Publications

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 (doi:10.1021/acs.jpcb.4c04100).
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 (doi:10.1021/acs.jpcb.4c01011).
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 (doi:10.1002/adom.202400801).
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 (doi:10.1002/jcc.27269; PMID: 38082539; preprint: doi:10.26434/chemrxiv-2023-545gw).
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 (doi:10.1016/j.cpc.2023.108933).
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 (doi:10.1021/acs.jctc.3c00973; PMID:37943896; preprint: doi:10.26434/chemrxiv-2023-mrm25) .
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 (doi:10.1021/acsnano.3c06047).
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 (doi:10.1063/5.0156327 PMID:37530109).
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 (doi:10.1016/j.bpc.2023.106992 PMID: 36933500).
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 (doi:10.1016/j.ijoes.2023.100077).
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 (doi:10.1039/D2RA08180F PMID: 36760282).
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 (doi:10.1039/d2cp02820d; PMID:36222412; selected as a 2022 PCCP HOT Article).
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 (doi:10.1021/acscatal.2c02993; preprint: doi:10.26434/chemrxiv-2022-0rb4h).
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 (doi:10.1021/acs.jpcb.2c02262; preprint: doi:10.26434/chemrxiv-2022-0zg7j).
46. "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).
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 (doi:10.1021/acs.jctc.1c00565; PMID:34468138).
44. "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).
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 (doi: 10.1039/d1ra04716g).
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 (doi: 10.1177/0003702820915506).
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 (doi: 10.1039/c9cp02593f; PMID:31508625).
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 (doi:10.1021/acs.jpca.8b12345).
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; doi:10.3390/molecules23102652; PMID:30332773).
38. "All-atom Simulations of Torque Generation in F₁-ATPase," Pu, J.; Nam, K.; Karplus, M., submitted.
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 (doi:10.1039/C7NR04874B).
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 (doi:10.1016/bs.mie.2016.05.054; PMID:27498639).
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 (doi:10.1063/1.4934880; PMID:26547162).
34. "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).
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 (doi:10.1063/1.4871871).
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 (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).
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 (doi:10.1016/j.bpc.2013.07.014).
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 (doi:10.1039/C3CP50965F; SI: movie_S1& movie_S2; preprint: arXiv:1304.0052 [q-bio.BM]).
28. "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).
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 (doi:10.1002/chem.201101821).

    --- Before IUPUI ---

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.
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 (doi:10.1021/jp808952m).
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 (doi:10.1002/jcc.21287).
23. "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.
22. "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).
21. "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).
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 (doi:10.1021/cr050293k).
19. "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). .
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 (doi:10.1021/ja061585l).
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. Theory Comput. 2006, 2, 895-904 (doi:10.1021/ct060032y).
16. "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).
15. "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).
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 (doi:10.1021/jp051184c).
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 (doi:10.1021/ja0434026).
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 (doi:10.1021/jp045574v).
11. "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).
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 (doi:10.1021/jp049529z).
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 (doi:10.1021/jp049972+).
8. "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).
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, 2475-2486 (doi:10.1021/jp037312j).
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 (doi:10.1021/jp036755k).
5. "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).
4. "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).
3. "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).
2. "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).
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 (doi:10.1063/1.1398581).