

J. Chem. Theory Comput. 2018, 14, 5203–5219. (arXiv:1807.06185).
(7) M. Ha, D. Y. Kim, N. Li, J. M. L. Madridejos, I. K. Park, I. S. Youn, J. Lee, C. Baig, M. Filatov, S. K. Min, et al.

“Adsorption of Carbon Tetrahalides on Coronene and Graphene”.

J. Phys. Chem. C, 2017, 121, 14968–14974.
(6) J. Lee, D. W. Small, E. Epifanovsky, and M. Head-Gordon.

“Coupled-Cluster Valence-Bond Singles and Doubles for Strongly Correlated Systems: Block-Tensor Based Implementation and Application to Oligoacenes”.

J. Chem. Theory Comput. 2017, 13, 602–615.
(5) I. S. Youn, D. Y. Kim, W. J. Cho, J. M. L. Madridejos, H. M. Lee, M. Ko laski, J. Lee, C. Baig, S. K. Shin, M. Filatov, et al.

“Halogen–π Interactions between Benzene and X2/CX4 (X = Cl, Br): Assessment of Various Density Functionals with Respect to CCSD(T)”.

J. Phys. Chem. A, 2016, 120, 9305–9314.
(4) N. M. Tubman, J. Lee, T. Y. Takeshita, M. Head-Gordon, and K. B. Whaley.

“A deterministic alternative to the full configuration interaction quantum Monte Carlo method”.

J. Chem. Phys. 2016, 145, 044112.
(3) M. E. Fornace*, J. Lee*, K. Miyamoto*, F. R. Manby, and T. F. Miller.

“Embedded Mean-Field Theory”.

J. Chem. Theory Comput. 2015, 11, 568–580.
(2) W. J. Cho, J. Kim, J. Lee, T. Keyes, J. E. Straub, and K. S. Kim.

“Limit of Metastability for Liquid and Vapor Phases of Water”.

Phys. Rev. Lett. 2014, 112, 157802.
(1) J. Y. Ko, S. W. Heo, J. H. Lee, H. B. Oh, H. Kim, and H. I. Kim.

“Host–Guest Chemistry in the Gas Phase: Complex Formation with 18-Crown-6 Enhances Helicity of Alanine-Based Peptides”.

J. Phys. Chem. A, 2011, 115, 14215–14220.