Publications

Sun, X. Hybrid equilibrium-nonequilibrium molecular dynamics approach for two-dimensional solute-pump/solvent-probe spectroscopy. J. Chem. Phys. 151, 194507 (2019)

Shao, Y., Mei, Y., Sundholm, D., and Kaila, V. R. I. Benchmarking the performance of time-dependent density functional theory methods on biochromophores. J. Chem. Theory Comput. 16, 587-600 (2019)

Wu, Z., Zhang, Y., Zhang, J. Z., Xia, K., and Xia, F. Determining optimal coarse-grained representation for biomolecules using internal cluster validation indexes. J. Comput. Chem. 41, 14-20 (2019)

Portillo-Ledesma, S. and Schlick, T. Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling. WIREs Comput. Mol. Sci. e1434 (2019)

Chen, J., Yin, B., Pang, L., Wang, W., Zhang, J. Z. H., and Zhu, T. Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies. J. Biomol. Struct. Dyn. 1-15 (2019)

Lu, J., Hou, X., Wang, C., and Zhang Y. Incorporating explicit water molecules and ligand conformation stability in machine-learning scoring functions. J. Chem. Inf. Model. 59, 4540-4549 (2019)

Chen, J., Pang, L., Wang, W., Wang, L., Zhang, J. Z. H., and Zhu, T. Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations. J. Biomol. Struct. Dyn. 1-15 (2019)

Li, K., Hou, X., Li, R., Bi, W., Yang, F., Chen, X., Xiao, P., Liu, T., Lu, T., Zhou, Y., Tian, Z., Shen, Y., Zhang, Y., Wang, J., Fang, H., Sun, J., and Yu, X. Identification and structure-function analyses of an allosteric inhibitor of the tyrosine phosphatase PTPN22. J. Biol. Chem. 294, 8653-8663 (2019)

Lu, J., Wang, C., and Zhang, Y. Predicting molecular energy using force-field optimized geometries and atomic vector representations learned from an improved deep tensor neural network. J. Chem. Theory Comput. 15, 4113-4121 (2019)

He, L., Bao, J., Yang, Y., Dong, S., Zhang, L., Qi, Y., and Zhang, J. Z. H. Study of SHMT2 inhibitors and their binding mechanism by computational alanine scanning. J. Chem. Inf. Model. 59, 3871-3878 (2019)

Zhang, L., Mei, D., Wu, Y., Shen, C., Hu, W., Zhang, L., Li, J., Wu, Y., and He, X. Syntheses, structures, optical properties, and electronic structures of Ba₆Cu₂GSn₄S₁₆ (G= Fe, Ni) and Sr₆D₂FeSn₄S₁₆ (D= Cu, Ag). J. Solid State Chem. 272, 69-77 (2019)

Zhang, Y., Xia, K., Cao, Z., Gräter, F., and Xia, F. A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data. Phys. Chem. Chem. Phys. 21, 9720-9727 (2019)

Zhang, Z., Liu, X., Yan, K., Tuckerman, M. E., and Liu, J. Unified efficient thermostat scheme for the canonical ensemble with holonomic or isokinetic constraints via molecular dynamics. J. Phys. Chem. A. 123, 6056-6079 (2019)

Shtukenberg, A. G., Tan, M., Vogt-Maranto, L., Chan, E. J., Xu, W., Yang, J., Tuckerman, M. E., Hu, C. T., and Kahr, B. Melt crystallization for paracetamol polymorphism. Cryst. Growth Des. 19, 4070-4080 (2019)

Zelovich, T., Vogt-Maranto, L., Hickner, M. A., Paddison, S. J., Bae, C., Dekel, D. R., and Tuckerman, M. E. Hydroxide ion diffusion in anion-exchange membranes at low hydration: Insights from ab initio molecular dynamics. Chem. Mater. 31, 5778-5787 (2019)

Tuckerman, M. E. Machine learning transforms how microstates are sampled. Science. 365, 982-983 (2019)

Luo, H., Hao, X., Gong, Y., Zhou, J., He, X., and Li, J. Rational crystal polymorph design of olanzapine. Cryst. Growth Des. 19, 2388-2395 (2019)

Verma, P., Wang, Y., Ghosh, S., He, X., and Truhlar, D. G. Revised M11 exchange-correlation functional for electronic excitation energies and ground-state properties. J. Phys. Chem. A. 123, 2966-2990 (2019)

Lu, Q., He, X., Hu, W., Chen, X., and Liu, J. Stability, vibrations, and diffusion of hydrogen gas in clathrate hydrates: Insights from ab initio calculations on condensed-phase crystalline structures. J. Phys. Chem. C. 123, 12052-12061 (2019)

Liu, J., Sun, H., Glover, W. J., and He, X. Prediction of excited-state properties of oligoacene crystals using fragment-based quantum mechanical method. J. Phys. Chem. A. 123, 5407-5417 (2019)

Verma, P., Janesko, B. G., Wang, Y., He, X., Scalmani, G., Frisch, M. J., and Truhlar, D. G. M11plus: A range-separated hybrid meta functional with both local and rung-3.5 correlation terms and high across-the-board accuracy for chemical applications. J. Chem. Theory Comput. 15, 4804-4815 (2019)

Han, Y., Liu, J., Huang, L., He, X., and Li, J. Predicting the phase diagram of solid carbon dioxide at high pressure from first principles. npj Quantum Materials. 4, 10 (2019)

Wang, M., Mei, Y., and Ryde, U. Host-guest relative binding affinities at density-functional theory level from semiempirical molecular dynamics simulations. J. Chem. Theory Comput. 15, 2659-2671 (2019)

Li, P., Liu, F., Shao, Y., and Mei, Y. Computational insights into endo/exo selectivity of the Diels-Alder reaction in explicit solvent at ab initio quantum mechanical/molecular mechanical level. J. Phys. Chem. B. 123, 5131-5138 (2019)

Xiao, Z., Cong, Y., Huang, K., Zhong, S., Zhang, J. Z. H., and Duan, L. Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy. Phys. Chem. Chem. Phys. 21, 20951-20964 (2019)

Sun, Z., Wang, X., Zhang, J. Z. H., and He, Q. Sulfur-substitution-induced base flipping in the DNA duplex. Phys. Chem. Chem. Phys. 21, 14923-14940 (2019)

Cao, H., Wang, J., He, L., Qi, Y., and Zhang, J. Z. H. DeepDDG: Predicting the stability change of protein point mutations using neural networks. J. Chem. Inf. Model. 59, 1508-1514 (2019)

Chen, J., Wang, X., Pang, L., Zhang, J. Z. H., and Zhu, T. Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations. Nucleic Acids Res. 47, 6618-6631 (2019)

Xu, M., Zhu, T., and Zhang, J. Z. H. Molecular dynamics simulation of zinc ion in water with an ab initio based neural network potential. J. Phys. Chem. A. 123, 6587-6595 (2019)

Duan, L., Guo, X., Cong, Y., Feng, G., Li, Y., and Zhang, J. Z. H. Accelerated molecular dynamics simulation for helical proteins folding in explicit water. Front Chem. 7, 540 (2019)

Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., and Hou, T. End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chem. Rev. 119, 9478-9508 (2019)

Duan, G., Ji, C., and Zhang, J. Z. H. A force consistent method for electrostatic energy calculation in fluctuating charge model. J. Chem. Phys. 151, 094105 (2019)

Chen, J., Gao, H., Ding, T., Ji, L., Zhang, J. Z. H., Gao, G., and Xia, F. Mechanistic studies of CO2 cycloaddition reaction catalyzed by amine-functionalized ionic liquids. Front Chem. 7, 615 (2019)

Liu, X., Zhao, Y., and Zhang, J. Z. H. Molecular mechanism of ligand bindings to Zika virus at SAM site. Chem. Phys. Lett. 735, 136771 (2019)

Felker, P. M., Lauvergnat, D., Scribano, Y., Benoit, D. M., and Bačić, Z. Intramolecular stretching vibrational states and frequency shifts of (H₂)₂ confined inside the large cage of clathrate hydrate from an eight-dimensional quantum treatment using small basis sets. The Journal of Chemical Physics, 151, 124311 (2019)

Mulvihill, E., Schubert, A., Sun, X., Dunietz, B. D., and Geva, E. A modified approach for simulating electronically nonadiabatic dynamics via the generalized quantum master equation. J. Chem. Phys. 150, 034101 (2019)

Wang, T., Su, X., Zhang, X., Huang, W., Huang, L., Zhang, X., Sun, X., Luo, Y., and Zhang, G. A combinatory approach towards the design of organic polymer luminescent materials. J. Mater. Chem. C. 7, 9917-9925 (2019)

Xu, M., Felker, P. M., Mamone, S., Horsewill, A. J., Rols, S., Whitby, R. J., and Bačić, Z. The endofullerene HF@C₆₀: Inelastic neutron scattering spectra from quantum simulations and experiment, validity of the selection rule, and symmetry breaking. J. Phys. Chem. Lett. 10, 5365−5371 (2019)

L. Petingi and T. Schlick, "Graph-Theoretic Partitioning of RNAs and Classification of Pseudoknots'', In: I. Holmes, C. Martín-Vide, M. Vega-Rodríguez, Editors, Algorithms for Computational Biology (AlCoB 2019), Lec. Notes in Comp. Sci. (LNCS) 11488: 68-79 (2019) 

Jain, S., Saju, S., Petingi, L., and Schlick, T. An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures. Methods. 162-163, 74-84 (2019)

Jung, J., Nishima, W., Daniels, M., Bascom, G., Kobayashi, C., Adedoyin, A., Wall. M., Lappala, A., Phillips, D., Fischer, W., Tung, C.-S., Schlick, T., Sugita, Y., and Sanbonmatsu,  K. Y. Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations. J. Comp. Chem. 40, 1919-1930 (2019)

Felker, P. M. and  Bačić, Z. Weakly bound molecular dimers: Intramolecular vibrational fundamentals, overtones, and tunneling splittings from full-dimensional quantum calculations using compact contracted bases of intramolecular and low-energy rigid-monomer intermolecular eigenstates. J. Chem. Phys. 151, 024305 (2019)

Zelovich, T., Long, Z., Hickner, M., Paddison, S. J., Bae, C., and Tuckerman, M. E. Ab initio molecular dynamics study of hydroxide diffusion mechanisms in nanoconfined structural mimics of anion exchange membranes. J. Phys. Chem. C. 123, 4638-4653 (2019)

Jeon, J. Y., Park, S. Han, J., Maurya, S., Mohanty, A. D. Tian, D. Saikia, N., Hickner, M. A., Ryu, C. Y., Tuckerman, M. E., Paddison, S. J., Kim, Y. S., and Bae, C. Synthesis of aromatic anion exchange membranes by Friedel–Crafts bromoalkylation and cross-linking of polystyrene block copolymers. Macromolecules. 52, 2139-2147 (2019)

Albaugh, A., Tuckerman, M. E., and Head-Gordon, T. Combining iteration-free polarization with large time step stochastic-isokinetic integration. J. Chem. Theory Comput. 15, 2195-2205 (2019)

Liu, W., Dai, X., Jih, J., Chan, K., Trang, P., Yu, X., Balogun, R., Mei, Y., Liu, F., Zhou, Z. H. Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development. PLOS Pathog. 15, e1007615 (2019)

Tong, Z., Huai, Z., Mei, Y., and Mo, Y. Influence of the protein environment on the electronic excitation of chromophores in the phycoerythrin 545 light-harvesting complex: A combined MD-QM/MM method with polarized protein-specific charge scheme. J. Phys. Chem. B. 123, 2040-2049 (2019)

Liu, W., Li, P., and Mei, Y. Discovery of SBF1 as an allosteric inhibitor targeting the PIF-pocket of 3-phosphoinositide-dependent protein kinase-1. J. Mol. Model. 25, 187 (2019)

Perišić, O., Portillo-Ledesma, S, and Schlick, T. Sensitive effect of linker histone binding mode and subtype on chromatin condensation. Nucleic Acids Res. 47, 4948-4957 (2019)

Zhao, P., Cao, H., Chen, Y., and Zhu, T. Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations. Chem. Phys. Lett. 728, 94-101 (2019)