Publications

201.

Shen,  Z. and Glover, W. J. Flexible boundary layer using exchange for embedding theories. I. Theory and implementationJ. Chem. Phys. 155, 224112 (2021) 

202.

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 cellseLife. 10, e72062 (2021)

203.

Brian, D. and Sun, X. Charge-transfer landscape manifesting the structure–rate relationship in the condensed phase via machine learningJ. Phys. Chem. B. 125, 13267–13278 (2021)

204.

Hu, Z., Brian, D., and Sun, X. Multi-state harmonic models with globally shared bath for nonadiabatic dynamics in the condensed phase. J. Chem. Phys. 155, 124105 (2021)

205.

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 drugsNanoscale. 13, 19218-19237 (2021)

206.

Li, M., Lu, W.C., and Zhang, J. Z.H. Introducing the effective polarizable bond (EPB) model in DNA simulationsChem. Phys. Lett. 785, 139160 (2021)

207.

Brian, D. and Sun, X. Generalized quantum master equation: A tutorial review and recent advances. Chin. J. Chem. Phys. 34, 497 (2021)

208.

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

209.

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)

210.

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

211.

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 waterNat. Commun. 12, 6880 (2021)

212.

Xu, M., Zhu, T., and Zhang, J. Z. H. Automated construction of neural network potential energy surface: The enhanced self-organizing incremental neural network deep potential method. J. Chem. Inf. Model. 61, 5425–5437 (2021)

213.

 Li, M., Cong, Y., Qi, Y., and Zhang, J. Z. H. Computational insights into the binding mechanism of OxyS sRNA with chaperone protein HfqBiomolecules. 11, 1653 (2021)

214.

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

215.

Pan, X., Yang, J., Van, R., Epifanovsky, E., Ho, J., Huang, J., Pu, J., Mei, Y., Nam, K., and Shao, Y. Machine-learning-assisted free energy simulation of solution-phase and enzyme reactionsJ. Chem. Theory Comput. 17, 5745–5758 (2021)

216.

Atsango, A. O., Tuckerman, M. E., and Markland, T. E. Characterizing and contrasting structural proton transport mechanisms in azole hydrogen bond networks using ab initio molecular dynamicsJ. Phys. Chem. Lett. 12, 8749–8756 (2021)

217.

Chan, E. J., Shtukenberg, A. G., Tuckerman, M. E., and Kahr, B. Crystal structure prediction as a tool for identifying components of disordered structures from powder diffraction: A case study of benzamide IICryst. Growth Des. 21, 5544–5557 (2021)

218.

Hu, Z., Sun, Z., and Sun, H. Simulation of negative ion photoelectron spectroscopy using a nuclear ensemble approach: Implications from a nuclear vibration effectJ. Phys. Chem. A. 125, 6621–6628 (2021)

219.

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

220.

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).

221.

Zhao, Y., Miao, Y., Zhi, F., Pan, Y., Zhang, J., Yang, X., Zhang, J. Z. H., and Zhang, L. Rational design of pepsin for enhanced thermostability via exploiting the guide of structural weakness on stabilityFront. Phys. 9, 755253 (2021)

222.

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 interactionsPhys. Chem. Chem. Phys. 23, 21001-21012 (2021)

223.

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

224.

Li, Z. and Zhang, J. Z. H. Quantitative analysis of ACE2 binding to coronavirus spike proteins: SARS-CoV-2 vs. SARS-CoV and RaTG13Phys. Chem. Chem. Phys. 23, 13926-13933 (2021)

225.

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 hydrolysisJ. Phys. Chem. B. 125, 8805–8813 (2021)

226.

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 mutantsJ. Phys. Chem. B. 125, 8313–8324 (2021)

227.

Pan, X., Wang, H., Li, C., Zhang, J. Z. H., and Ji, C. MolGpka: A web server for small molecule pKa prediction using a graph-convolutional neural networkJ. Chem. Inf. Model. 61, 3159–3165 (2021)

228.

Kaplan, M., Wang, Y., Chreifi, G., Zhang, L., Chang, Y.-W., and Jensen, G. J. Programmed flagellar ejection in caulobacter crescentus leaves PL-subcomplexesJ. Mol. Biol. 433, 1670042 (2021)

229.

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

230.

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 analysisJ. Chem. Inf. Model. 61, 3529–3542 (2021)

231.

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

232.

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 surfaceJ. Phys. Chem. A. 125, 6437–6449 (2021)

233.

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 materialsJ. Chem. Phys. 154, 214108 (2021)

234.

Zhao, X., Zhang, P., Li, Y., Wu, S., Li, F., Wang, Y., Liang, S., He, X., Zeng, Y., and Liu, Z. Glucose–lipopeptide conjugates reveal the role of glucose modification position in complexation and the potential of malignant melanoma therapy. J. Med. Chem. 64, 11483–11495 (2021)

235.

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)

236.

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)

237.

Shan, J., Pan, X., Wang, X., Xiao, X., and Ji, C. FragRep: A web server for structure-based drug design by fragment replacement. J. Chem. Inf. Model. 60, 5900–5906 (2020)

238.

Felker, P. M. and Bačić, Z. HDO−CO complex: D‑bonded and H‑bonded isomers and intra- and intermolecular rovibrational states from full-dimensional and fully coupled quantum calculationsJ. Phys. Chem. A. 125, 980−989 (2021)

239.

Cendagorta, J. R., Shen, H., Bačić, Z., and Tuckerman, M. E. Enhanced sampling path integral methods using neural network potential energy surfaces with application to diffusion in hydrogen hydratesAdv. Theory Simul. 4, 2000258 (2020)

240.

Bao, J., He, X., and Zhang, J. Z. H. Development of a new scoring function for virtual screening: APBScoreJ. Chem. Inf. Model. 60, 6355–6365 (2020)

241.

Shan, J. and Ji, C. MolOpt: A web server for drug design using bioisosteric transformationCurr. Comput. Aided Drug Des. 16, 460 - 466 (2020)

242.

Zhang, Y., Cao, Z., Zhang, J. Z. H., and Xia, F. Double-well ultra-coarse-grained model to describe protein conformational transitions. J. Chem. Theory Comput. 16, 6678–6689 (2020)

243.

Du, J., Li, W., Liu, B., Zhang, Y., Yu, J., Hou, X., and Fang, H. An in silico mechanistic insight into HDAC8 activation facilitates the discovery of new small-molecule activators.  Bioorg. Med. Chem. 28, 115607 (2020)

244.

Chin, C.-H., Zhu, T., and Zhang, J. Z. H. Reaction mechanism and product branching ratios of OH+C2H3F reaction: A theoretical study. Chin. J. Chem. Phys. 33, 203 (2020)

245.

Li, M., Lu, W.C., and Zhang, J. Z. H. A three-point coarse-grained model of five-water cluster with permanent dipoles and quadrupoles. Phys. Chem. Chem. Phys. 22, 26289-26298 (2020)

246.

Zeng, J., Cao, L., Xu, M., Zhu, T., and Zhang. J. Z. H. Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation. Nat. Commun. 11, 5713 (2020)

247.

Burnham, C. J., Futera, Z., Bačić, Z., and English, N. J. Hydrogen intramolecular stretch redshift in the electrostatic environment of type II clathrate hydrates from Schrödinger equation treatment. Appl. Sci. 10, 8504 (2020)

248.

Hu, Z., Tong, Z., Cheung, M. S., Dunietz, B. D., Geva, E., and Sun, X. Photoinduced charge transfer dynamics in the carotenoid–porphyrin–C60 triad via the linearized semiclassical nonequilibrium Fermi’s golden rule. J. Phys. Chem. B. 124, 9579–9591 (2020)

249.

Hu, W., Li, P., Wang, J.-N., Xue, Y., Mo, Y., Zheng, J., Pan, X., Shao, Y., Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semiempirical reference potential. 3. Gaussian smoothing on density-of-states. J. Chem. Theory Comput. 16, 6814–6822 (2020)

250.

Han, J., Zhang, P., Aksu, H., Maiti, B., Sun, X., Geva, E., Dunietz, B. D., and Cheung, M. S. On the interplay between electronic structure and polarizable force fields when calculating solution-phase charge-transfer rates. J. Chem. Theory Comput. 16, 6481–6490 (2020)

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