Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation von Snyder, Ryan, Kim, Bryant, Pan, Xiaoliang, Shao, Yihan, Pu, Jingzhi

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Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations von Zhou, Yan, Pu, Jingzhi

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Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations von Ojeda-May, Pedro, Pu, Jingzhi

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Photoinduced Site-Selective Functionalization of Aliphatic C–H Bonds by Pyridine N‑oxide Based HAT Catalysts von Wang, Ban, Ascenzi Pettenuzzo, Cristina, Singh, Jujhar, Mccabe, Gavin E., Clark, Logan, Young, Ryan, Pu, Jingzhi, Deng, Yongming

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Trapping the ATP binding state leads to a detailed understanding of the F₁-ATPase mechanism von Nam, Kwangho, Pu, Jingzhi, Karplus, Martin

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Assessing the accuracy of the isotropic periodic sum method through Madelung energy computation von Ojeda-May, Pedro, Pu, Jingzhi

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Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical Calculations von Ojeda-May, Pedro, Pu, Jingzhi

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Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force von Kim, Bryant, Snyder, Ryan, Nagaraju, Mulpuri, Zhou, Yan, Ojeda-May, Pedro, Keeton, Seth, Hege, Mellisa, Shao, Yihan, Pu, Jingzhi

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H-loop histidine catalyzes ATP hydrolysis in the E. coli ABC-transporter HlyB von YAN ZHOU, OJEDA-MAY, Pedro, JINGZHI PU

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Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method von Zhou, Yan, Ojeda-May, Pedro, Nagaraju, Mulpuri, Kim, Bryant, Pu, Jingzhi

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Tests of second-generation and third-generation density functionals for thermochemical kinetics von YAN ZHAO, JINGZHI PU, LYNCH, Benjamin J, TRUHLAR, Donald G

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Mechanisms and Free Energies of Enzymatic Reactions von Gao, Jiali, Ma, Shuhua, Major, Dan T, Nam, Kwangho, Pu, Jingzhi, Truhlar, Donald G

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Multiscale QM/MM Simulations of ATP Hydrolysis Mechanism in ABC-Transporters von Pu, Jingzhi

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How subunit coupling produces the γ-subunit rotary motion in F 1 -ATPase von Pu, Jingzhi, Karplus, Martin

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Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability von Kim, Bryant, Shao, Yihan, Pu, Jingzhi

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DFT/MM Simulations for Cycloreversion Reaction of Cyclobutane Pyrimidine Dimer with Deprotonated and Protonated E283 von Xue, Pei, Huang, Donglian, Pu, Jingzhi, Zhou, Yan

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Generalized Hybrid-Orbital Method for Combining Density Functional Theory with Molecular Mechanicals von Pu, Jingzhi, Gao, Jiali, Truhlar, Donald G.

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Revealing intrinsic changes of DNA induced by spore photoproduct lesion through computer simulation von Hege, Mellisa, Li, Lei, Pu, Jingzhi

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Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions von Pan, Xiaoliang, Yang, Junjie, Van, Richard, Epifanovsky, Evgeny, Ho, Junming, Huang, Jing, Pu, Jingzhi, Mei, Ye, Nam, Kwangho, Shao, Yihan

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Photoactivities of thiophene monomer/polymer transition in gel–based photoelectrochemical assembly: A theoretical/experimental approach von Kasem, Kasem K., Pu, Jingzhi, Cox, Logan

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