Academic Appointments

All Publications

  • ChemPix: automated recognition of hand-drawn hydrocarbon structures using deep learning CHEMICAL SCIENCE Weir, H., Thompson, K., Woodward, A., Choi, B., Braun, A., Martinez, T. J. 2021

    View details for DOI 10.1039/d1sc02957f

    View details for Web of Science ID 000673126700001

  • The non-adiabatic nanoreactor: towards the automated discovery of photochemistry CHEMICAL SCIENCE Pieri, E., Lahana, D., Chang, A. M., Aldaz, C. R., Thompson, K. C., Martinez, T. J. 2021

    View details for DOI 10.1039/d1sc00775k

    View details for Web of Science ID 000648669700001

  • TeraChem Cloud: A High-Performance Computing Service for Scalable Distributed GPU-Accelerated Electronic Structure Calculations. Journal of chemical information and modeling Seritan, S. n., Thompson, K. n., Martínez, T. J. 2020


    The encapsulation and commoditization of electronic structure arise naturally as interoperability, and the use of nontraditional compute resources (e.g., new hardware accelerators, cloud computing) remains important for the computational chemistry community. We present TeraChem Cloud, a high-performance computing service (HPCS) that offers on-demand electronic structure calculations on both traditional HPC clusters and cloud-based hardware. The framework is designed using off-the-shelf web technologies and containerization to be extremely scalable and portable. Within the HPCS model, users can quickly develop new methods and algorithms in an interactive environment on their laptop while allowing TeraChem Cloud to distribute ab initio calculations across all available resources. This approach greatly increases the accessibility of hardware accelerators such as graphics processing units (GPUs) and flexibility for the development of new methods as additional electronic structure packages are integrated into the framework as alternative backends. Cost-performance analysis indicates that traditional nodes are the most cost-effective long-term solution, but commercial cloud providers offer cutting-edge hardware with competitive rates for short-term large-scale calculations. We demonstrate the power of the TeraChem Cloud framework by carrying out several showcase calculations, including the generation of 300,000 density functional theory energy and gradient evaluations on medium-sized organic molecules and reproducing 300 fs of nonadiabatic dynamics on the B800-B850 antenna complex in LH2, with the latter demonstration using over 50 Tesla V100 GPUs in a commercial cloud environment in 8 h for approximately $1250.

    View details for DOI 10.1021/acs.jcim.9b01152

    View details for PubMedID 32267693

  • Construction of reaction networks using the ab initio nanoreaction coupled to a kinetic model Meisner, J., Zhu, X., Thompson, K., Hirai, H., Martinez, T. AMER CHEMICAL SOC. 2019
  • Methane combustion studied using the ab initio nanoreactor approach combined with kinetic modeling Meisner, J., Zhu, X., Hirai, H., Thompson, K., Martinez, T. AMER CHEMICAL SOC. 2019
  • Geodesic interpolation for reaction pathways JOURNAL OF CHEMICAL PHYSICS Zhu, X., Thompson, K. C., Martinez, T. J. 2019; 150 (16)

    View details for DOI 10.1063/1.5090303

    View details for Web of Science ID 000466698700009

  • Thinking inside boxes: Modularizing electronic structure and ab initio molecular dynamics Seritan, S., Thompson, K., Fales, S., Song, C., Parrish, R., Hohenstein, E., Martinez, T. AMER CHEMICAL SOC. 2019
  • Large-Scale Functional Group Symmetry-Adapted Perturbation Theory on Graphical Processing Units JOURNAL OF CHEMICAL THEORY AND COMPUTATION Parrish, R. M., Thompson, K. C., Martinez, T. J. 2018; 14 (3): 1737–53


    Symmetry-adapted perturbation theory (SAPT) is a valuable method for analyzing intermolecular interactions. The functional group SAPT partition (F-SAPT) has been introduced to provide additional insight into the origins of noncovalent interactions. Until now, SAPT analysis has been too costly for large ligand-protein complexes where it could provide key insights for chemical modifications that might improve ligand binding. In this paper, we present a large-scale implementation of a variant of F-SAPT. Two pragmatic choices are made from the outset to render the problem tractable: (1) Ab initio computation of dispersion and exchange-dispersion is replaced with Grimme's empirical dispersion correction. (2) Basis sets with augmented functions are avoided to allow for efficient integral screening. These choices allow the F-SAPT analysis to be written largely in terms of Coulomb and exchange matrix builds which have been implemented efficiently on graphical processing units (GPUs). Our formulation of F-SAPT is routinely applicable to molecules with well over 3000 atoms and 25,000 basis functions and is particularly optimized for the case where one monomer is significantly larger than the other. This is demonstrated explicitly with results from F-SAPT analysis of the full indinavir @ HIV-II protease complex (PDB ID 1HSG ) in a polarized double-ζ basis.

    View details for PubMedID 29345933