Publications

Associate Professor

Department of Chemistry and Chemical Biology
Indiana University Indianapolis
402 N. Blackford St., LD 326
Indianapolis, IN, USA

[ORCID]   [Google Scholar]   [GitHub]   [CV]   [E-mail]

Publications

  1. “Enhancing Gaussian Process Regression-Accelerated QM/MM Free Energy Simulations Using Atomic Environment Descriptors,” Snyder, R.; Li, D.; Ho, Tinh; Kim, B.; Qazi, H.; Pan, X.; Shao, Y.; Pu, J. J. Chem. Phys. 2026, 164, 114111 (DOI: 10.1063/5.0315012; preprint: ChemRxiv DOI:10.26434/chemrxiv-2025-hg8n7).
  2. “Anisotropically Shaped Plasmonic WO3–x Nanostructure-Driven Ultrasensitive SERS Detection and Machine Learning-Based Differentiation of Nitro-Explosives,” Simas, M. V.; Davis Jr, G. A.; Hati, S.; Pu, J.; Goodpaster, J. V.; Sardar, R. ACS Appl. Mater. Interfaces 2025, 17, 11309–11324 (DOI:10.1021/acsami.4c19673).
  3. “CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed,” Hwang, W.; Austin, S. L.; Blondel, A.; Boittier, E. D.; Boresch, S.; Buck, M.; Buckner, J.; Caflisch, A.; Chang, H.-T.; Cheng, X.; Choi, K. Y.; Chu, J.-W.; Crowley, M. F.; Cui, Q.; Damjanovic, A.; Deng, Y.; Devereux, M.; Ding, X.; Feig, M. F.; Gao, J.; Glowacki, D. R.; Gonzales, J. E.; Hamaneh, M. B.; Harder, E. D.; Hayes, R. L.; Huang, J.; Huang, Y.; Hudson, P. S.; Im, W.; Islam, S. M.; Jiang, W.; Jones, M. R.; Kaser, S.; Kearns, F. L.; Kern, N. R.; Klauda, J. B.; Lazaridis, T.; Lee, J.; Lemkul, J. A.; Liu, X.; Luo, Y.; MacKerell, Jr. A. D.; Major, D. T.; Meuwly, M.; Nam, K.; Nilsson, L.; Ovchinnikov, V.; Paci, E.; Park, S.; Pastor, R. W.; Pittman, A. R.; Post, C. B.; Prasad, S.; Pu, J.; Qi, Y.; Rathinavelan, T.; Roe, D. R.; Roux, B.; Rowley, C. N.; Shen, J.; Simmonett, A. C.; Sodt, A. J.; Topfer, K.; Upadhyay, M.; van der Vaart, A.; Vazquez-Salazar, L. I.; Venable, R. M.; Warrensford, L. C.; Woodcock, H. L.; Wu, Y.; Brooks, III C. L.; Brooks, B. R.; Karplus, M. J. Phys. Chem. B. 2024, 128 , 9976-10042 (DOI:10.1021/acs.jpcb.4c04100).
  4. “Design of Light‐Induced Solid‐State Plasmonic Rulers via Tethering Photoswitchable Molecular Machines to Gold Nanostructures Displaying Angstrom Length Resolution,” Langlais, S. R.; Hati, S.; Simas, M. V.; Pu, J.; Muhoberac, B. B.; Sardar, R. Adv. Opt. Mater. 2024, 12 , 2400801 (DOI:10.1002/adom.202400801).
  5. “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.
  6. “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).
  7. “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)
  8. “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).
  9. “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).
  10. “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).
  11. “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).
  12. “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, 1000077 (DOI:10.1016/j.ijoes.2023.100077).
  13. “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).
  14. “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 (selected as a 2022 PCCP HOT Article) (DOI:10.1039/D2CP02820D).
  15. “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).
  16. “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).
  17. “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).
  18. “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).
  19. “Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force,” Bryant, K.; 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).
  20. “Interligand Communication in a Metal Mediated LL’CT System – A Case Study,” Dille, S. A.; Colston, K.; Ratvasky, S. C.; Pu, J.; Basu, P. RSC Adv. 2021, 11, 24381-24386 (DOI:10.1039/D1RA04716G).
  21. “Identifying Thermal Decomposition Products of Nitrate Ester Explosives via Gas Chromatography/Vacuum UV (VUV) Spectroscopy: An Experimental and Computational Study,” Cruse, C. A.; Pu, J.; Goodpaster, J. V. Applied Spec. 2020, 74, 1486-1495 (DOI:10.1177/0003702820915506).
  22. “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).
  23. “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).
  24. “Mapping Free Energy Paths 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 (DOI:10.3390/molecules23102652).
  25. “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).
  26. “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 in Enzymology (Computational approaches for studying enzyme mechanism) 2016, 577, 185-212 (invited Article) (DOI:10.1016/bs.mie.2016.05.054).
  27. “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).
  28. “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).
  29. “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).
  30. “Reaction Path-Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in QM/MM Simulations,” Zhou, Y.; Pu, J. J. Chem. Theory Comput. 2014, 10, 3038-3054 (DOI:10.1021/ct4009624).
  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 (DOI:10.1021/ct400724d).
  32. “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).
  33. “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; see also arXiv:1304.0052).
  34. “Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Cyclobutane Dimers Formed via 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).
  35. “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 IU

  1. “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.
  2. “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).
  3. “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).
  4. “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) .
  5. “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).
  6. “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).
  7. “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).
  8. “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).
  9. “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).
  10. “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).
  11. “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).
  12. “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).
  13. “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).
  14. “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/ja043402).
  15. “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).
  16. “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).
  17. “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).
  18. “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+).
  19. “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).
  20. “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).
  21. “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).
  22. “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).
  23. “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).
  24. “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).
  25. “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).
  26. “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).