Publications

Portillo-Ledesma, S., Li, Z., and Schlick, T. Genome modeling: From chromatin fibers to genes. Curr. Opin. Struct. Biol. 78, 102506 (2023)

Yao, S., Van, R., Pan, X., Park, J. H., Mao, Y., Pu, J., Mei, Y., and Shao, Y. Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations. RSC Adv. 13, 4565-4577 (2023)

Xia, S., Zhang, D., and Zhang, Y. Multitask deep ensemble prediction of molecular energetics in solution: From quantum mechanics to experimental properties. J. Chem. Theory Comput. 19, 659–668 (2023)

Li, Z. and Schlick, T. Hi-BDiSCO: Folding 3D mesoscale genome structures from Hi-C data using brownian dynamics. Nucleic Acids Res. gkad1121 (2023)

Pan, X., Snyder, R., Wang, J.-N., Lander, C., Wickizer, C., Van, R., Chesney, A., Xue, Y., Mao, Y., Mei, Y., Pu, J., and Shao, Y. Training machine learning potentials for reactive systems: A Colab tutorial on basic models.  J. Comput. Chem. (2023)

Zhao, C., Yang, G., Zhang, S., He, X., Zhong, Y., and Gao, X. Enhanced breathing effect of nanoporous UIO-66-DABA metal–organic frameworks with coordination defects for high selectivity and rapid adsorption of Hg(II). ACS Appl. Nano Mater. 6, 18372–18380 (2023)

Yue, J., Li, Y., Li, F., Zhang, P., Li, Y., Xu, J., Zhang, Q., Zhang, C., He, X., Wang, Y., and Liu, Z. Discovery of Mcl-1 inhibitors through virtual screening, molecular dynamics simulations and in vitro experiments. Comput. Biol. Med. 152, 106350 (2023)

Xiong, L., He, X., and Yang, J. Origin of humidity influencing the excited state electronic properties of silicon quantum dot based light-emitting diodes. Phys. Chem. Chem. Phys. 24, 28222-28231 (2022)

Jiang, Y., Cai, Z., Yuan, Q., Cao, W., Hu, Z., Sun, H., Wang, X.-B., and Sun, Z. Highly structured water networks in microhydrated dodecaborate clusters. J. Phys. Chem. Lett. 13, 11787–11794 (2022)

Zelovich, T., Hensen, T., and Tuckerman, M. E. A Green’s function approach for determining surface induced broadening and shifting of molecular energy levels. Nano Lett. 22, 9854–9860 (2022)

Guo, X.-K. and Zhang, Y. CovBinderInPDB: A structure-based covalent binder database. J. Chem. Inf. Model. 62, 6057–6068 (2022)

Felker, P. M. and Bačić, Z. Intermolecular vibrational states of HF trimer from rigorous nine-dimensional quantum calculations: Strong coupling between intermolecular bending and stretching vibrations and the importance of the three-body interactions. J. Chem. Phys. 157, 194103 (2022)

Liu, Z., Xu, W., Tuckerman, M. E., and Sun, X. Imaginary-time open-chain path-integral approach for two-state time correlation functions and applications in charge transfer. J. Chem. Phys. 157, 114111 (2022)

Hu, Z., Liu, Z., and Sun, X. Effects of heterogeneous protein environment on excitation energy transfer dynamics in the Fenna–Matthews–Olson complex. J. Phys. Chem. B 126, 9271–9287 (2022)

Shakiba, M., Smith, B., Li, W., Dutra, M., Jain, A., Sun, X., Garashchuk, S., and Akimov, A. Libra: A modular software library for quantum nonadiabatic dynamics. Software Impacts 14, 100445 (2022)

Bai, Y., Vogt-Maranto, L., Tuckerman, M. E., and Glover, W. J. Machine learning the Hohenberg-Kohn map for molecular excited states. Nat. Commun. 13, 7044 (2022)

Liu, X., Zheng, L., Qin, C., Zhang, J. Z. H., and Sun, Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedure. J. Comput. Aided Mol. Des. 36, 735–752 (2022)

Liu, X., Zheng, L., Cong, Y., Gong, Z., Yin, Z., Zhang, J. Z. H., Liu, Z., and Sun, Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant. J. Comput. Aided Mol. Des. 36, 879–894 (2022).

Liu, X., Humeniuk, A., and Glover, W. J. Conical intersections in solution with polarizable embedding: Integral-exact direct reaction field. J. Chem. Theory Comput. 18, 6826–6839 (2022)

Cao, W., Hu, Z., Peng, X., Sun, H., Sun, Z., and Wang, X.-B. Annihilating actinic photochemistry of the pyruvate anion by one and two water molecules. J. Am. Chem. Soc. 144, 19317–19325 (2022)

Portillo-Ledesma, S., Wagley, M., and Schlick, T. Chromatin transitions triggered by LH density as epigenetic regulators of the genome. Nucleic Acids Res. 50, 10328–10342 (2022)

Luo, F., Zhao, J., Liu, S., Xue, Y., Tang, D., Yang, J., Mei, Y., ... and Xie, Y. Ursolic acid augments the chemosensitivity of drug-resistant breast cancer cells to doxorubicin by AMPK-mediated mitochondrial dysfunction. Biochem. Pharmacol. 205, 115278 (2022)

Felker, P. M. and Bačić, Z. Noncovalently bound molecular complexes beyond diatom–diatom systems: full-dimensional, fully coupled quantum calculations of rovibrational states. Phys. Chem. Chem. Phys. 24, 24655-24676 (2022)

Hong, R. S., Mattei, A., Sheikh, A. Y., and Tuckerman, M. E. A data-driven and topological mapping approach for the a priori prediction of stable molecular crystalline hydrates. Proc. Natl. Acad. Sci. U.S.A. 119, e2204414119 (2022)

Li, X., Jia, X., Paz, A. S. P., Cao, Y., and Glover, W. J. Evidence for water antibonding orbital mixing in the hydrated electron from its oxygen 1s X-ray absorption spectrum. J. Am. Chem. Soc. 144, 19668–19672 (2022)

Hu, Z. and Sun, X. All-atom nonadiabatic semiclassical mapping dynamics for photoinduced charge transfer of organic photovoltaic molecules in explicit solvents. J. Chem. Theory Comput. 18, 5819–5836 (2022)

Zhang, F., Wei, M., Chen, H., Ji, L., Nie, Y., and Kang, J. The genomic stability regulator PTIP is required for proper chromosome segregation in mitosis. Cell Div. 17, 5 (2022)

Xiong, D., Zhao, X., Luo, S., Zhang, J. Z. H., and Duan, L. Molecular mechanism of the non-covalent orally targeted SARS-CoV-2 Mpro inhibitor S-217622 and computational assessment of its effectiveness against nainstream variants. J. Phys. Chem. Lett. 13, 38, 8893–8901 (2022)

Zhang, Y., Wang, Y., Xia, F., Cao, Z., and Xu, X. Accurate and efficient estimation of Lennard–Jones interactions for coarse-grained particles via a potential matching method. J. Chem. Theory Comput. 18, 4879–4890 (2022)

Liu, L., Luo, C., Zhang, J., He, X., Shen, Y., Yan, B., ... and Jiang, L. Synergistic effect of bio‐inspired nanochannels: Hydrophilic DNA probes at inner wall and hydrophobic coating at outer surface for highly sensitive detection. Small 18, 2201925 (2022)

Zhao, Y., Miao, Y., Cong, Y., Wang, J., Zhi, F., Pan, Y., ... Zhang, J. Z. H. and Zhang, L. High-level expression and improved pepsin activity by enhancing the conserved domain stability based on a scissor-like model. LWT 167, 113877 (2022)

Liu, D., Zhao, W., and Yuan, Q. Breaking the linear relation in the dissociation of nitrogen on iron surfaces. ChemPhysChem 23, e202200147 (2022)

Yin, Y., Ding, F., and Yuan, Q. Stabilization of black phosphorene by edge-selective adsorption of C₆₀ molecules. J. Phys. Chem. C 126, 6874–6879 (2022)

Liang, J., Chen, Y., Bu, S., Song, S., Yang, J., Wang, M., and Yuan, Q. Computational study of the C₂P₄ monolayer as a stable two-dimensional material with high carrier mobility: Implications for nanoelectronic devices. ACS Appl. Nano Mater. 5, 6972–6979 (2022)

Pan, Y., Bao, J., Zhang, X., Ni, H., Zhao, Y., Zhi, F., Fang, B., He, X., Zhang, J. Z. H., and Zhang, L. Rational design of P450 aMOx for improving anti-Markovnikov selectivity based on the “butterfly” model. Front. Mol. Biosci. 9, 888721 (2022)

Chen, Y. and Yuan, Q. Carbon induced segregation of Ni atoms in Cu-Ni alloy. Chem. Phys. Lett. 806, 139979 (2022)

Humeniuk, A. and Glover, W. J. Efficient CPU and GPU implementations of multicenter integrals over long-range operators using Cartesian Gaussian functions. Comput. Phys. Commun. 280, 108467 (2022)

Wang, B., Mao, J., Wei, M., Qi, Y., and Zhang, J. Z. H. SeBPPI: A sequence-based protein-protein binding predictor. J. Comput. Biophys. Chem. 21, 729-737 (2022)

Yan, S., Zhu, Q., Jain, S., and Schlick, T. Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression. Nat. Commun. 13, 4284 (2022)

Li, T., Yu, L., Sun, J., Liu, J., and He, X. Ionization of D571 is coupled with SARS-CoV-2 spike up/down equilibrium revealing the pH-dependent allosteric mechanism of receptor-binding domains. J. Phys. Chem. B 126, 4828–4839 (2022)

Zhu, Q., Petingi, L., and Schlick, T. RNA-as-graphs motif atlas—dual graph library of RNA modules and viral frameshifting-element applications. Int. J. Mol. Sci. 23, 9249 (2022)

Ren, L., Jing, Z., Xia, F., Zhang, J. Z., and Li, Y. Toxic effect of fullerene and its derivatives upon the transmembrane β2-adrenergic receptors. Molecules 27, 4562 (2022)

Yang, C., Chen, E. A., and Zhang, Y. Protein–ligand docking in the machine-learning era. Molecules 27, 4568 (2022)

Gu, S., Chin, C.-H., Zhu, T., and Zhang, Z. H. Theoretical investigations on photodissociation dynamics of deuterated alkyl halides CD₃CH₂F. Chin. J. Chem. Phys. 35, 431 (2022)

Zhang, C., Miao, Y., Feng, Y., Wang, J., Tian, Z., Dong, J., ... and Zhang, L. Umami polypeptide detection system targeting the human T1R1 receptor and its taste-presenting mechanism. Biomaterials 287, 121660 (2022)

Chen, S., Ding, X., Sun, C. Wang, F., He, X., Watts, A., and Zhao X. Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake. Int. J. Mol. Sci. 23, 6913 (2022)

Zhang, H., Saravanan, K. M., Yang, Y., Wei, Y., Yi, P., and Zhang, J. Z. H. Generating and screening de novo compounds against given targets using ultrafast deep learning models as core components. Brief. Bioinform. 23, bbac226 (2022)

Xiong, D., Zhao, X., Luo, S., Cong, Y., Zhang, J. Z. H., and Duan, L. Immune escape mechanisms of SARS-CoV-2 delta and omicron variants against two monoclonal antibodies that received emergency use authorization. J. Phys. Chem. Lett. 13, 6064–6073 (2022)

Wang, H., Pan, X., Zhang, Y., Wang, X., Xiao, X., and Ji, C. MolHyb: A web server for structure-based drug design by molecular hybridization. J. Chem. Inf. Model. 62, 2916–2922 (2022)

Liu, J., Lan, J., and He, X. Toward high-level machine learning potential for water based on quantum fragmentation and neural networks. J. Phys. Chem. A (2022)