Publications

Zhang, D., et al. DPA-2: A large atomic model as a multi-task learner. npj Comput. Mater. 10, 293 (2024)

Sun, X. and Liu, Z. Reduced density matrix dynamics in multistate harmonic models via time-convolution and time-convolutionless quantum master equations with quantum-mechanical and semiclassical kernels. J. Chem. Phys. 161, 184105 (2024)

Zeng., H., Kou, Y., and Sun, X. How sophisticated are neural networks needed to predict long-term nonadiabatic dynamics?  J. Chem. Theory Comput. 20, 9832–9848 (2024)

Feng, Y., Cong, Y., Zhao, Y., Zhang, C., Song, H., Fang, B., Yang, F., Zhang, H., Zhang, J. Z.H., Zhang, L. "Blade of polarized water molecule” is the key to hydrolase catalysis regulation. J. Chem. Inf. Model.  64, 7987–7997(2024)

Cao, W., Hu, Z., Sun, H., and Wang, X.-B. Photoelectron spectroscopy and computational study on microsolvated [B₁₀H₁₀]^2– clusters and comparisons to their [B₁₂H₁₂]^2– analogues. J. Phys. Chem. A 128, 6981-6988 (2024)

Shu, Y., Yue, J., Li, Y., Yin, Y., Wang, J., Li, T., He, X., Liang, S., Zhang, G., Liu, Z., and Wang, Y. Development of human lactate dehydrogenase a inhibitors: High-throughput screening, molecular dynamics simulation and enzyme activity assay. J. Comput. Aided Mol. Des. 38, 28 (2024)

Yue, J., Yin, Y., Feng, X., Xu, J., Li, Y., Li, T., Liang, S., He, X., Liu, Z., and Wang, Y. Discovery of the inhibitor targeting the SLC7A11/xCT axis through in silico and in vitro experiments. Int. J. Mol. Sci.  25, 8284 (2024)

Zhu, J., Guo, P., Zhang, J., Jiang, Y., Chen, S., Liu, J., Jiang, J., Lan, J., Zeng, X. C., He, X., and Yang, J. Superdiffusive rotation of interfacial water on noble metal surface. J. Am. Chem. Soc. 146, 16281-16294 (2024)

Wan, Z., Chen, Z., Chen, H., Jiang, Y., Zhang, J., Wang, Y., Wang, J., Sun, H., Zhu, Z., Zhu, J., Yang, L., Ye, W., Zhang, S., Xie, X., Zhang, Y., Zhuang, X., He, X., and Yang, J. XRDMatch: a semi-supervised learning framework to efficiently discover room temperature lithium superionic conductors. Energy Environ. Sci. 17, 9487-9498 (2024)

Chen, Z., Li, H., Zhang, C., Zhang, H., Zhao, Y., Cao, J., He, T., Xu, L., Xiao, H., Li, Y., Shao, H., Yang, X., He, X., and Fang, G. Crystal structure prediction using generative adversarial network with data-driven latent space fusion strategy. J. Chem. Theory Comput. 20, 9627–9641 (2024)

Chen, Y., Wan, Z., Li, Y., He, X., Wei, X., and Han, J. Graph curvature flow-based masked attention. J. Chem. Inf. Model. 64, 8153–8163 (2024)

Wang, S., Wang, K., Song, K., Lai, Z. W., Li, P., Li, D., Sun, Y., Mei, Y., Xu, C., and Liao, M. Structures of the Mycobacterium tuberculosis efflux pump EfpA reveal the mechanisms of transport and inhibition. Nat. Commun. 15, 7710 (2024)

Zhou, X., Huang, Z., and He, X. Diffusion Monte Carlo method for barrier heights of multiple proton exchanges and complexation energies in small water, ammonia, and hydrogen fluoride clusters. J. Chem. Phys. 160, 054103 (2024)

Li, H., Sun, M., Lei, F., Liu, J., Chen, X., Li, Y., Wang, Y., Lu, J., Yu, D., Gao, Y., Xu, J., Chen, H., Li, M., Yi, Z., He, X., and Chen, L. Methyl rosmarinate is an allosteric inhibitor of SARS-cov-2 3 C L protease as a potential candidate against SARS-cov-2 infection. Antivir. Res. 224, 105841 (2024)

Trillot, S., Lam, J., Ispas, S., Kandy, A. K. A., Tuckerman, M. E., Tarrat, N., and Benoit, M. Elaboration of a neural-network interatomic potential for silica glass and melt. Comput. Mater. Sci. 236, 112848 (2024)

Xia, W., Xiao, J., Bian, H., Zhang, J, Zhang, J. Z. H., and Zhang, H. Deep learning-based construction of a drug-like compound database and its application in virtual screening of HsDHODH inhibitors. Methods 225, 44-51 (2024)

Zhou, M., Zhao, F., Yu, L., Liu, J., Wang, J., and Zhang, J. Z. H. An efficient approach to the accurate prediction of mutational effects in antigen binding to the MHC1. Molecules 29, 881 (2024)

Peng, X., Cao, W. Hu, Z., Yang, Y., Sun, Z., Wang, X.-B., and Sun, H. Observation of a super-tetrahedral cluster of acetonitrile-solvated dodecaborate dianion via dihydrogen bonding. J. Chem. Phys. 160, 054308 (2024)

Hu, Z., Shao, Q., Li, Z., Sun, Z., Wang, X.-B., and Sun, H. Deprotonated sulfamic acid and its homodimers: Does sulfamic acid adopt zwitterion during cluster growth? J. Chem. Phys. 160, 054303 (2024)

Han. C., Zhang, D., Xia, S., and Zhang, Y. Accurate prediction of NMR chemical shifts: Integrating DFT calculations with three-dimensional graph neural networks. J. Chem. Theory Comput. 20, 5250–5258 (2024)

Han. C., Zhang, D., Xia, S., and Zhang, Y. Accurate prediction of NMR chemical shifts: Integrating DFT calculations with three-dimensional graph neural networks. J. Chem. Theory Comput. 20, 5250–5258 (2024)

Wang, S., Oliveira-Silveira, J., Fang, G., and Kang, J. High-content analysis identified synergistic drug interactions between INK128, an mTOR inhibitor, and HDAC inhibitors in a non-small cell lung cancer cell line. BMC Cancer 24, 335 (2024)

Simkó, I., Felker, P. M., and Bačić, Z. HCl trimer: HCl-stretch excited intramolecular and intermolecular vibrational states from 12D fully coupled quantum calculations employing contracted intra- and inter-molecular bases. J. Chem. Phys. 160, 164304 (2024)

Liu, X., Gong, J., Jiang, Y., He, X., and Yang, J. Optimizing cell voltage dependence on size of carbon nanotube-based electrodes in Na-ion and K-ion batteries. Phys. Chem. Chem. Phys. 26, 12027-12034 (2024)

Yue, J., Xu, J., Yin, Y., Shu, Y., Li, Y., Li, T., Zou, Z., Wang, Z., Li, F., Zhang, M., Liang, S., He, X., Liu, Z., and Wang, Y. Targeting the PDK/PDH axis to reverse metabolic abnormalities by structure-based virtual screening with in vitro and in vivo experiments. Int. J. Biol. Macromol. 262, 129970 (2024)

Yang, Y., Chen, S., Zhang, M., Shi, Y., Luo, J., Huang, Y., Gu, Z., Hu, W., Zhang, Y., He, X., and Yu, C. Mesoporous nanoperforators as membranolytic agents via nano- and molecular-scale multi-patterning. Nat. Commun. 15, 1891 (2024)

Humeniuk, A and Glover, W. J. Multistate, polarizable QM/MM embedding scheme based on the direct reaction field method: Solvatochromic shifts, analytical gradients and optimizations of conical intersections in solution. J. Chem. Theory Comput. 20, 2111–2126 (2024)

Gu, W. and Zhang, J. Z.H. Substituent effects on the selectivity of ambimodal [6+4]/[4+2] cycloaddition. Phys. Chem. Chem. Phys. 26, 9636-9644 (2024)

Wang, M., Mei, Y., and Ryde, U. Convergence criteria for single-step free-energy calculations: the relation between the Π bias measure and the sample variance. Chem. Sci.15, 8786-8799 (2024)

Zhu, Y., Feng, Y., Wang, J., Yuan, Z., Miao, Y., Miao, T., Gao, B., and Zhang, L. Selective Esterification Design of Lipases for TAG Synthesis Based on the Unique Structure of Curved DHA. ACS Food Sci. Technol. (2024)

Zhu, S., Liu, S., Zhang, C., Xin, X., Liu, Z., Zhang, L., Li, B., Yuan, Y. Pathway and enzyme engineering for the bioconversion of lignin derivatives into homoeriodictyol in Saccharomyces cerevisiae. Green Chem. 26, 5260-5272 (2024)

Wang, L., Xue, B., Zhang, X., Gao, Y., Xu, P., Dong, B., Zhang, L., Zheng, L., Li, L., and Liu, W. Extracellular Matrix-Mimetic Intrinsic Versatile Coating Derived from Marine Adhesive Protein Promotes Diabetic Wound Healing through Regulating the Microenvironment. ACS Nano 18, 14726–14741 (2024)

Quarta, G. and Schlick, T. Riboswitch Distribution in the Human Gut Microbiome Reveals Common Metabolite Pathways. J. Phys. Chem. B 128, 4336–4343 (2024)

Portillo-Ledesma, S. and Schlick, T. Regulation of chromatin architecture by protein binding: insights from molecular modeling. Biophys. Rev. (2024)

Zhang, Y., Zhang, Z., Ke, D., Pan, X., Wang, X., Xiao, X., and Ji, C. FragGrow: A web server for structure-based drug design by fragment growing within constraints. J. Chem. Inf. Model. 64, 3970–3976 (2024)

Liu, Z. and Sun, X. Instantaneous Marcus theory for photoinduced charge transfer dynamics in multistate harmonic model systems. J. Phys. Condens. Matter 36, 31 (2024)

Sun, X. and Liu, Z. Semiclassical Approaches to Perturbative Time-Convolution and Time-Convolutionless Quantum Master Equations for Electronic Transitions in Multistate Systems. J. Chem. Phys. 160, 174113 (2024)

Liu, Z., Song, Z., and Sun, X. All-atom photoinduced charge transfer dynamics in condensed phase via multistate nonlinear-response instantaneous Marcus theory. J. Chem. Theory Comput. 20, 3993–4006 (2024)

Liu, Z., Lyu. N., Hu, Z., Zeng, H., Batista, V. S., and Sun, X. Benchmarking various nonadiabatic semiclassical mapping dynamics methods with tensor-train thermo-field dynamics. J. Chem. Phys. 161, 024102 (2024)

Kuroshima, D., Kilgour, M., Tuckerman, M. E., and Rogal, J. Machine learning classification of local environments in molecular crystals. J. Chem. Theory Comput. (2024)

Fu, H., Zhang, M., Leng, J., Hu, W., Zhu, T., and Zhang, Y. Predicting two-photon absorption spectra of octupolar molecules: A deep-learning approach based exclusively on molecular structures. J. Phys. Chem. A 128, 431–438 (2024)

Zelovich, T., Dekel, D. R., and Tuckerman, M. E. Electrostatic potential of functional cations as a predictor of hydroxide diffusion pathways in nanoconfined environments of anion exchange membranes. J. Phys. Chem. Lett. 15, 408–415 (2024)

Portillo-Ledesma, S., Chung, S., Hoffman, J., and Schlick, T. Regulation of chromatin architecture by transcription factor binding. eLife 12, RP91320 (2024)

Wang, S., Liu, F., Li, P., Wang, J.-N., Mo, Y., Lin, B., and Mei, Y. Potent inhibitors targeting cyclin-dependent kinase 9 discovered via virtual high-throughput screening and absolute binding free energy calculations. Phys. Chem. Chem. Phys. (2024)

Wan, Z., Shi, M., Gong, Y., Lucci, M., Li, J., Zhou, J., Yang, X.-L., Lelli, M., He X., and Mao, J. Multitasking pharmacophores support cabotegravir-based long-acting HIV pre-exposure prophylaxis (PrEP). Molecules 29, 376 (2024)

Mao, J., Jin, X., Shi, M., Heidenreich, D., Brown, L. J., Brown, R. C. D., Lelli, M., He, X., and Glaubitz, C. Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins. Sci. Adv. 10,  eadj0384 (2024)

Sun, X., Zhang, X., and Liu, Z. Generalized nonequilibrium Fermi’s golden rule and its semiclassical approximations for electronic transitions between multiple states. J. Chem. Phys. 160, 034108 (2024)

Zhang, X., Feng, Y., Hua, Y., Zhang, C., Fang, B., Long, X., Pan, Y., Gao, B., Zhang, J. Z. H., Li, L., Ni, H., and Zhang, L. Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylation. Appl. Microbiol. Biotechnol. 108,  84 (2024)

Xiao, J., Chen, Y., Zhang, L.F., Wang, H., and Zhu, T. A machine learning-based high-precision density functional method for drug-like molecules. Artificial Intelligence Chemistry 2, 100037 (2024)

Liang, J. and Yuan, Q. Effects of graphitic- and pyridinic-N co-doping on structure regulation and ORR activity of N-doped graphene. Appl. Surf. Sci. 648, 159025 (2024)