Evidence map›Paper›PMID 40302849›Full record

ArticleThe journal of physical chemistry. C, Nanomaterials and interfaces2025

Automated Pynta-Based Curriculum for ML-Accelerated Calculation of Transition States.

Trevor Price, Saurabh Sivakumar, Matthew S Johnson, Judit Zádor, Ambarish Kulkarni

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Article in The journal of physical chemistry. C, Nanomaterials and interfaces, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

5 authors.

Trevor PriceDepartment of Chemical Engineering, University of California, Davis, California 95616, United States.
Saurabh SivakumarDepartment of Chemical Engineering, University of California, Davis, California 95616, United States.
Matthew S JohnsonCombustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States.
Judit ZádorCombustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States.ORCID https://orcid.org/0000-0002-9123-8238
Ambarish KulkarniDepartment of Chemical Engineering, University of California, Davis, California 95616, United States.ORCID https://orcid.org/0000-0001-9834-8264

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Microkinetic models (MKMs) are widely used within the computational heterogeneous catalysis community to investigate complex reaction mechanisms, to rationalize experimental trends, and to accelerate the rational design of novel catalysts. However, constructing these models requires computationally expensive and manually tedious density functional theory (DFT) calculations for identifying transition states for each elementary reaction within the MKM. To address these challenges, we demonstrate a novel protocol that uses the open-source kinetics workflow tool Pynta to automate the iterative training of a reactive machine learning potential (rMLP). Specifically, using the silver-catalyzed partial oxidation of methanol as a prototypical example, we first demonstrate our workflow by training an rMLP to accelerate the parallel calculation of DFT-quality transition states for all 53 reactions, achieving a 7× speedup compared to a DFT-only strategy. Detailed analysis of our training curriculum reveals the shortcomings of using an adaptive sampling scheme with a single rMLP model to describe all reactions within the MKM simultaneously. We show that these limitations can be overcome using a balanced "reaction class" approach that uses multiple rMLP models, each describing a single class of similar transition states. Finally, we demonstrate that our Pynta-based workflow is also compatible with large pretrained foundational models. For example, by fine-tuning a top-performing graph neural network potential trained on the OC20 dataset, we observe an impressive 20× speedup with an 89% success rate in identifying transition states. This work highlights the synergistic potential of integrating automated tools with machine learning to advance catalysis research.

Identifiers

PMID40302849
PMCPMC12035851

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.