Difference between revisions of "Publications"
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+ | <li value="60"> | ||
+ | "CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed," Hwang, W.; Austin, S.; Blondel, A.; Boittier, E.; Boresch, S.; Buck, M.; Buckner, J.; Caflisch, A.; Chang, H.-T.; Cheng, X.; Choi, Y. K.; Chu, J.-W.; Crowley, M.; Cui, Q.; Damjanovic, A.; Deng, Y.; Devereux, M.; Ding, X.; Feig, M.; Gao, J.; Glowacki, D.; Gonzales, J.; Hamaneh, M.; Harder, E.; Hayes, R.; Huang, J.; Huang, Y.; Hudson, P.; Im, W.; Islam, S.; Jiang, W.; Jones, M.; Käser, S.; Kearns, F. ; Kern, N.; Klauda, J.; Lazaridis, T.; Lee, J.; Lemkul, J.; Liu, X.; Luo, Y.; MacKerell, A.; Major, D.; Meuwly, M.; Nam, K.; Nilsson, L.; Ovchinnikov, V.; Paci, E.; Park, S.; Pastor, R.; Pittman, A.; Post, C.; Prasad, S.; '''Pu, J.'''; Qi, Y.; Rathinavelan, T.; Roe, D.; Roux, B.; Rowley, C.; Shen, J.; Simmonett, A.; Sodt, A.; Topfer, K.; Upadhyay, M.; van der Vaart, A.; Vazquez-Salazar, L. I.; Venable, R.; Warrensford, L.; Woodcock, H. L.; Wu, Y.; Brooks, Charles; Brooks, B.; Karplus, M. ''J. Phys. Chem. B'' '''2024''', ''128'', 9976-10042 ([https://doi.org/10.1021/acs.jpcb.4c04100 doi:10.1021/acs.jpcb.4c04100]). | ||
+ | </li> | ||
+ | |||
+ | <li value="59"> | ||
+ | "DFT/MM Simulations for Cycloreversion Reaction of Cyclobutane Pyrimidine Dimer with Deprotonated and Protonated E283," Xue, P.; Huang, D.; '''Pu, J.'''; Zhou, Y. ''J. Phys. Chem. B'' '''2024''', ''128'', 6670–6683 ([https://doi.org/10.1021/acs.jpcb.4c01011 doi:10.1021/acs.jpcb.4c01011]). | ||
+ | </li> | ||
+ | |||
+ | <li value="58"> | ||
+ | "Design of Light-Induced Solid-State Plasmonic Rulers via Tethering Photoswitchable Molecular Machines to Gold Nanostructures Displaying Angstrom Length Resolution," Langlais, S.; Hati, S.; Simas, V.; '''Pu, J.'''; Muhoberac, B.; Sardar, R. ''Adv. Optical Mater.'' '''2024''', 2400801 ([https://doi.org/10.1002/adom.202400801 doi:10.1002/adom.202400801]). | ||
+ | </li> | ||
+ | |||
+ | <li value="57"> | ||
+ | "Training Machine Learning Potentials for Reactive Systems: A Colab Tutorial on Basic Models," Pan, X.; Snyder, R.; Wang, J.-N.; Lander, C.; Wickizer, C.; Van, R.; Chesney, A.; Xue, Y.; Mao, Y.; Mei, Y.; '''Pu, J.'''; Shao, Y. ''J. Comput. Chem.'' '''2024''', ''45'', 638-647 ([http://doi.org/10.1002/jcc.27269 doi:10.1002/jcc.27269]; [https://pubmed.ncbi.nlm.nih.gov/38082539/ PMID: 38082539]; preprint: [https://doi.org/10.26434/chemrxiv-2023-545gw doi:10.26434/chemrxiv-2023-545gw]). | ||
+ | </li> | ||
+ | |||
+ | <li value="56"> | ||
+ | "Polyrate 2023: A Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics. New Version Announcement," Meana-Paneda, R.; Zheng, J.; Bao, J. L.; Zhang, S.; Lynch, B. J.; Corchado, J. C.; Chuang, Y.-Y.; Fast, P. L.; Hu, W.-P.; Liu, Y.-P.; Lynch, G. C.; Nguyen, K. A.; Jackels, C. F.; Fernandez-Ramos, A.; Ellingson, B. A.; Melissas, V. S.; Villa, J.; Rossi, I.; Coitino, E. L.; '''Pu, J.'''; Albu, T. V.; Zhang, R. M.; Xu, X.; Ratkiewicz, A.; Steckler, R.; Garrett, B. C.; Isaacson, A. D.; Truhlar, D. G. ''Comput. Phys. Commun.'' '''2024''', ''294'', 108933 ([https://doi.org/10.1016/j.cpc.2023.108933 doi:10.1016/j.cpc.2023.108933]). | ||
+ | </li> | ||
+ | |||
+ | <li value="55"> | ||
+ | "Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions," Pan, X.; Van, R.; '''Pu, J.'''; Nam, K.; Mao, Y.; Shao, Y. ''J. Chem. Theory Comput.'' '''2023''', ''19'', 8234-8244 ([https://doi.org/10.1021/acs.jctc.3c00973 doi:10.1021/acs.jctc.3c00973]; [https://pubmed.ncbi.nlm.nih.gov/37943896/ PMID:37943896]; preprint: [https://doi.org/10.26434/chemrxiv-2023-mrm25 doi:10.26434/chemrxiv-2023-mrm25]) | ||
+ | . | ||
+ | </li> | ||
+ | |||
+ | <li value="54"> | ||
+ | "Hybrid Metal-Ligand Interfacial Dipole Engineering of Functional Plasmonic Nanostructures for Extraordinary Responses of Optoelectronic Properties," Hati, S.; Yang, X.; Gupta, P.; Muhoberac, B.; '''Pu, J.'''; Zhang, J.; Sardar, R. ''ACS Nano'' '''2023''', ''17'', 17499-17515 ([https://doi.org/10.1021/acsnano.3c06047 doi:10.1021/acsnano.3c06047]). | ||
+ | </li> | ||
+ | |||
+ | <li value="53"> | ||
+ | "Bridging Semiempirical and Ab Initio QM/MM Potentials by Gaussian Process Regression and Its Sparse Variants for Free Energy Simulation," Snyder, R.; Kim, B.; Pan, X.; Shao, Y.; '''Pu, J.''' ''J. Chem. Phys.'' '''2023''', ''159'', 054107 ([https://doi.org/10.1063/5.0156327 doi:10.1063/5.0156327] [https://pubmed.ncbi.nlm.nih.gov/37530109/ PMID:37530109]). | ||
+ | </li> | ||
+ | |||
+ | <li value="52"> | ||
+ | "Revealing Intrinsic Changes of DNA Induced by Spore Photoproduct Lesion through Computer Simulation," Hege, M.; Li, L.; '''Pu, J.''' ''Biophys. Chem.'' '''2023''', ''296'', 106992 ([https://www.sciencedirect.com/science/article/pii/S0301462223000431?dgcid=author doi:10.1016/j.bpc.2023.106992] [https://pubmed.ncbi.nlm.nih.gov/36933500/ PMID: 36933500]). | ||
+ | </li> | ||
+ | |||
+ | <li value="51"> | ||
+ | "Photoactivities of Thiophene Monomer/Polymer Transition in Gel-Based Photoelectrochemical Assembly: A Theoretical/Experimental Approach." Kasem, K.; '''Pu, J.'''; Cox, L. ''Int. J. Electrochem. Sci.'' '''2023''', ''18'', 100077 ([https://doi.org/10.1016/j.ijoes.2023.100077 doi:10.1016/j.ijoes.2023.100077]). | ||
+ | </li> | ||
+ | |||
+ | <li value="50"> | ||
+ | "Machine Learning Based Implicit Solvent Model for Aqueous-Solution Alanine Dipeptide Molecular Dynamics Simulations," Yao, S.; Van, R.; Pan, X.; Park, J. H.; Mao, Y.; '''Pu, J.'''; Mei, Y.; Shao, Y. ''RSC Adv.'' '''2023''', ''13'', 4565-4577 ([https://doi.org/10.1039/D2RA08180F doi:10.1039/D2RA08180F] [https://pubmed.ncbi.nlm.nih.gov/36760282/ PMID: 36760282]). | ||
+ | </li> | ||
+ | |||
+ | <li value="49"> | ||
+ | "Facilitating Ab Initio QM/MM Free Energy Simulations by Gaussian Process Regression with Derivative Observations," Snyder, R.; Kim, B.; Pan, X.; Shao, Y.; '''Pu, J.''' ''Phys. Chem. Chem. Phys.'' '''2022''', ''24'', 25134-25143 ([https://pubs.rsc.org/en/content/articlehtml/2022/cp/d2cp02820d doi:10.1039/d2cp02820d]; [https://pubmed.ncbi.nlm.nih.gov/36222412/ PMID:36222412]; selected as a [https://rsc.li/pccp-hot22 2022 ''PCCP'' HOT Article]). | ||
+ | </li> | ||
+ | |||
+ | <li value="48"> | ||
+ | "Photoinduced Site-Selective Functionalization of Aliphatic C-H Bonds by Pyridine N-oxide Based HAT Catalysts," Wang, B.; Ascenzi Pettenuzzo, C.; Singh, J.; Mccabe, G.; Clark, L.; Young, R.; '''Pu, J.'''; Deng, Y. ''ACS Catalysis'' '''2022''', ''12'', 10441-10448 ([https://doi.org/10.1021/acscatal.2c02993 doi:10.1021/acscatal.2c02993]; preprint: [https://doi.org/10.26434/chemrxiv-2022-0rb4h doi:10.26434/chemrxiv-2022-0rb4h]). | ||
+ | </li> | ||
+ | |||
+ | <li value="47"> | ||
+ | "Accelerating ab initio QM/MM Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian," Pan, X.; Van, R.; Epifanovsky, E.; Liu, J.; '''Pu, J.'''; Nam, K.; Shao, Y. ''J. Phys. Chem. B'' '''2022''', ''126'', 4226-4235 ([https://doi.org/10.1021/acs.jpcb.2c02262 doi:10.1021/acs.jpcb.2c02262]; preprint: [https://doi.org/10.26434/chemrxiv-2022-0zg7j doi:10.26434/chemrxiv-2022-0zg7j]). | ||
+ | </li> | ||
+ | |||
+ | <li value="46"> | ||
+ | "Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability," Kim, B.; Shao, Y.; '''Pu, J.''' ''J. Chem. Theory Comput.'' '''2021''', ''17'', 7682-7695 ([https://doi.org/10.1021/acs.jctc.1c00567 doi:10.1021/acs.jctc.1c00567]; [https://pubmed.ncbi.nlm.nih.gov/34723536/ PMID:34723536]). | ||
+ | </li> | ||
+ | |||
+ | <li value="45"> | ||
+ | "Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions," Pan, X.; Yang, J.; Van, R.; Epifanovsky, E.; Ho, J.; Huang, J.; '''Pu, J.''', Mei, Y.; Nam, K.; Shao, Y. ''J. Chem. Theory Comput.'' '''2021''', ''17'', 5745-5758 ([https://doi.org/10.1021/acs.jctc.1c00565 doi:10.1021/acs.jctc.1c00565]; [https://pubmed.ncbi.nlm.nih.gov/34468138/ PMID:34468138]). | ||
+ | </li> | ||
+ | |||
+ | <li value="44"> | ||
+ | "Reaction Path-Force Matching in Collective Variables: Determining <i>Ab Initio</i> QM/MM Free Energy Profiles by Fitting Mean Force," Kim, B.; Snyder, R.; Nagaraju, M.; Zhou, Y.; Ojeda-May, P.; Keeton, S.; Hege, M.; Shao, Y.; '''Pu, J.''' ''J. Chem. Theory Comput.'' '''2021''', ''17'', 4961-4980 ([https://doi.org/10.1021/acs.jctc.1c00245 doi: 10.1021/acs.jctc.1c00245]; [https://pubmed.ncbi.nlm.nih.gov/34283604/ PMID:34283604]). | ||
+ | </li> | ||
+ | |||
+ | <li value="43"> | ||
+ | "Interligand Communication in a Metal Mediated LL’CT System - A Case Study," Dille, S.; Colston, K.; Ratvasky, S. C.; '''Pu, J.'''; Basu, P. ''RSC Adv.'' '''2021''', ''11'', 24381–24386 ([https://doi.org/10.1039/d1ra04716g doi: 10.1039/d1ra04716g]). | ||
+ | </li> | ||
+ | |||
+ | <li value="42"> | ||
+ | "Identifying Thermal Decomposition Products of Nitrate Ester Explosives Using Gas Chromatography–Vacuum Ultraviolet Spectroscopy: An Experimental and Computational Study," Cruse, C.; '''Pu, J.'''; Goodpaster, J. V. ''Appl. Spectrosc.'' '''2020''', ''74'', 1486-1495 ([https://doi.org/10.1177/0003702820915506 doi: 10.1177/0003702820915506]). | ||
+ | </li> | ||
+ | |||
+ | <li value="41"> | ||
+ | "Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. II. Recalibrating Semi-Empirical Parameters with Force Matching," Pan, X.; Li, P.; Ho, J.; '''Pu, J.'''; Mei, Y.; Shao, Y. ''Phys. Chem. Chem. Phys.'' '''2019''', ''21'', 20595-20605 ([http://dx.doi.org/10.1039/c9cp02593f doi: 10.1039/c9cp02593f]; [https://pubmed.ncbi.nlm.nih.gov/31508625/ PMID:31508625]). | ||
+ | </li> | ||
+ | |||
+ | <li value="40"> | ||
+ | "Exploring Cycloreversion Reaction of Cyclobutane Pyrimidine Dimers Quantum Mechanically," Huang, D.; Chen, S.; '''Pu, J.'''; Tan, X.; Zhou, Y. ''J. Phys. Chem. A'' '''2019''', ''123'', 2025-2039 ([http://dx.doi.org/10.1021/acs.jpca.8b12345 doi:10.1021/acs.jpca.8b12345]). | ||
+ | </li> | ||
+ | |||
+ | <li value="39"> | ||
+ | "Mapping Free Energy Pathways for ATP Hydrolysis in the ''E. coli'' ABC Transporter HlyB by the String Method," Zhou, Y.; Ojeda-May, P.; Nagaraju, M.; Kim, B.; '''Pu, J.''' ''Molecules'' '''2018''', ''23'', 2652 (QM/MM Special Issue; [http://dx.doi.org/10.3390/molecules23102652 doi:10.3390/molecules23102652]; [https://www.ncbi.nlm.nih.gov/pubmed/?term=30332773 PMID:30332773]). | ||
+ | </li> | ||
+ | |||
+ | <li value="38"> | ||
+ | "All-atom Simulations of Torque Generation in F<sub>1</sub>-ATPase," '''Pu, J.'''; Nam, K.; Karplus, M., submitted. | ||
+ | </li> | ||
+ | |||
+ | <li value="37"> | ||
+ | "Elucidating the Role of Surface Passivating Ligand Structural Parameters in Hole Wave Function Delocalization in Semiconductor Cluster Molecules," Teunis, M. B.; Mulpuri, N.; Dutta, P; '''Pu, J.'''; Muhoberac, B. B.; Sardar, R.; Agarwal, M. ''Nanoscale'' '''2017''', ''9'', 14127-14138 ([http://dx.doi.org/10.1039/C7NR04874B doi:10.1039/C7NR04874B]). | ||
+ | </li> | ||
+ | |||
+ | <li value="36"> | ||
+ | "Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path-Force Matching QM/MM Method," Zhou, Y.; Ojeda-May, P.; Nagaraju, M.; '''Pu, J.''' ''Methods Enzymol.'' '''2016''', ''577'', 185-212 ([http://dx.doi.org/10.1016/bs.mie.2016.05.054 doi:10.1016/bs.mie.2016.05.054]; [https://www.ncbi.nlm.nih.gov/pubmed/?term=27498639 PMID:27498639]). | ||
+ | </li> | ||
+ | |||
+ | <li value="35"> | ||
+ | "Treating Electrostatics with Wolf Summation in Combined Quantum Mechanical and Molecular Mechanical Simulations," Ojeda-May, P.; '''Pu, J.''' ''J. Chem. Phys.'' '''2015''', ''143'', 174111 ([http://dx.doi.org/10.1063/1.4934880 doi:10.1063/1.4934880]; [https://www.ncbi.nlm.nih.gov/pubmed/?term=26547162 PMID:26547162]). | ||
+ | </li> | ||
+ | |||
+ | <li value="34"> | ||
+ | "Trapping the ATP Binding State Leads to a Detailed Understanding of the F<sub>1</sub>-ATPase Mechanism," Nam, K.; '''Pu, J.'''; Karplus, M. ''Proc. Natl. Acad. Sci. USA'' '''2014''', ''111'', 17851-17856 ([http://dx.doi.org/10.1073/pnas.1419486111 doi:10.1073/pnas.1419486111]). | ||
+ | </li> | ||
+ | |||
+ | <li value="33"> | ||
+ | "Assessing the Accuracy of the Isotropic Periodic Sum Method through Madelung Energy Computation," Ojeda-May, P.; '''Pu, J.''' ''J. Chem. Phys.'' '''2014''', ''140'', 164106 ([http://dx.doi.org/10.1063/1.4871871 doi:10.1063/1.4871871]). | ||
+ | </li> | ||
<li value="32"> | <li value="32"> | ||
− | " | + | "Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations," Zhou, Y.; '''Pu, J.''' ''J. Chem. Theory Comput.'' '''2014''', ''10'', 3038-3054 |
+ | ([http://dx.doi.org/10.1021/ct4009624 doi:10.1021/ct4009624]). | ||
</li> | </li> | ||
<li value="31"> | <li value="31"> | ||
− | " | + | "Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical Calculations," Ojeda-May, P.; '''Pu, J.''' ''J. Chem. Theory Comput.'' '''2014''', ''10'', 134-145 ([http://dx.doi.org/10.1021/ct400724d doi:10.1021/ct400724d]). |
</li> | </li> | ||
<li value="30"> | <li value="30"> | ||
− | " | + | "Replica Exchange Molecular Dynamics Simulations of an α/β-type Small Acid Soluble Protein (SASP)," Ojeda-May, P.; '''Pu, J.''' ''Biophys. Chem.'' '''2013''', ''184'', 17-21 ([http://dx.doi.org/10.1016/j.bpc.2013.07.014 doi:10.1016/j.bpc.2013.07.014]). |
</li> | </li> | ||
<li value="29"> | <li value="29"> | ||
− | " | + | "H-loop Histidine Catalyzes ATP Hydrolysis in the ''E. coli'' ABC-Transporter HlyB," Zhou, Y.; Ojeda-May, P.; '''Pu, J.''' ''Phys. Chem. Chem. Phys.'' '''2013''', ''15'', 15811-15815 ([http://dx.doi.org/10.1039/C3CP50965F doi:10.1039/C3CP50965F]; SI: [[Media:QMMM_HlyB_GAC_Movie_S1_240x200.mpg|movie_S1]]& [[Media:QMMM_HlyB_SAC_Movie_S2_240x200.mpg|movie_S2]]; preprint: [http://arxiv.org/abs/1304.0052 arXiv:1304.0052] [q-bio.BM]). |
</li> | </li> | ||
<li value="28"> | <li value="28"> | ||
− | "Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Dimers | + | "Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Cyclobutane Dimers Formed by Photoreaction between a Thymine and a Toluene residue in the Dinucleotide Framework," Liu, D.; Zhou, Y.; '''Pu, J.'''; Li, L. ''Chem. Eur. J.'' '''2012''', ''18'', 7823-7833 ([http://dx.doi.org/10.1002/chem.201200816 doi:10.1002/chem.201200816]). |
</li> | </li> | ||
<li value="27"> | <li value="27"> | ||
− | "Chemical Synthesis, Crystal Structure and Enzymatic Evaluation of a Dinucleotide Spore Photoproduct Analogue Containing Formacetal Linker," Lin, G.; Chen, C.-H; Pink, M.; '''Pu, J.'''; Li, L. ''Chem. Eur. J.'' '''2011''', ''17'', 9658-9668. | + | "Chemical Synthesis, Crystal Structure and Enzymatic Evaluation of a Dinucleotide Spore Photoproduct Analogue Containing Formacetal Linker," Lin, G.; Chen, C.-H; Pink, M.; '''Pu, J.'''; Li, L. ''Chem. Eur. J.'' '''2011''', ''17'', 9658-9668 |
+ | ([http://dx.doi.org/10.1002/chem.201101821 doi:10.1002/chem.201101821]). | ||
</li> | </li> | ||
− | ''' --- Before IUPUI ---''' | + | </ol> |
+ | |||
+ | ''' --- Before IUPUI ---''' | ||
+ | <ol> | ||
<li value="26"> | <li value="26"> | ||
"How Biomolecular Motors Work: Synergy between Single Molecule Experiments and Single Molecule Simulations," Karplus, M.; '''Pu, J.''', in Springer Series in Chemical Physics '''2010''', ''96'' (''Single Molecule Spectroscopy in Chemistry, Physics, and Biology''), pp. 271-285. | "How Biomolecular Motors Work: Synergy between Single Molecule Experiments and Single Molecule Simulations," Karplus, M.; '''Pu, J.''', in Springer Series in Chemical Physics '''2010''', ''96'' (''Single Molecule Spectroscopy in Chemistry, Physics, and Biology''), pp. 271-285. | ||
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<li value="25"> | <li value="25"> | ||
− | "A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function," Xie, W.; '''Pu, J.'''; Gao, J. ''J. Phys. Chem. A'' '''2009''', ''113'', 2109-2116. | + | "A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function," Xie, W.; '''Pu, J.'''; Gao, J. ''J. Phys. Chem. A'' '''2009''', ''113'', 2109-2116 ([http://dx.doi.org/10.1021/jp808952m doi:10.1021/jp808952m]). |
</li> | </li> | ||
<li value="24"> | <li value="24"> | ||
− | "CHARMM: The Biomolecular Simulation Program," Brooks, B. R.; Brooks III, C. L.; MacKerell, Jr., A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; '''Pu, J.'''; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. ''J. Comput. Chem.'' '''2009''', ''30'', 1545-1614. | + | "CHARMM: The Biomolecular Simulation Program," Brooks, B. R.; Brooks III, C. L.; MacKerell, Jr., A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; '''Pu, J.'''; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. ''J. Comput. Chem.'' '''2009''', ''30'', 1545-1614 ([http://dx.doi.org/10.1002/jcc.21287 doi:10.1002/jcc.21287]). |
</li> | </li> | ||
<li value="23"> | <li value="23"> | ||
− | "How | + | "How Subunit Coupling Produces the Rotary Motion in F<sub>1</sub>-ATPase," '''Pu, J.'''; Karplus, M. ''Proc. Natl. Acad. Sci. USA'' '''2008''', ''105'', 1192-1197 (track II, direction submission) ([http://dx.doi.org/10.1073/pnas.0708746105 doi:10.1073/pnas.0708746105]); selected by [http://f1000.com/1102040 Faculty of 1000]. |
</li> | </li> | ||
<li value="22"> | <li value="22"> | ||
− | "Development of a Polarizable Intermolecular Potential Function for Liquid Amides and Alkanes," Xie, W.; '''Pu, J.'''; MacKerell, Jr. A. D.; Gao, J. ''J. Chem. | + | "Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes," Xie, W.; '''Pu, J.'''; MacKerell, Jr. A. D.; Gao, J. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 1878-1889 ([http://dx.doi.org/10.1021/ct700146x doi:10.1021/ct700146x]). |
</li> | </li> | ||
<li value="21"> | <li value="21"> | ||
− | " | + | "Multicoefficient Gaussian-3 Calculation of the Rate Constant for the OH + CH<sub>4</sub> Reaction and its <sup>12</sup>C/<sup>13</sup>C Kinetic Isotope Effect with Emphasis on the Effects of Coordinate System and Torsional Treatment," Ellingson, B. A.; '''Pu, J.'''; Lin, H.; Zhao, Y.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2007''', ''111'', 11706-11717 ([http://dx.doi.org/10.1021/jp072843j doi:10.1021/jp072843j]). |
</li> | </li> | ||
<li value="20"> | <li value="20"> | ||
− | " | + | "Mechanisms and Free Energies of Enzymatic Reactions," Gao, J.; Ma, S.; Major, D. T.; Nam, K.; '''Pu, J.'''; Truhlar, D. G. ''Chem. Rev.'' '''2006''', ''106'', 3188-3209 ([http://dx.doi.org/10.1021/cr050293k doi:10.1021/cr050293k]). |
</li> | </li> | ||
<li value="19"> | <li value="19"> | ||
− | "Multidimensional Tunneling, Recrossing, and Transmission Coefficient for Enzymatic Reactions," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''Chem. Rev.'' '''2006''', ''106'', 3140-3169. | + | "Multidimensional Tunneling, Recrossing, and Transmission Coefficient for Enzymatic Reactions," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''Chem. Rev.'' '''2006''', ''106'', 3140-3169 ([http://dx.doi.org/10.1021/cr050308e doi:10.1021/cr050308e]). |
+ | . | ||
</li> | </li> | ||
<li value="18"> | <li value="18"> | ||
− | "Hydride Transfer Reaction Catalyzed by Hyperthermophilic Dihydrofolate Reductase is Dominated by Quantum Mechanical Tunneling and is Promoted by Both Inter- and Intramonomeric Correlated Motions," Pang, J.; '''Pu, J.'''; Gao, J.; Truhlar, D. G; Allemann, R. K. ''J. Am. Chem. Soc.'' '''2006''', ''128'', 8015-8023. | + | "Hydride Transfer Reaction Catalyzed by Hyperthermophilic Dihydrofolate Reductase is Dominated by Quantum Mechanical Tunneling and is Promoted by Both Inter- and Intramonomeric Correlated Motions," Pang, J.; '''Pu, J.'''; Gao, J.; Truhlar, D. G; Allemann, R. K. ''J. Am. Chem. Soc.'' '''2006''', ''128'', 8015-8023 ([http://dx.doi.org/10.1021/ja061585l doi:10.1021/ja061585l]). |
</li> | </li> | ||
<li value="17"> | <li value="17"> | ||
− | "Searching for Saddle Points by Using the Nudged Elastic Band Method: An Implementation for Gas-Phase Systems," Gonzalez-Garcia, N.; Pu, J.; Gonzalez-Lafont, A.; Lluch, J. M.; Truhlar, D. G. ''J. Chem. | + | "Searching for Saddle Points by Using the Nudged Elastic Band Method: An Implementation for Gas-Phase Systems," Gonzalez-Garcia, N.; '''Pu, J.'''; Gonzalez-Lafont, A.; Lluch, J. M.; Truhlar, D. G. ''J. Chem. Theory Comput.'' '''2006''', ''2'', 895-904 ([http://dx.doi.org/10.1021/ct060032y doi:10.1021/ct060032y]). |
</li> | </li> | ||
<li value="16"> | <li value="16"> | ||
− | "Nonperfect Synchronization of Reaction Center Rehybridization in the Transition State of the | + | "Nonperfect Synchronization of Reaction Center Rehybridization in the Transition State of the Hydride Transfer Catalyzed by Dihydrofolate Reductase," '''Pu, J.'''; Ma, S.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G.; Kohen, A. ''J. Am. Chem. Soc.'' '''2005''', ''127'', 14879-14886 ([http://dx.doi.org/10.1021/ja054170t doi:10.1021/ja054170t]). |
</li> | </li> | ||
<li value="15"> | <li value="15"> | ||
− | "Generalized Hybrid Orbital Method for Combined | + | "Generalized Hybrid-Orbital Method for Combined Density Functional Theory and Molecular Mechanics," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''ChemPhysChem'' '''2005''', ''6'', 1853-1865 ([http://dx.doi.org/10.1002/cphc.200400602 doi:10.1002/cphc.200400602]). |
</li> | </li> | ||
<li value="14"> | <li value="14"> | ||
− | "Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. B'' '''2005''', ''109'', 8551-8556. | + | "Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. B'' '''2005''', ''109'', 8551-8556 ([http://dx.doi.org/10.1021/jp051184c doi:10.1021/jp051184c]). |
</li> | </li> | ||
<li value="13"> | <li value="13"> | ||
− | "Temperature Dependence of Carbon-13 Kinetic Isotope Effects of Importance to Global Climate Change," Lin, H.; Zhao, Y.; Ellingson, B. A.; '''Pu, J.'''; Truhlar, D. G. ''J. Am. Chem. Soc.'' '''2005''', ''127'', 2830-2831. | + | "Temperature Dependence of Carbon-13 Kinetic Isotope Effects of Importance to Global Climate Change," Lin, H.; Zhao, Y.; Ellingson, B. A.; '''Pu, J.'''; Truhlar, D. G. ''J. Am. Chem. Soc.'' '''2005''', ''127'', 2830-2831 ([http://dx.doi.org/10.1021/ja0434026 doi:10.1021/ja0434026]). |
</li> | </li> | ||
<li value="12"> | <li value="12"> | ||
− | "Benchmark Calculations of Reaction Energies, Barrier Heights, and Transition State Geometries for Hydrogen Abstraction from Methanol by a Hydrogen Atom," '''Pu, J.'''; Truhlar, D. G. ''J. Phys. Chem. A'' '''2005''', ''109'', 773-778. | + | "Benchmark Calculations of Reaction Energies, Barrier Heights, and Transition State Geometries for Hydrogen Abstraction from Methanol by a Hydrogen Atom," '''Pu, J.'''; Truhlar, D. G. ''J. Phys. Chem. A'' '''2005''', ''109'', 773-778 ([http://dx.doi.org/10.1021/jp045574v doi:10.1021/jp045574v]). |
</li> | </li> | ||
<li value="11"> | <li value="11"> | ||
− | "Use of Block | + | "Use of Block Hessians for the Optimization of Molecular Geometries," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Theory Comput.'' '''2005''', ''1'', 54-60 ([http://dx.doi.org/10.1021/ct0400020 doi:10.1021/ct0400020]). |
</li> | </li> | ||
<li value="10"> | <li value="10"> | ||
− | "Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 5454-5463. | + | "Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 5454-5463 ([http://dx.doi.org/10.1021/jp049529z doi:10.1021/jp049529z]). |
</li> | </li> | ||
<li value="9"> | <li value="9"> | ||
− | "Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics using Partial Electronic Structure Hessians," Lin, H.; '''Pu, J.'''; Albu, T. V.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 4112-4124. | + | "Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics using Partial Electronic Structure Hessians," Lin, H.; '''Pu, J.'''; Albu, T. V.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 4112-4124 ([http://dx.doi.org/10.1021/jp049972+ doi:10.1021/jp049972+]). |
</li> | </li> | ||
<li value="8"> | <li value="8"> | ||
− | "Tests of Second-Generation Density Functionals for Thermochemical Kinetics," Zhao, Y.; '''Pu, J.'''; Lynch, B. J. Truhlar, D. G. ''Phys. Chem. Chem. Phys.'' '''2004''', ''6'', 673-676. | + | "Tests of Second-Generation and Third-Generation Density Functionals for Thermochemical Kinetics," Zhao, Y.; '''Pu, J.'''; Lynch, B. J. Truhlar, D. G. ''Phys. Chem. Chem. Phys.'' '''2004''', ''6'', 673-676 ([http://dx.doi.org/10.1039/B316260E doi:10.1039/B316260E]). |
</li> | </li> | ||
<li value="7"> | <li value="7"> | ||
− | "Benchmark Results for Hydrogen Atom Transfer between Carbon Centers and Validation of Electronic Structure Methods for Bond Energies and Barrier Heights," Dybala-Defratyka, A.; Paneth, P.; '''Pu, J.'''; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 2475- | + | "Benchmark Results for Hydrogen Atom Transfer between Carbon Centers and Validation of Electronic Structure Methods for Bond Energies and Barrier Heights," Dybala-Defratyka, A.; Paneth, P.; '''Pu, J.'''; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 2475-2486 ([http://dx.doi.org/10.1021/jp037312j doi:10.1021/jp037312j]). |
</li> | </li> | ||
<li value="6"> | <li value="6"> | ||
− | "Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 632-650. | + | "Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics," '''Pu, J.'''; Gao, J.; Truhlar, D. G. ''J. Phys. Chem. A'' '''2004''', ''108'', 632-650 ([http://dx.doi.org/10.1021/jp036755k doi:10.1021/jp036755k]). |
</li> | </li> | ||
<li value="5"> | <li value="5"> | ||
− | "Lateral Confinement of Image Electron | + | "Lateral Confinement of Image Electron Wave Function by an Interfacial Dipole Lattice," Dutton, G.; '''Pu, J.'''; Truhlar, D. G.; Zhu, X. -Y. ''J. Chem. Phys.'' '''2003''', ''118'', 4337 ([http://dx.doi.org/10.1063/1.1556848 doi:10.1063/1.1556848]). |
</li> | </li> | ||
<li value="4"> | <li value="4"> | ||
− | "Tests of Potential Energy Surfaces for H + CH<sub>4</sub> → CH<sub>3</sub> + H<sub>2</sub>: Deuterium and Muonium Kinetic Isotope Effects for the Forward and Reverse Reaction," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Phys.'' '''2002''', ''117'', 10675. | + | "Tests of Potential Energy Surfaces for H + CH<sub>4</sub> → CH<sub>3</sub> + H<sub>2</sub>: Deuterium and Muonium Kinetic Isotope Effects for the Forward and Reverse Reaction," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Phys.'' '''2002''', ''117'', 10675 ([http://dx.doi.org/10.1063/1.1518471 doi:10.1063/1.1518471]). |
</li> | </li> | ||
<li value="3"> | <li value="3"> | ||
− | " | + | "Validation of Variational Transition State Theory with Multidimensional Tunneling Contributions against Accurate Quantum Mechanical Dynamics for H + CH<sub>4</sub> → CH<sub>3</sub> + H<sub>2</sub> in an Extended Temperature Interval," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Phys.'' '''2002''', ''117'', 1479 ([http://dx.doi.org/10.1063/1.1485063 doi:10.1063/1.1485063]). |
</li> | </li> | ||
<li value="2"> | <li value="2"> | ||
− | "Parametrized Direct Dynamics Study of Rate Constants of H with CH<sub>4</sub> from 250 to 2400 K," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Phys.'' '''2002''', ''116'', 1468. | + | "Parametrized Direct Dynamics Study of Rate Constants of H with CH<sub>4</sub> from 250 to 2400 K," '''Pu, J.'''; Truhlar, D. G. ''J. Chem. Phys.'' '''2002''', ''116'', 1468 ([http://dx.doi.org/10.1063/1.1427917 doi:10.1063/1.1427917]). |
</li> | </li> | ||
<li value="1"> | <li value="1"> | ||
− | "Test of Variational Transition State Theory with Multidimensional Tunneling Contributions Against an Accurate Full-Dimensional Rate Constant Calculation for a Six-Atom system," '''Pu, J.'''; Corchado, J. C.; Truhlar, D. G. ''J. Chem. Phys.'' '''2001''', ''115'', 6266. | + | "Test of Variational Transition State Theory with Multidimensional Tunneling Contributions Against an Accurate Full-Dimensional Rate Constant Calculation for a Six-Atom system," '''Pu, J.'''; Corchado, J. C.; Truhlar, D. G. ''J. Chem. Phys.'' '''2001''', ''115'', 6266 ([http://dx.doi.org/10.1063/1.1398581 doi:10.1063/1.1398581]). |
</li> | </li> | ||
</ol> | </ol> |
Latest revision as of 14:55, 17 October 2024
- "CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed," Hwang, W.; Austin, S.; Blondel, A.; Boittier, E.; Boresch, S.; Buck, M.; Buckner, J.; Caflisch, A.; Chang, H.-T.; Cheng, X.; Choi, Y. K.; Chu, J.-W.; Crowley, M.; Cui, Q.; Damjanovic, A.; Deng, Y.; Devereux, M.; Ding, X.; Feig, M.; Gao, J.; Glowacki, D.; Gonzales, J.; Hamaneh, M.; Harder, E.; Hayes, R.; Huang, J.; Huang, Y.; Hudson, P.; Im, W.; Islam, S.; Jiang, W.; Jones, M.; Käser, S.; Kearns, F. ; Kern, N.; Klauda, J.; Lazaridis, T.; Lee, J.; Lemkul, J.; Liu, X.; Luo, Y.; MacKerell, A.; Major, D.; Meuwly, M.; Nam, K.; Nilsson, L.; Ovchinnikov, V.; Paci, E.; Park, S.; Pastor, R.; Pittman, A.; Post, C.; Prasad, S.; Pu, J.; Qi, Y.; Rathinavelan, T.; Roe, D.; Roux, B.; Rowley, C.; Shen, J.; Simmonett, A.; Sodt, A.; Topfer, K.; Upadhyay, M.; van der Vaart, A.; Vazquez-Salazar, L. I.; Venable, R.; Warrensford, L.; Woodcock, H. L.; Wu, Y.; Brooks, Charles; Brooks, B.; Karplus, M. J. Phys. Chem. B 2024, 128, 9976-10042 (doi:10.1021/acs.jpcb.4c04100).
- "DFT/MM Simulations for Cycloreversion Reaction of Cyclobutane Pyrimidine Dimer with Deprotonated and Protonated E283," Xue, P.; Huang, D.; Pu, J.; Zhou, Y. J. Phys. Chem. B 2024, 128, 6670–6683 (doi:10.1021/acs.jpcb.4c01011).
- "Design of Light-Induced Solid-State Plasmonic Rulers via Tethering Photoswitchable Molecular Machines to Gold Nanostructures Displaying Angstrom Length Resolution," Langlais, S.; Hati, S.; Simas, V.; Pu, J.; Muhoberac, B.; Sardar, R. Adv. Optical Mater. 2024, 2400801 (doi:10.1002/adom.202400801).
- "Training Machine Learning Potentials for Reactive Systems: A Colab Tutorial on Basic Models," Pan, X.; Snyder, R.; Wang, J.-N.; Lander, C.; Wickizer, C.; Van, R.; Chesney, A.; Xue, Y.; Mao, Y.; Mei, Y.; Pu, J.; Shao, Y. J. Comput. Chem. 2024, 45, 638-647 (doi:10.1002/jcc.27269; PMID: 38082539; preprint: doi:10.26434/chemrxiv-2023-545gw).
- "Polyrate 2023: A Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics. New Version Announcement," Meana-Paneda, R.; Zheng, J.; Bao, J. L.; Zhang, S.; Lynch, B. J.; Corchado, J. C.; Chuang, Y.-Y.; Fast, P. L.; Hu, W.-P.; Liu, Y.-P.; Lynch, G. C.; Nguyen, K. A.; Jackels, C. F.; Fernandez-Ramos, A.; Ellingson, B. A.; Melissas, V. S.; Villa, J.; Rossi, I.; Coitino, E. L.; Pu, J.; Albu, T. V.; Zhang, R. M.; Xu, X.; Ratkiewicz, A.; Steckler, R.; Garrett, B. C.; Isaacson, A. D.; Truhlar, D. G. Comput. Phys. Commun. 2024, 294, 108933 (doi:10.1016/j.cpc.2023.108933).
- "Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions," Pan, X.; Van, R.; Pu, J.; Nam, K.; Mao, Y.; Shao, Y. J. Chem. Theory Comput. 2023, 19, 8234-8244 (doi:10.1021/acs.jctc.3c00973; PMID:37943896; preprint: doi:10.26434/chemrxiv-2023-mrm25) .
- "Hybrid Metal-Ligand Interfacial Dipole Engineering of Functional Plasmonic Nanostructures for Extraordinary Responses of Optoelectronic Properties," Hati, S.; Yang, X.; Gupta, P.; Muhoberac, B.; Pu, J.; Zhang, J.; Sardar, R. ACS Nano 2023, 17, 17499-17515 (doi:10.1021/acsnano.3c06047).
- "Bridging Semiempirical and Ab Initio QM/MM Potentials by Gaussian Process Regression and Its Sparse Variants for Free Energy Simulation," Snyder, R.; Kim, B.; Pan, X.; Shao, Y.; Pu, J. J. Chem. Phys. 2023, 159, 054107 (doi:10.1063/5.0156327 PMID:37530109).
- "Revealing Intrinsic Changes of DNA Induced by Spore Photoproduct Lesion through Computer Simulation," Hege, M.; Li, L.; Pu, J. Biophys. Chem. 2023, 296, 106992 (doi:10.1016/j.bpc.2023.106992 PMID: 36933500).
- "Photoactivities of Thiophene Monomer/Polymer Transition in Gel-Based Photoelectrochemical Assembly: A Theoretical/Experimental Approach." Kasem, K.; Pu, J.; Cox, L. Int. J. Electrochem. Sci. 2023, 18, 100077 (doi:10.1016/j.ijoes.2023.100077).
- "Machine Learning Based Implicit Solvent Model for Aqueous-Solution Alanine Dipeptide Molecular Dynamics Simulations," Yao, S.; Van, R.; Pan, X.; Park, J. H.; Mao, Y.; Pu, J.; Mei, Y.; Shao, Y. RSC Adv. 2023, 13, 4565-4577 (doi:10.1039/D2RA08180F PMID: 36760282).
- "Facilitating Ab Initio QM/MM Free Energy Simulations by Gaussian Process Regression with Derivative Observations," Snyder, R.; Kim, B.; Pan, X.; Shao, Y.; Pu, J. Phys. Chem. Chem. Phys. 2022, 24, 25134-25143 (doi:10.1039/d2cp02820d; PMID:36222412; selected as a 2022 PCCP HOT Article).
- "Photoinduced Site-Selective Functionalization of Aliphatic C-H Bonds by Pyridine N-oxide Based HAT Catalysts," Wang, B.; Ascenzi Pettenuzzo, C.; Singh, J.; Mccabe, G.; Clark, L.; Young, R.; Pu, J.; Deng, Y. ACS Catalysis 2022, 12, 10441-10448 (doi:10.1021/acscatal.2c02993; preprint: doi:10.26434/chemrxiv-2022-0rb4h).
- "Accelerating ab initio QM/MM Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian," Pan, X.; Van, R.; Epifanovsky, E.; Liu, J.; Pu, J.; Nam, K.; Shao, Y. J. Phys. Chem. B 2022, 126, 4226-4235 (doi:10.1021/acs.jpcb.2c02262; preprint: doi:10.26434/chemrxiv-2022-0zg7j).
- "Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability," Kim, B.; Shao, Y.; Pu, J. J. Chem. Theory Comput. 2021, 17, 7682-7695 (doi:10.1021/acs.jctc.1c00567; PMID:34723536).
- "Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions," Pan, X.; Yang, J.; Van, R.; Epifanovsky, E.; Ho, J.; Huang, J.; Pu, J., Mei, Y.; Nam, K.; Shao, Y. J. Chem. Theory Comput. 2021, 17, 5745-5758 (doi:10.1021/acs.jctc.1c00565; PMID:34468138).
- "Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force," Kim, B.; Snyder, R.; Nagaraju, M.; Zhou, Y.; Ojeda-May, P.; Keeton, S.; Hege, M.; Shao, Y.; Pu, J. J. Chem. Theory Comput. 2021, 17, 4961-4980 (doi: 10.1021/acs.jctc.1c00245; PMID:34283604).
- "Interligand Communication in a Metal Mediated LL’CT System - A Case Study," Dille, S.; Colston, K.; Ratvasky, S. C.; Pu, J.; Basu, P. RSC Adv. 2021, 11, 24381–24386 (doi: 10.1039/d1ra04716g).
- "Identifying Thermal Decomposition Products of Nitrate Ester Explosives Using Gas Chromatography–Vacuum Ultraviolet Spectroscopy: An Experimental and Computational Study," Cruse, C.; Pu, J.; Goodpaster, J. V. Appl. Spectrosc. 2020, 74, 1486-1495 (doi: 10.1177/0003702820915506).
- "Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. II. Recalibrating Semi-Empirical Parameters with Force Matching," Pan, X.; Li, P.; Ho, J.; Pu, J.; Mei, Y.; Shao, Y. Phys. Chem. Chem. Phys. 2019, 21, 20595-20605 (doi: 10.1039/c9cp02593f; PMID:31508625).
- "Exploring Cycloreversion Reaction of Cyclobutane Pyrimidine Dimers Quantum Mechanically," Huang, D.; Chen, S.; Pu, J.; Tan, X.; Zhou, Y. J. Phys. Chem. A 2019, 123, 2025-2039 (doi:10.1021/acs.jpca.8b12345).
- "Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method," Zhou, Y.; Ojeda-May, P.; Nagaraju, M.; Kim, B.; Pu, J. Molecules 2018, 23, 2652 (QM/MM Special Issue; doi:10.3390/molecules23102652; PMID:30332773).
- "All-atom Simulations of Torque Generation in F1-ATPase," Pu, J.; Nam, K.; Karplus, M., submitted.
- "Elucidating the Role of Surface Passivating Ligand Structural Parameters in Hole Wave Function Delocalization in Semiconductor Cluster Molecules," Teunis, M. B.; Mulpuri, N.; Dutta, P; Pu, J.; Muhoberac, B. B.; Sardar, R.; Agarwal, M. Nanoscale 2017, 9, 14127-14138 (doi:10.1039/C7NR04874B).
- "Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path-Force Matching QM/MM Method," Zhou, Y.; Ojeda-May, P.; Nagaraju, M.; Pu, J. Methods Enzymol. 2016, 577, 185-212 (doi:10.1016/bs.mie.2016.05.054; PMID:27498639).
- "Treating Electrostatics with Wolf Summation in Combined Quantum Mechanical and Molecular Mechanical Simulations," Ojeda-May, P.; Pu, J. J. Chem. Phys. 2015, 143, 174111 (doi:10.1063/1.4934880; PMID:26547162).
- "Trapping the ATP Binding State Leads to a Detailed Understanding of the F1-ATPase Mechanism," Nam, K.; Pu, J.; Karplus, M. Proc. Natl. Acad. Sci. USA 2014, 111, 17851-17856 (doi:10.1073/pnas.1419486111).
- "Assessing the Accuracy of the Isotropic Periodic Sum Method through Madelung Energy Computation," Ojeda-May, P.; Pu, J. J. Chem. Phys. 2014, 140, 164106 (doi:10.1063/1.4871871).
- "Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations," Zhou, Y.; Pu, J. J. Chem. Theory Comput. 2014, 10, 3038-3054 (doi:10.1021/ct4009624).
- "Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical Calculations," Ojeda-May, P.; Pu, J. J. Chem. Theory Comput. 2014, 10, 134-145 (doi:10.1021/ct400724d).
- "Replica Exchange Molecular Dynamics Simulations of an α/β-type Small Acid Soluble Protein (SASP)," Ojeda-May, P.; Pu, J. Biophys. Chem. 2013, 184, 17-21 (doi:10.1016/j.bpc.2013.07.014).
- "H-loop Histidine Catalyzes ATP Hydrolysis in the E. coli ABC-Transporter HlyB," Zhou, Y.; Ojeda-May, P.; Pu, J. Phys. Chem. Chem. Phys. 2013, 15, 15811-15815 (doi:10.1039/C3CP50965F; SI: movie_S1& movie_S2; preprint: arXiv:1304.0052 [q-bio.BM]).
- "Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Cyclobutane Dimers Formed by Photoreaction between a Thymine and a Toluene residue in the Dinucleotide Framework," Liu, D.; Zhou, Y.; Pu, J.; Li, L. Chem. Eur. J. 2012, 18, 7823-7833 (doi:10.1002/chem.201200816).
- "Chemical Synthesis, Crystal Structure and Enzymatic Evaluation of a Dinucleotide Spore Photoproduct Analogue Containing Formacetal Linker," Lin, G.; Chen, C.-H; Pink, M.; Pu, J.; Li, L. Chem. Eur. J. 2011, 17, 9658-9668 (doi:10.1002/chem.201101821).
--- Before IUPUI ---
- "How Biomolecular Motors Work: Synergy between Single Molecule Experiments and Single Molecule Simulations," Karplus, M.; Pu, J., in Springer Series in Chemical Physics 2010, 96 (Single Molecule Spectroscopy in Chemistry, Physics, and Biology), pp. 271-285.
- "A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function," Xie, W.; Pu, J.; Gao, J. J. Phys. Chem. A 2009, 113, 2109-2116 (doi:10.1021/jp808952m).
- "CHARMM: The Biomolecular Simulation Program," Brooks, B. R.; Brooks III, C. L.; MacKerell, Jr., A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. J. Comput. Chem. 2009, 30, 1545-1614 (doi:10.1002/jcc.21287).
- "How Subunit Coupling Produces the Rotary Motion in F1-ATPase," Pu, J.; Karplus, M. Proc. Natl. Acad. Sci. USA 2008, 105, 1192-1197 (track II, direction submission) (doi:10.1073/pnas.0708746105); selected by Faculty of 1000.
- "Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes," Xie, W.; Pu, J.; MacKerell, Jr. A. D.; Gao, J. J. Chem. Theory Comput. 2007, 3, 1878-1889 (doi:10.1021/ct700146x).
- "Multicoefficient Gaussian-3 Calculation of the Rate Constant for the OH + CH4 Reaction and its 12C/13C Kinetic Isotope Effect with Emphasis on the Effects of Coordinate System and Torsional Treatment," Ellingson, B. A.; Pu, J.; Lin, H.; Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2007, 111, 11706-11717 (doi:10.1021/jp072843j).
- "Mechanisms and Free Energies of Enzymatic Reactions," Gao, J.; Ma, S.; Major, D. T.; Nam, K.; Pu, J.; Truhlar, D. G. Chem. Rev. 2006, 106, 3188-3209 (doi:10.1021/cr050293k).
- "Multidimensional Tunneling, Recrossing, and Transmission Coefficient for Enzymatic Reactions," Pu, J.; Gao, J.; Truhlar, D. G. Chem. Rev. 2006, 106, 3140-3169 (doi:10.1021/cr050308e). .
- "Hydride Transfer Reaction Catalyzed by Hyperthermophilic Dihydrofolate Reductase is Dominated by Quantum Mechanical Tunneling and is Promoted by Both Inter- and Intramonomeric Correlated Motions," Pang, J.; Pu, J.; Gao, J.; Truhlar, D. G; Allemann, R. K. J. Am. Chem. Soc. 2006, 128, 8015-8023 (doi:10.1021/ja061585l).
- "Searching for Saddle Points by Using the Nudged Elastic Band Method: An Implementation for Gas-Phase Systems," Gonzalez-Garcia, N.; Pu, J.; Gonzalez-Lafont, A.; Lluch, J. M.; Truhlar, D. G. J. Chem. Theory Comput. 2006, 2, 895-904 (doi:10.1021/ct060032y).
- "Nonperfect Synchronization of Reaction Center Rehybridization in the Transition State of the Hydride Transfer Catalyzed by Dihydrofolate Reductase," Pu, J.; Ma, S.; Garcia-Viloca, M.; Gao, J.; Truhlar, D. G.; Kohen, A. J. Am. Chem. Soc. 2005, 127, 14879-14886 (doi:10.1021/ja054170t).
- "Generalized Hybrid-Orbital Method for Combined Density Functional Theory and Molecular Mechanics," Pu, J.; Gao, J.; Truhlar, D. G. ChemPhysChem 2005, 6, 1853-1865 (doi:10.1002/cphc.200400602).
- "Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase," Pu, J.; Gao, J.; Truhlar, D. G. J. Phys. Chem. B 2005, 109, 8551-8556 (doi:10.1021/jp051184c).
- "Temperature Dependence of Carbon-13 Kinetic Isotope Effects of Importance to Global Climate Change," Lin, H.; Zhao, Y.; Ellingson, B. A.; Pu, J.; Truhlar, D. G. J. Am. Chem. Soc. 2005, 127, 2830-2831 (doi:10.1021/ja0434026).
- "Benchmark Calculations of Reaction Energies, Barrier Heights, and Transition State Geometries for Hydrogen Abstraction from Methanol by a Hydrogen Atom," Pu, J.; Truhlar, D. G. J. Phys. Chem. A 2005, 109, 773-778 (doi:10.1021/jp045574v).
- "Use of Block Hessians for the Optimization of Molecular Geometries," Pu, J.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1, 54-60 (doi:10.1021/ct0400020).
- "Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method," Pu, J.; Gao, J.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 5454-5463 (doi:10.1021/jp049529z).
- "Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics using Partial Electronic Structure Hessians," Lin, H.; Pu, J.; Albu, T. V.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 4112-4124 (doi:10.1021/jp049972+).
- "Tests of Second-Generation and Third-Generation Density Functionals for Thermochemical Kinetics," Zhao, Y.; Pu, J.; Lynch, B. J. Truhlar, D. G. Phys. Chem. Chem. Phys. 2004, 6, 673-676 (doi:10.1039/B316260E).
- "Benchmark Results for Hydrogen Atom Transfer between Carbon Centers and Validation of Electronic Structure Methods for Bond Energies and Barrier Heights," Dybala-Defratyka, A.; Paneth, P.; Pu, J.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 2475-2486 (doi:10.1021/jp037312j).
- "Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics," Pu, J.; Gao, J.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 632-650 (doi:10.1021/jp036755k).
- "Lateral Confinement of Image Electron Wave Function by an Interfacial Dipole Lattice," Dutton, G.; Pu, J.; Truhlar, D. G.; Zhu, X. -Y. J. Chem. Phys. 2003, 118, 4337 (doi:10.1063/1.1556848).
- "Tests of Potential Energy Surfaces for H + CH4 → CH3 + H2: Deuterium and Muonium Kinetic Isotope Effects for the Forward and Reverse Reaction," Pu, J.; Truhlar, D. G. J. Chem. Phys. 2002, 117, 10675 (doi:10.1063/1.1518471).
- "Validation of Variational Transition State Theory with Multidimensional Tunneling Contributions against Accurate Quantum Mechanical Dynamics for H + CH4 → CH3 + H2 in an Extended Temperature Interval," Pu, J.; Truhlar, D. G. J. Chem. Phys. 2002, 117, 1479 (doi:10.1063/1.1485063).
- "Parametrized Direct Dynamics Study of Rate Constants of H with CH4 from 250 to 2400 K," Pu, J.; Truhlar, D. G. J. Chem. Phys. 2002, 116, 1468 (doi:10.1063/1.1427917).
- "Test of Variational Transition State Theory with Multidimensional Tunneling Contributions Against an Accurate Full-Dimensional Rate Constant Calculation for a Six-Atom system," Pu, J.; Corchado, J. C.; Truhlar, D. G. J. Chem. Phys. 2001, 115, 6266 (doi:10.1063/1.1398581).