Publications

Zhang, J., Kriebel, C. N., Wan, Z., Shi, M., Glaubitz, C., and He, X. Automated fragmentation quantum mechanical calculation of 15N and 13C chemical shifts in a membrane protein. J. Chem. Theory Comput. 19, 7405–7422 (2023)

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

Zelovich, T., Dekel, D. R., and Tuckerman, M. E. Functional groups in anion exchange membranes: Insights from Ab initio molecular dynamics. J. Membr. Sci. 678, 121638 (2023)

Zhang, H., Saravanan, K. M., and Zhang, J. Z. H. DeepBindGCN: Integrating molecular vector representation with graph convolutional neural networks for protein–ligand interaction prediction. Molecules 28, 4691 (2023)

Bajpai, S., Petkov, B. K., Tong, M., Abreu, C. R. A., Nair, N. N., and Tuckerman, M. E. An interoperable implementation of collective-variable based enhanced sampling methods in extended phase space within the OpenMM package. J. Comput. Chem. 44, 2166-2183 (2023)

Vindel-Zandbergen, P., Kȩdziera, D., Żółtowski, M., Kłos, J., Żuchowski, P., Felker, P. M., Lique, F., and Bačić, Z. H₂O–HCN complex: A new potential energy surface and intermolecular rovibrational states from rigorous quantum calculations. J. Chem. Phys. 159, 174302 (2023)

Zhang, C., Verma, P., Wang, J., Liu, Y., He, X., Wang, Y., Truhlar, D. G., and Liu, Z. Performance of screened-exchange functionals for band gaps and lattice constants of crystals. J. Chem. Theory Comput. 19, 311–323 (2023)

Yan, S., Zhu, Q., Hohl, J., Dong, A., and Schlick, T. Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability. Proc. Natl. Acad. Sci. U.S.A. 120, e2221324120 (2023)

Li, Y., Wang, Y., Zhang, R. M., He, X., and Xu, X. Comprehensive theoretical study on four typical intramolecular hydrogen shift reactions of peroxy radicals: Multireference character, recommended model chemistry, and kinetics. J. Chem. Theory Comput. 19, 3284–3302 (2023)

Xia, S., Chen, E., and Zhang, Y. Integrated molecular modeling and machine learning for drug design. J. Chem. Theory Comput. 19, 7478–7495 (2023)

Yang, Y., Lyu, X., Cong, Y., Miao, T., Fang, B., Zhang, C., Shen, Q., Matthews, M., Fisher, A. J., Zhang, J. Z. H., Zhang, L., and Yang, R. A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction. Int. J. Biol. Macromol. 253, 127093 (2023)

Zhang, H., Saravanan, K. M., Wei, Y., Jiao, Y., Yang, Y., Pan, Y., Wu, X., and Zhang, J. Z. H. Deep learning-based bioactive therapeutic peptide generation and screening. J. Chem. Inf. Model. 63, 835–845 (2023)

Liu, X., Zheng, L., Qin, C., Cong, Y., Zhang, J. Z. H., and Sun, Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: III. Force-field comparison, three-trajectory realization and further dielectric augmentation. Molecules 28, 2767 (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)

Liu, Y., Liu, J., and He, X. Different pKa shifts of internal GLU8 in human β-endorphin amyloid revealing a coupling of internal ionization and stepwise fibril disassembly. J. Phys. Chem. B 127, 1089–1096 (2023)

Zeng, J., Cao, L., & Zhu, T. (2023). Neural network potentials. In Quantum Chemistry in the Age of Machine Learning (pp. 279-294). Elsevier.

Liu, X., Zheng, L., Qin, C., Li, Y., Zhang, J. Z. H., and Sun, Z. Screening power of end-point free-energy calculations in cucurbituril host–guest systems. J. Chem. Inf. Model. 63, 6938–6946 (2023)

Long, Z. and Tuckerman, M. E. Hydroxide diffusion in functionalized cylindrical nanopores as idealized models of anion exchange membrane environments: An ab initio molecular dynamics study. J. Phys. Chem. C 127, 2792–2804 (2023)

Li, M., Cong, Y., Qi, Y., and Zhang, J. Z. H. Binding of berberine derivates to G-quadruplex: insight from a computational study. Phys. Chem. Chem. Phys. 25, 10741-10748 (2023)

Jiang, G., Hu, Z., Bai, L., Zhong, C., Lu, S., Han, B., Sun, Z., Zhu, S., Liang, Y., and Sun, H. Origins of near-infrared-II emission tail and fluorescence enhancement of the albumin-chaperoned cyanine dyes from a multiscale computational study. J. Mater. Chem. C (2023)

Ma, M., Feng, Y., Miao, Y., Shen, Q., Tang, S., Dong, J., Zhang, J. Z. H., and Zhang, L. Revealing the sequence characteristics and molecular mechanisms of ACE inhibitory peptides by comprehensive characterization of 160,000 tetrapeptides. Foods 12, 1573 (2023)

Li, C., Zhang, A., Wang, L., Zuo, J., Zhu, C., Xu, J., Wang, M., and Zhang, J. Z. H. Development of a polynomial scoring function P3-Score for improved scoring and ranking powers. Chem. Phys. Lett. 824, 140547 (2023)

Li, Y., Yang, J., and He, X. Characterizing polyproline II conformational change of collagen superhelix unit on adsorption on gold surface. Nanoscale Adv. 5, 5322-5331 (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)

Zhu, X., Liu, X., Xia, F., and Liu, L. Theoretical study on the copper-catalyzed ortho-selective C-H functionalization of naphthols with α-phenyl-α-diazoesters. Molecules 28, 1767 (2023)

Liu, J. and He, X. Recent advances in quantum fragmentation approaches to complex molecular and condensed-phase systems. WIREs Comput Mol Sci. 13, e1650 (2023)

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

Tuckerman, M. E. The curse of dimensionality loses its power. Nat. Comput. Sci. 2, 6–7 (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)

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)

Metz, M. P., Shahbaz, M., Song, H., Vogt-Maranto, L., Tuckerman, M. E., and Szalewicz, K. Crystal structure predictions for 4-amino-2,3,6-trinitrophenol using a tailor-made first-principles-based force field. Cryst. Growth Des. 22, 1182–1195 (2022)

Zelovich, T., Simari, C., Nicotera, I., Dekel, D. R., and Tuckerman, M. E. The impact of carbonation on hydroxide diffusion in nano-confined anion exchange membranes. J. Mater. Chem. A. 10, 11137-11149 (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)

Xu, M., Felker, P. M., and Bačić, Z. H₂O inside the fullerene C₆₀: Inelastic neutron scattering spectrum from rigorous quantum calculations. J. Chem. Phys. 156, 124101 (2022)

Qu, K., Xu, J., Xue, Y., Guo, J., Gao, Z., Song, Y.-Y., and Mei, Y. Near infrared light-driven photothermal effect on homochiral Au/TiO2 nanotube arrays for enantioselective desorption. Anal. Chem. 94, 588–592 (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)

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)

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)

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)

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

Li, Y., Li, Y., Ning, C., Yue, J., Zhang, C., He, X., … & Liu, Z. Discovering inhibitors of TEAD palmitate binding pocket through virtual screening and molecular dynamics simulation. Comput. Biol. Chem. 98, 107648 (2022)

Yang, C. and Zhang, Y. Delta machine learning to improve scoring-ranking-screening performances of protein–ligand scoring functions. J. Chem. Inf. Model  62, 2696–2712 (2022)

Zheng, L., Yang, Y., Bao, J., He, L., Qi, Y., and Zhang, J. Z. H. Discovery of novel inhibitors of CDK2 using docking and physics- based binding free energy calculation. Chem. Biol. Drug Des. 1– 12 (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)

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)

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)

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)

 Kleimeier, N. F., Liu, Y., Turner, A. M., Young, L. A., Chin, C.-H., Yang, T., He, X., Lo, J., Cheng, B. M., and Kaiser, R. I. Excited state photochemically driven surface formation of benzene from acetylene ices on Pluto and in the outer solar system. Phys. Chem. Chem. Phys. 24, 1424-1436 (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)

Miao, Y., Ni, H., Zhang, X., Zhi, F., Long, X., Yang, X., He, X., and Zhang, L. Investigating mechanism of sweetness intensity differences through dynamic analysis of sweetener–T1R2–membrane systems. Food Chem. 374, 131807 (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, 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)

Hu, A., Zhang, J.-Z., Wang, J., Li, C.-C., Yuan, M., Deng, G., … He, X., … and Song, B.-L. Cholesterylation of Smoothened is a calcium-accelerated autoreaction involving an intramolecular ester intermediate. Cell Res. 32, 288–301 (2022)

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

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)

Zelovich, T., Vogt-Maranto, L., Simari, C., Nicotera, E., Hickner, M. A., Paddison, S. J., Bae, C., Dekel, D. R., and Tuckerman, M. E. Non-monotonic temperature dependence of hydroxide ion diffusion in anion exchange membranes. Chem. Mater. 34, 2133–2145 (2022)

Cao, L., Zeng, J., Wang, B., Zhu, T., and Zhang, J. Z. H. Ab initio neural network MD simulation of thermal decomposition of a high energy material CL-20/TNT. Phys. Chem. Chem. Phys. 24, 11801-11811 (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)

Spittle, S., Poe, D., Doherty, B., Kolodziej, C., Heroux, L., Haque, M. A., … Tuckerman, M., … and Sangoro, J. Evolution of microscopic heterogeneity and dynamics in choline chloride-based deep eutectic solvents. Nat. Commun. 13, 219 (2022)

Yang, L., Feng, J., Wang, J. N., Gao, Z., Xu, J., Mei, Y., and Song, Y. Y. Engineering large-scaled electrochromic semiconductor films as reproductive SERS substrates for operando investigation at the solid/liquid interfaces. Chin. Chem. Lett. (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)

Ding, T., Zha, J., Zhang, D., Zhang, J., Yuan, H., Xia, F, and Gao, G. CO₂ atmosphere enables efficient catalytic hydration of ethylene oxide by ionic liquids/organic bases at low water/epoxide ratios. Green Chem. 23, 3386-3391 (2021)

Zhu, X., Hu, C. T., Erriah, B., Vogt-Maranto, L., Yang, J., Yang, Y., Qiu, M., Fellah, N., Tuckerman, M. E., Ward, M. D., and Kahr, B. Imidacloprid crystal polymorphs for disease vector control and pollinator protection. J. Am. Chem. Soc. 143, 17144–17152 (2021)

Cong, Y., Feng, Y., Ni, H., Zhi, F., Miao, Y., Fang, B., Zhang, L., and Zhang, J. Z. H. Anchor-Locker binding mechanism of the coronavirus spike protein to human ACE2: Insights from computational analysis. J. Chem. Inf. Model. 61, 3529–3542 (2021)

Bao, J., He, X., and Zhang, J. Z. H. DeepBSP—a machine learning method for accurate prediction of protein–ligand docking structures. Chem. Inf. Model. 61, 2231–2240 (2021)

Jia, X., Ge, H., and Mei, Y. Free energy change estimation: The divide and conquer MBAR method. J. Comput. Chem. 42, 1204-1211 (2021)

Dong, G., Hu, Z., Sun, X., and Dong, H. Structural reconstruction of optically invisible state in a single molecule via scanning tunneling microscope. J. Phys. Chem. Lett. 12, 10034–10039 (2021)

Li, M., Lu, W.C., and Zhang, J. Z. H. Ultra-coarse-graining modeling of liquid water. J. Chem. Phys. 154, 224506 (2021)

Shao, G., Bao, J., Pan, X., He, X., Qi, Y., and Zhang, J. Z. Computational analysis of residue-specific binding free energies of androgen receptor to ligands. Front. Biosci. 8, 646524 (2021)

Xia, W., He, L., Bao, J., Qi, Y., and Zhang, J. Z. H. Insights into small molecule inhibitor bindings to PD-L1 with residue-specific binding free energy calculation. J. Biomol. Struct. Dyn. 1-9 (2021)

Lv, Y., Luo, S., Huang, K., Wang, H., Dong, S., Cong, Y., Zhang, J. Z. H., and Duan, L. Investigating effects of bridging water on the binding of neuraminidase−ligands using computational alanine scanning combined with interaction entropy method. J. Mol. Liq. 336, 116214 (2021)

Wang, X, Yan, J., Zhang, H., Xu, Z., and Zhang, J. Z. H. An electrostatic energy-based charge model for molecular dynamics simulation. J. Chem. Phys. 154, 134107 (2021)

Chen, R., Miao, Y., Hao, X., Gao, B., Ma, M., Zhang, J. Z. H., Wang, R., Li, S., He, X., and Zhang, L. Investigation on the characteristics and mechanisms of ACE inhibitory peptides by a thorough analysis of all 8000 tripeptides via binding free energy calculation. Food Sci. Nutr. 9, 2943-2953 (2021)

Zheng, L., Chen, Y., Bao, J., He, L., Dong, S., Qi, Y., and Zhang, J. Z. H. Discovery of novel inhibitors of SARS-CoV-2 main protease. J. Biomol. Struct. Dyn. 1-9 (2021)

Zelovich, T. and Tuckerman, M. E. OH− and H3O+ Diffusion in model AEMs and PEMs at low hydration: Insights from ab initio molecular dynamics. Membranes. 11, 355 (2021)

Yin, Y., Chen, H., and Yuan, Q. Strain-induced bandgap engineering in C₃N nanotubes. Chem. Phys. Lett. 768, 138390 (2021)

Xue, Y., Wang, J.-N., Hu, W., Zheng, J., Li, Y., Pan, X., Mo, Y., Shao, Y., Wang, L., and Mei, Y. Affordable ab initio path integral for thermodynamic properties via molecular dynamics simulations using semiempirical reference potential. J. Phys. Chem. A 125, 10677–10685 (2021)

Schlick, T. and Portillo-Ledesma, S. Biomolecular modeling thrives in the age of technology. Nat. Comput. Sci. 1, 321-331 (2021)

Schlick, T., Zhu, Q., Jain, S., and Yan, S. Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element. Biophys. J. 120, 1040-1053 (2021)

Zhao, X., Luo, S., Huang, K., Xiong, D., Zhang, J. Z. H., and Duan, L. Targeting mechanism for SARS-CoV-2 in silico: interaction and key groups of TMPRSS2 toward four potential drugs. Nanoscale. 13, 19218-19237 (2021)

Huai, Z., Tong, Z., Mei, Y., and Mo, Y. Theoretical study of the spectral differences of the Fenna–Matthews–Olson protein from different species and their mutants. J. Phys. Chem. B. 125, 8313–8324 (2021)

Shi, M., Jin, X., Wan, Z., and He, X. Automated fragmentation quantum mechanical calculation of ¹³C and ¹H chemical shifts in molecular crystals. J. Chem. Phys. 154, 064502 (2021)

Yang, C. and Zhang, Y. Lin_F9: A linear empirical scoring function for protein–ligand docking. J. Chem. Inf. Model. 61, 4630–4644 (2021)

Tinnin, J., Aksu, H., Tong, Z., Zhang, P., Geva, E., Dunietz, B. D., Sun, X., and Cheung, M. S. CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials. J. Chem. Phys. 154, 214108 (2021)

Zeng, J., Weng, J., Zhang, Y., Xia, F., Cui, Q., and Xu, X. Conformational features of Ras: Key hydrogen-bonding interactions of Gln61 in the intermediate state during GTP hydrolysis. J. Phys. Chem. B. 125, 8805–8813 (2021)

Hao, X., Liu, J., Ali, I., Luo, H., Han, Y., Hu, W., Liu, J., He, X. and Li, J. Ab initio determination of crystal stability of di-p-tolyl disulfide. Sci. Rep. 11, 7076 (2021)

Paz, A. S., Baleeva, N. S., and Glover, W. J. Active orbital preservation for multiconfigurational self-consistent field. J. Chem. Phys. 155, 071103 (2021)

Xu, M., Zhu, T., and Zhang, J. Z. H. Automatically constructed neural network potentials for molecular dynamics simulation of zinc proteins. Front. Chem. 9, 692200 (2021)

Liu, J., Yang, J., Zeng, X. C., Xantheas, S. S., Yagi, K., and He, X. Towards complete assignment of the infrared spectrum of the protonated water cluster H+(H₂O)₂₁. Nat. Commun. 12, 6141 (2021)

Li, Z. and Zhang, J. Z. H. Quantitative analysis of ACE2 binding to coronavirus spike proteins: SARS-CoV-2 vs. SARS-CoV and RaTG13. Phys. Chem. Chem. Phys. 23, 13926-13933 (2021)

Gómez-García, P. A., Portillo-Ledesma, S., Neguembor, M. V., Pesaresi, M., Oweis, W., Rohrlich, T., Wieser, S., Meshorer, E., Schlick, T., Cosma, M. P., Lakadamyali, M. Mesoscale modeling and single-nucleosome tracking reveal remodeling of clutch folding and dynamics in stem cell differentiation. Cell Rep. 34, 108614 (2021)

Felker, P. M. and Bačić, Z. Intra- and intermolecular rovibrational states of HCl-H₂O and DCl-H₂O dimers from full-dimensional and fully coupled quantum calculations. Chin. J. Chem. Phys. 34, 6 (2021)

Shen, C., Jin, X., Glover, J. W., and He, X. Accurate prediction of absorption spectral shifts of proteorhodopsin using a fragment-based quantum mechanical method. Molecules. 26, 4486 (2021)

Wang, X., Li, X., He, X., and Zhang, J. Z. H. A fixed multi-site interaction charge model for an accurate prediction of the QM/MM interactions. Phys. Chem. Chem. Phys. 23, 21001-21012 (2021)

Yusufova, N., Kloetgen, A., Teater, M., Osunsade, A., Camarillo, J. M., Chin, C. R., Doane, A. S., Venters, B. J., Portillo-Ledesma, S., Conway, J., Phillip, J. M., Elemento, O., Scott, D. W., Béguelin, W., Licht, J. D., Kelleher, N. L., Staudt, L. M., Skoultchi, A. I., Keogh, M.-C., Apostolou, E., Mason, C. E., Imielinski, M., Schlick, T., David, Y., Tsirigos, A., Allis, C. D., Soshnev, A. A., Cesarman, E., and Melnick, A. M. Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture. Nature. 589, 299-305 (2021)

Duan, L., Dong, S., Huang, K., Cong, Y., Luo, S., and Zhang, J. Z. H. Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/Bcl-2 binding to Bad/Bax. Phys. Chem. Chem. Phys. 23, 2025-2037 (2021)

Swygert, S. G., Lin, D., Portillo-Ledesma, S., Lin, P.-Y., Hunt, D. R., Kao, C.-F., Schlick, T., Noble, W. S., Tsukiyama, T. Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. eLife. 10, e72062 (2021)

Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: A theoretical study. Phys. Chem. Chem. Phys. 23, 12408-12420 (2021)

Sun, Z., Gong, Z., Xia, F., and He, X. Ion dynamics and selectivity of Na_v channels from molecular dynamics simulation. Chem. Phys. 548, 111245 (2021)

Dai, D., Wang, X., Liu, Y., Yang, X.-L., Glaubitz, C., Denysenkov, V., He, X., Prisner, T., and Mao, J. Room-temperature dynamic nuclear polarization enhanced NMR spectroscopy of small biological molecules in water. Nat. Commun. 12, 6880 (2021)

Felker, P. M., Liu, Y., Li, J., and Bačić, Z. DCl–H₂O, HCl–D₂O, and DCl–D₂O dimers: Inter- and intramolecular vibrational states and frequency shifts from fully coupled quantum calculations on a full-dimensional neural network potential energy surface. J. Phys. Chem. A. 125, 6437–6449 (2021)

Zelovich, T., Winey, K. I., and Tuckerman, M. E. Hydronium ion diffusion in model proton exchange membranes at low hydration: Insights from ab initio molecular dynamics. J. Mater. Chem. A. 9, 2448-2458 (2021)

Rogal, J., & Tuckerman, M. E. (2021). Pathways in Classification Space: Machine Learning as a Route to Predicting Kinetics of Structural Transitions in Atomic Crystals. In Multiscale Dynamics Simulations (pp. 312-348).

Abreu, C. R. A. and Tuckerman, M. E. Hamiltonian based resonance-free approach for enabling very large time steps in multiple time-scale molecular dynamics. Mol. Phys. e1923848 (2021)

Abreu, C. R. A. and Tuckerman, M. E. Multiple timescale molecular dynamics with very large time steps: avoidance of resonances. Eur. Phys. J. B. 94, 231 (2021)

Wen, W., Huang, D., Bao, J., Zhang, J. Z. H. Residue-specific binding mechanisms of PD-L1 to its monoclonal antibodies by computational alanine scanning. Phys. Chem. Chem. Phys. 23, 15591-15600 (2021)

Hong, R. S., Chan, E. J., Vogt-Maranto, L., Mattei, A., Sheikh, A. Y., and Tuckerman, M. E. Insights into the polymorphic structures and enantiotropic layer-slip transition in paracetamol form III from enhanced molecular dynamics. Cryst. Growth Des. 21, 886-896 (2021)

Li, N., Gao, Y., Qiu, F., and Zhu, T. Benchmark force fields for the molecular dynamic simulation of G-quadruplexes. Molecules. 26, 5379 (2021)

Zhang, B., Ma, Y., Jin, X., Wang, Y., Suo, B., He, X., and Jin, Z. GridMol2. 0: Implementation and application of linear‐scale quantum mechanics methods and molecular visualization. Int. J. Quantum Chem. 120, e26402 (2020)

Zha, J., Zhang, Y., Xia, K., Gräter, F., and Fei Xia. Coarse-grained simulation of mechanical properties of single microtubules with micrometer length. Front. Biosci. 7, 632122 (2020)

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