Joseph Kelly

All Publications

• Two-Dimensional Electronic Spectroscopy in the Condensed Phase Using Equivariant Transformer Accelerated Molecular Dynamics Simulations. The journal of physical chemistry letters Kelly, J., Hu, F., Damiani, A., Chen, M. S., Snider, A., Son, M., Lee, A., Gupta, P., Montoya-Castillo, A., Zuehlsdorff, T. J., Schlau-Cohen, G. S., Isborn, C. M., Markland, T. E. 2025: 5561-5569

  Abstract

  Two-dimensional electronic spectroscopy (2DES) provides rich information about how the electronic states of molecules, proteins, and solid-state materials interact with each other and their surrounding environment. Atomistic molecular dynamics simulations offer an appealing route to uncover how nuclear motions mediate electronic energy relaxation and their manifestation in electronic spectroscopies but are computationally expensive. Here we show that by using an equivariant transformer-based machine learning architecture trained with only 2500 ground state and 100 excited state electronic structure calculations, one can construct accurate machine-learned potential energy surfaces for both the ground-state electronic surface and excited-state energy gap. We demonstrate the utility of this approach for simulating the dynamics of Nile blue in ethanol, where we experimentally validate and decompose the simulated 2DES to establish the nuclear motions of the chromophore and the solvent that couple to the excited state, connecting the spectroscopic signals to their molecular origin.

  View details for DOI 10.1021/acs.jpclett.5c00911

  View details for PubMedID 40434198

• Electron transfer at electrode interfaces via a straightforward quasiclassical fermionic mapping approach. The Journal of chemical physics Jung, K. A., Kelly, J., Markland, T. E. 2023; 159 (1)

  Abstract

  Electron transfer at electrode interfaces to molecules in solution or at the electrode surface plays a vital role in numerous technological processes. However, treating these processes requires a unified and accurate treatment of the fermionic states of the electrode and their coupling to the molecule being oxidized or reduced in the electrochemical processes and, in turn, the way the molecular energy levels are modulated by the bosonic nuclear modes of the molecule and solvent. Here we present a physically transparent quasiclassical scheme to treat these electrochemical electron transfer processes in the presence of molecular vibrations by using an appropriately chosen mapping of the fermionic variables. We demonstrate that this approach, which is exact in the limit of non-interacting fermions in the absence of coupling to vibrations, is able to accurately capture the electron transfer dynamics from the electrode even when the process is coupled to vibrational motions in the regimes of weak coupling. This approach, thus, provides a scalable strategy to explicitly treat electron transfer from electrode interfaces in condensed-phase molecular systems.

  View details for DOI 10.1063/5.0156136

  View details for PubMedID 37409707