67 Publications (Page 1 of 3)
2023
Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation. The Journal of Chemical Physics
. | Journal Article
 
Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions. Journal of Chemical Theory and Computation
. | Journal Article
 
Hybrid Metal-Ligand Interfacial Dipole Engineering of Functional Plasmonic Nanostructures for Extraordinary Responses of Optoelectronic Properties.
Hati, Sumon⋅Yang, Xuehui⋅Gupta, Prashant⋅Muhoberac, Barry B⋅Pu, Jingzhi⋅Zhang, Jing and Sardar, Rajesh
ACS nano, August 14, 2023. | Journal Article
 
Hybrid Metal–Ligand Interfacial Dipole Engineering of Functional Plasmonic Nanostructures for Extraordinary Responses of Optoelectronic Properties. ACS Nano
. | Journal Article
 
Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations. RSC Advances
. | Journal Article
 
Revealing intrinsic changes of DNA induced by spore photoproduct lesion through computer simulation.
Hege, Mellisa⋅Li, Lei and Pu, Jingzhi
Biophysical chemistry, vol. 296, pp. 106992, May 2023. | Journal Article
 
Training machine learning potentials for reactive systems: A Colab tutorial on basic models.
Pan, Xiaoliang⋅Snyder, Ryan⋅Wang, Jia-Ning⋅Lander, Chance⋅Wickizer, Carly⋅Van, Richard⋅Chesney, Andrew⋅Xue, Yuanfei⋅Mao, Yuezhi⋅Mei, Ye⋅Pu, Jingzhi and Shao, Yihan
Journal of computational chemistry, December 11, 2023. | Journal Article
2022
Accelerating ab initio QM/MM Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semi-empirical QM/MM Hamiltonian
Pan, Xiaoliang⋅Van, Richard⋅Epifanovsky, Evgeny⋅Liu, Jian⋅Pu, Jingzhi⋅Nam, Kwangho and Shao, Yihan
American Chemical Society (ACS)
 
Accelerating Ab Initio Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian
Pan, Xiaoliang⋅Van, Richard⋅Epifanovsky, Evgeny⋅Liu, Jian⋅Pu, Jingzhi⋅Nam, Kwangho and Shao, Yihan
The Journal of Physical Chemistry B. | Journal Article
 
Facilitating ab initio QM/MM free energy simulations by Gaussian process regression with derivative observations.
Snyder, Ryan⋅Kim, Bryant⋅Pan, Xiaoliang⋅Shao, Yihan and Pu, Jingzhi
Physical chemistry chemical physics : PCCP, October 12, 2022. | Journal Article
 
Facilitating ab initio QM/MM free energy simulations by Gaussian process regression with derivative observations. Physical Chemistry Chemical Physics
 
Photoinduced Site-Selective Functionalization of Aliphatic C–H Bonds by Pyridine N-oxide Based HAT Catalysts. ACS Catalysis
Wang, Ban⋅Pettenuzzo, Cristina Ascenzi⋅Singh, Jujhar⋅Mccabe, Gavin E.⋅Clark, Logan⋅Young, Ryan⋅Pu, Jingzhi and Deng, Yongming
2021
Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability.
Kim, Bryant⋅Kim, Bryant⋅Shao, Yihan⋅Shao, Yihan⋅Pu, Jingzhi and Pu, Jingzhi
Journal of chemical theory and computation, November 1, 2021. | Journal Article
 
Interligand communication in a metal mediated LL\primeCT system – a case study
Dille, Sara A.⋅Colston, Kyle J.⋅Ratvasky, Stephen C.⋅Pu, Jingzhi and Basu, Partha
pp. 24381–24386. | Journal Article
 
Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions
Pan, Xiaoliang⋅Pan, Xiaoliang⋅Yang, Junjie⋅Yang, Junjie⋅Van, Richard⋅Van, Richard⋅Epifanovsky, Evgeny⋅Epifanovsky, Evgeny⋅Ho, Junming⋅Ho, Junming⋅Huang, Jing⋅Huang, Jing⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Mei, Ye⋅Mei, Ye⋅Nam, Kwangho⋅Nam, Kwangho⋅Shao, Yihan and Shao, Yihan
Journal of Chemical Theory and Computation. | Journal Article
 
Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force
Kim, Bryant⋅Snyder, Ryan⋅Nagaraju, Mulpuri⋅Zhou, Yan⋅Ojeda-May, Pedro⋅Keeton, Seth⋅Hege, Mellisa⋅Shao, Yihan and Pu, Jingzhi
Journal of Chemical Theory and Computation. | Journal Article
2020
EXPRESS: Identifying Thermal Decomposition Products of Nitrate Ester Explosives Using Gas Chromatography-Vacuum Ultraviolet Spectroscopy: An Experimental and Computational Study
Cruse, Courtney⋅Cruse, Courtney⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Goodpaster, John Vincent and Goodpaster, John Vincent
Applied spectroscopy, pp. 3702820915506, 2020-Mar-20. | Journal Article
 
EXPRESS: Identifying Thermal Decomposition Products of Nitrate Ester Explosives Using Gas Chromatography–Vacuum Ultraviolet Spectroscopy: An Experimental and Computational Study
Cruse, Courtney⋅Cruse, Courtney⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Goodpaster, John Vincent and Goodpaster, John Vincent
Applied Spectroscopy, pp. 3702820915506, 2020-03-20. | Journal Article
2019
Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching.
Pan, Xiaoliang⋅Pan, Xiaoliang⋅Li, Pengfei⋅Li, Pengfei⋅Ho, Junming⋅Ho, Junming⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Mei, Ye⋅Mei, Ye⋅Shao, Yihan and Shao, Yihan
Physical chemistry chemical physics : PCCP, September 11, 2019. | Journal Article
 
Exploring Cycloreversion Reaction of Cyclobutane Pyrimidine Dimers Quantum Mechanically
Huang, Donglian⋅Chen, Shanfeng⋅Pu, Jingzhi⋅Tan, Xuecai and Zhou, Yan
The journal of physical chemistry. A, vol. 123, (no. 10), pp. 2039, 2019-Mar-14. | Journal Article
2018
Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method
Zhou, Yan⋅Ojeda-May, Pedro⋅Nagaraju, Mulpuri⋅Kim, Bryant and Pu, Jingzhi
Molecules (Basel, Switzerland), vol. 23, (no. 10), pp. 2652, 2018-Oct-16. | Journal Article
2017
Elucidating the role of surface passivating ligand structural parameters in hole wave function delocalization in semiconductor cluster molecules
Teunis, Meghan B⋅Teunis, Meghan B⋅Teunis, Meghan B⋅Teunis, Meghan B⋅Nagaraju, Mulpuri⋅Nagaraju, Mulpuri⋅Nagaraju, Mulpuri⋅Nagaraju, Mulpuri⋅Dutta, Poulami⋅Dutta, Poulami⋅Dutta, Poulami⋅Dutta, Poulami⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Muhoberac, Barry B⋅Muhoberac, Barry B⋅Muhoberac, Barry B⋅Muhoberac, Barry B⋅Sardar, Rajesh⋅Sardar, Rajesh⋅Sardar, Rajesh⋅Sardar, Rajesh⋅Agarwal, Mangilal⋅Agarwal, Mangilal⋅Agarwal, Mangilal and Agarwal, Mangilal
Nanoscale, vol. 9, (no. 37), pp. 14138, 2017-Sep-28. | Journal Article
 
Elucidating the role of surface passivating ligand structural parameters in hole wave function delocalization in semiconductor cluster moleculesElectronic supplementary information (ESI) available: UV-visible absorption, PL, 1H NMR, XRD, EDS, and FTIR spectra; a TEM image of mixed Py-DTC-/OLA-passivated (CdSe)34 SCMs; tables of HOMO and LUMO energies of ligands; and temperature dependent PL decay constants. See DOI: 10.1039/c7nr04874b
Teunis, Meghan B⋅Teunis, Meghan B⋅Teunis, Meghan B⋅Teunis, Meghan B⋅Nagaraju, Mulpuri⋅Nagaraju, Mulpuri⋅Nagaraju, Mulpuri⋅Nagaraju, Mulpuri⋅Dutta, Poulami⋅Dutta, Poulami⋅Dutta, Poulami⋅Dutta, Poulami⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Pu, Jingzhi⋅Muhoberac, Barry B⋅Muhoberac, Barry B⋅Muhoberac, Barry B⋅Muhoberac, Barry B⋅Sardar, Rajesh⋅Sardar, Rajesh⋅Sardar, Rajesh⋅Sardar, Rajesh⋅Agarwal, Mangilal⋅Agarwal, Mangilal⋅Agarwal, Mangilal and Agarwal, Mangilal
(no. 37), pp. 14138, 20170928. | Journal Article
2016
Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path-Force Matching QM/MM Method.
Zhou, Y⋅Ojeda-May, P⋅Nagaraju, M and Pu, J
Methods in enzymology, vol. 577, pp. 185-212, 2016. | Journal Article
2015
Multiscale QM/MM Simulations of ATP Hydrolysis Mechanism in ABC-Transporters
Pu, Jingzhi
Biophysical Journal, vol. 108, (no. 2), pp. 146a, 2015-01-27. | Journal Article