Taka AA, Lu S-Y, Gowland D, Zuehlsdorff TJ, Corzo HH, Pribram-Jones A, Shi L, Hratchian HP, Isborn CM. Comparison of Linear Response Theory, Projected Initial Maximum Overlap Method, and Molecular Dynamics-Based Vibronic Spectra: The Case of Methylene Blue. Journal of Chemical Theory and Computation. 2022;18(5):3039-3051.
Bhat HS, Collins K, Gupta P, Isborn CM. Dynamic Learning of Correlation Potentials for a Time-Dependent Kohn-Sham System. In: Firoozi R, Mehr N, Yel E, Antonova R, Bohg J, Schwager M, Kochenderfer M, Firoozi R, Mehr N, Yel E, et al. Proceedings of The 4th Annual Learning for Dynamics and Control Conference. Vol. 168. PMLR; 2022. pp. 546–558.
We develop methods to learn the correlation potential for a time-dependent Kohn-Sham (TDKS) system in one spatial dimension. We start from a low-dimensional two-electron system for which we can numerically solve the time-dependent Schrodinger equation; this yields electron densities suitable for training models of the correlation potential. We frame the learning problem as one of optimizing a least-squares objective subject to the constraint that the dynamics obey the TDKS equation. Applying adjoints, we develop efficient methods to compute gradients and thereby learn models of the correlation potential. Our results show that it is possible to learn values of the correlation potential such that the resulting electron densities match ground truth densities. We also show how to learn correlation potential functionals with memory, demonstrating one such model that yields reasonable results for trajectories outside the training set.
Shedge SV, Zuehlsdorff TJ, Khanna A, Conley S, Isborn CM. Explicit environmental and vibronic effects in simulations of linear and nonlinear optical spectroscopy. The Journal of Chemical Physics. 2021;154(8):084116.
Dunnett AJ, Gowland D, Isborn CM, Chin AW, Zuehlsdorff TJ. Influence of non-adiabatic effects on linear absorption spectra in the condensed phase: Methylene blue. The Journal of Chemical Physics. 2021;155(14):144112.
Lu S-Y, Zuehlsdorff TJ, Hong H, Aguirre VP, Isborn CM, Shi L. The Influence of Electronic Polarization on Nonlinear Optical Spectroscopy. The Journal of Physical Chemistry B. 2021;125(44):12214-12227.
Seritan S, Bannwarth C, Fales BS, Hohenstein EG, Isborn CM, Kokkila-Schumacher SIL, Li X, Liu F, Luehr N, Snyder JW, et al. TeraChem: A graphical processing unit-accelerated electronic structure package for large-scale ab initio molecular dynamics. WIREs Computational Molecular Science. 2021;11(2):e1494.
Abstract TeraChem was born in 2008 with the goal of providing fast on-the-fly electronic structure calculations to facilitate ab initio molecular dynamics studies of large biochemical systems such as photoswitchable proteins and multichromophoric antenna complexes. Originally developed for videogaming applications, graphics processing units (GPUs) offered a low-cost parallel computer architecture that became more accessible for general-purpose GPU computing with the release of CUDA in 2007. The evaluation of the electron repulsion integrals (ERIs) is a major bottleneck in electronic structure codes and provides an attractive target for acceleration on GPUs. Thus, highly efficient routines for evaluation of and contractions between the ERIs and density matrices were implemented in TeraChem. Electronic structure methods were developed and implemented to leverage these integral contraction routines, resulting in the first quantum chemistry package designed from the ground up for GPUs. This GPU acceleration makes TeraChem capable of performing large-scale ground and excited state calculations in the gas and condensed phase. Today, TeraChem’s speed forms the basis for a suite of quantum chemistry applications, including optimization and dynamics of proteins, automated and interactive chemical discovery tools, and large-scale nonadiabatic dynamics simulations. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry Structure and Mechanism > Computational Biochemistry and Biophysics
Zuehlsdorff TJ, Shedge SV, Lu S-Y, Hong H, Aguirre VP, Shi L, Isborn CM. Vibronic and Environmental Effects in Simulations of Optical Spectroscopy. Annual Review of Physical Chemistry. 2021;72(1):165-188.
Including both environmental and vibronic effects is important for accurate simulation of optical spectra, but combining these effects remains computationally challenging. We outline two approaches that consider both the explicit atomistic environment and the vibronic transitions. Both phenomena are responsible for spectral shapes in linear spectroscopy and the electronic evolution measured in nonlinear spectroscopy. The first approach utilizes snapshots of chromophore-environment configurations for which chromophore normal modes are determined. We outline various approximations for this static approach that assumes harmonic potentials and ignores dynamic system-environment coupling. The second approach obtains excitation energies for a series of time-correlated snapshots. This dynamic approach relies on the accurate truncation of the cumulant expansion but treats the dynamics of the chromophore and the environment on equal footing. Both approaches show significant potential for making strides toward more accurate optical spectroscopy simulations of complex condensed phase systems.
Zuehlsdorff TJ, Hong H, Shi L, Isborn CM. Influence of Electronic Polarization on the Spectral Density. The Journal of Physical Chemistry B. 2020;124(3):531-543.
Accurate spectral densities are necessary for computing realistic exciton dynamics and nonlinear optical spectra of chromophores in condensed-phase environments, including multichromophore pigment–protein systems. However, due to the significant computational cost of computing spectral densities from first principles, requiring many thousands of excited-state calculations, most simulations of realistic systems rely on treating the environment as fixed-point charges. Here, using a number of representative systems ranging from solvated chromophores to the photoactive yellow protein (PYP), we demonstrate that the quantum mechanical (QM) electronic polarization of the environment is key to obtaining accurate spectral densities and line shapes within the cumulant framework. We show that the QM environment can enhance or depress the coupling of fast chromophore degrees of freedom to the energy gap, altering the electronic–vibrational coupling and the resulting vibronic progressions in the absorption spectrum. In analyzing the physical origin of peaks in the spectral density, we identify vibrational modes that couple the electron and the hole as being particularly sensitive to the QM screening of the environment. For PYP, we reveal the need for careful determination of the appropriate QM region to obtain reliable spectral densities. Our results indicate that the QM polarization of the environment can be crucial not just for excitation energies but also for electronic–vibrational coupling in complex systems with implications for the correct modeling of linear and nonlinear optical spectroscopy in the condensed phase as well as energy transfer in pigment–protein complexes.