About this blog

Hi, welcome to my blog. I would like to use this blog to share some thoughts on software development, machine learning, computational chemistry, and my hobbies, such as homelab, 3D printing, photography, and maybe games (?).

About the username “tautomer”

It was the end of 2015 (or beginning of 2016). I was about to register an account for an online game the World of Warships (WoWS). I had a hard time to pick a username. Suddenly, I noticed the paper I was reading, which was sitting just by my right hand. The title of the paper was “Enol Tautomers of Watson−Crick Base Pair Models Are Metastable Because of Nuclear Quantum Effects”. Since then, I have been using this username in many different places.

About me

I am theoretical chemist trying to understand chemical reactions through molecular dynamics simulations. Currently, I am working on building a deep neural network framework for predicting excited state properties. Before joining LANL as a postdoc, I did my PhD at University of Rochester. You can download my resume here.

Skills

• Software development
• Scientific machine learning
• Molecular dynamics
• Quantum chemistry
• High-performance computing

Work experience

• Postdoc, Theoretical Division, Los Alamos National Laboratory. Jan 2022 - now
• Research assistant, Department of Chemistry, University of Rochester. Jan 2016 - Dec 2021

Education

• University of Rochester, Ph.D. in theoretical chemistry, Dec. 2021
• Wuhan University, B.S. in chemistry, Jul. 2014

Publications

For the ones listed with a cover art, I made all of them.

• Theoretical
  • Li, X.; Lubbers, N.; Tretiak, S.; Barros, K.; Zhang, Y. Machine Learning Framework for Modeling Exciton-Polaritons in Molecular Materials. J. Chem. Theory Comput. 2024, 20, 891-901
  • Li, X.; Zhang, Y. First-principles molecular quantum electrodynamics theory at all coupling strengths. Submitted to Nat. Commun.
  • Weight, B. M.; Li, X.; Zhang, Y. Theory and Modeling of Light-Matter Interactions in Chemistry: Current and Future. Phys. Chem. Chem. Phys. 2023, 25, 31554-31577 with front outside cover
  • Freixas, V. M.; Malone, W.; Li, X.; Song, H.; Negrín-Yuvero, H.; Pérez‐Castillo, R.; White, A.; Nelson, T.; Makhov, D. V.; Shalashilin, D. V.; Zhang, Y.; Fedik, N.; Kulichenko, M.; Messerly, R. A.; Mohanam, L. N.; Sharifzadeh, S.; Bastida, A.; Mukamel, S.; Fernandez‐Alberti, S.; Tretiak, S. NEXMD V2.0 Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations. J. Chem. Theory and Comput. 2023, 19, 5356–5368
  • Mandal, A.; Taylor, M. A. D.; Weight, B. M.; Koessler E. R.; Li, X.; Huo, P. Theoretical Advances in Polariton Chemistry and Molecular Cavity Quantum Electrodynamics. Chem. Rev. 2023, 123, 9786–9879
  • Mandal, A.; Li, X.; Huo, P. Theory of Vibrational Polariton Chemistry in the Collective Coupling Regime. J. Chem. Phys. 2022, 156, 014101
  • Li, X.; Mandal, A.; Huo, P. Theory of Mode-Selective Chemistry through Polaritonic Vibrational Strong Coupling. J. Phys. Chem. Lett. 2021, 12, 6974–6982
  • Li, X.; Huo, P. Investigating Tunneling-Controlled Chemical Reactions through Ab Initio Ring Polymer Molecular Dynamics. J. Phys. Chem. Lett. 2021, 12, 6714–6721 with inner cover
  • Li, X.; Mandal, A.; Huo, P. Cavity Frequency-Dependent Theory for Vibrational Polariton Chemistry. Nat. Commun. 2021, 12, 1315 Featured article

• Nanoscience (during bachelor’s)

  • Wang, J.; Wei, Y.; Hu, X.; Fang, YY.; Li, X.; Liu, J.; Wang, S.; Yuan, Q. Protein Activity Regulation: Inhibition by Closed-Loop Aptamer-Based Structures and Restoration by Near-IR Stimulation. J. Am. Chem. Soc. 2015, 137, 10576-10584
  • Wu, S.; Shi. E.; Yang, Y.; Xu, W.; Li, X.; Cao, A. Direct fabrication of carbon nanotube-graphene hybrid films by a blown bubble method. Nano Res. 2015, 8, 1746-1754
  • Yang, Y.; Li, P.; Wu, S.; Li, X.; Shi, E.; Shen, Q.; Wu, D.; Xu, W.; Cao, A.; Yuan, Q. Hierarchically Designed Three‐Dimensional Macro/Mesoporous Carbon Frameworks for Advanced Electrochemical Capacitance Storage. Chem. Eur. J. 2015, 21, 6157-6164
  • Hu, X.; Wei, T.; Wang, J.; Liu, ZE.; Li, X.; Zhang, B.; Li, Z.; Li, L.; Yuan, Q. Near-infrared-light mediated ratiometric luminescent sensor for multimode visualized assays of explosives. Anal. Chem. 2014, 86, 10484-10491
  • Wang, J.; Wei, T.; Li, X.; Zhang, B.; Wang, J.; Huang, C.; Yuan, Q. Near-Infrared-Light-Mediated Imaging of Latent Fingerprints based on Molecular Recognition. Angew. Chem. Int. Ed. 2014, 53, 1616-1620 with inside back cover
  • Li, LL.; Xie, M.; Wang. J.; Li, X.; Wang, C.; Yuan, Q.; Pang, DW.; Lu, Y.; Tan, W. A vitamin-responsive mesoporous nanocarrier with DNA aptamer-mediated cell targeting. Chem. Commun. 2013, 49, 5823-5825

Technical side of this blog

This blog is made using Jekyll by Peter Roelants and is hosted on GitHub Pages. To know more how this blog is made, and how he converted notebooks to blog posts see hosting Jupyter notebooks on a blog. The gallery code is modified from this repo and the css is modified based on the gallery.css provided here. The syntax highlight theme is One Dark taken from here.

Please get in touch with me if you have any comments or questions. You can contact me via the channels below: