James Dean, PhD

Machine Learning Innovations in Chemistry

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Located in Pittsburgh, PA

Resume

Scientist specializing in the intersection of chemistry, machine learning, and software engineering. Computational and experimental background. Highly-motivated researcher, enjoying challenging problems and learning new skills.

Selected Skills

Languages

  • Python (Fluent)
  • JavaScript / HTML / CSS (Intermediate)
  • R / C / MatLab / Fortran (Rusty)

Data Science Packages

  • Scikit-Learn
  • XGBoost
  • Imbalanced-Learn
  • TensorFlow / Keras
  • TPOT
  • Optuna
  • Pandas
  • Numpy

Visualization Tools

  • Matplotlib / PyPlot
  • Seaborn
  • Manim
  • Blender
  • Adobe Substance Painter
  • Origin
  • Microsoft Office

Miscellaneous Tools

  • Git / Git LFS
  • Jenkins CI
  • Atlassian Jira
  • SaltStack
  • Vagrant
  • MongoDB
  • React
  • Environment Modules
  • Redux
  • Cucumber / Gherkin

Cheminformatics Packages

  • RDKit
  • OpenBabel
  • PyMatGen
  • Atomic Simulation Environment (ASE)
  • XenonPy
  • MatMiner
  • Materials Studio

Density-Functional Theory

  • CP2K
  • VASP
  • Quantum Espresso
  • Gaussian

Experience

Data Scientist

PPG Industries, Inc. January 2022 - Present
  • Worked closely with experimental chemists and other ML researchers to accelerate R&D.
  • Developed novel ML tooling for the in-silico analysis of a variety of chemical systems.
  • Engineered software to automate data extraction and processing from internal archives and databases.
  • Delivered presentations training colleagues in software engineering and cheminformatics best-practices.

Computational Scientist

Mat3ra (formerly Exabyte.io) January 2021 - December 2021
  • Supported a team of scientists and engineers as a subject-matter expert in Machine Learning (ML) applications in chemistry.
  • Employed a variety of ML tooling including TensorFlow / Keras (neural networks), Scikit-Learn, and XGBoost.
  • Developed predictive models of chemical properties in a variety of systems (low-D materials, small molecules, perovskites, etc.).
  • Created scientific visualizations to communicate research findings to colleagues, customers, and other stakeholders.
  • Led the design and implementation of a new user-facing ML toolkit, with regression, classification, and clustering capabilities.
  • Delivered new features, bugfixes, and tests for both Python (backend) and JavaScript (frontend) in an Agile environment.
  • Engaged directly with Fortune-500 and Federal Government researchers for continued customer feedback.

PhD Candidate

CANELa Lab, University of Pittsburgh September 2016 - January 2021
  • Delivered a PhD thesis at the intersection of ML and computational chemistry for the high-throughput screening of catalysts.
  • Applied genetic programming to train a model of molecule adsorption to bimetallic materials (published in Science Advances).
  • Worked closely with experimental collaborators to guide the synthesis of new nanoparticles and rationalize experimental results.
  • Led the creation and publication of a database of 5,454 bimetallic nanoparticles of catalytic relevance (published in ACS Nano).
  • Discovered a new crystal structure candidate for CuZrO3 (peer review) via a genetic algorithm and Density-Functional Theory.
  • Led the preparation of 2 proposals (and assisted in 2 others), successfully obtaining over 12-million CPU-hours of compute time.
  • Delivered 6 publications to high-impact scientific journals (H-index 5) and presented results at 14 scientific conferences.
  • Trained junior students (PhDs, Masters, and Undergraduates) in computational chemistry and ML.

Summer Undergraduate Researcher

Keith Lab, University of Pittsburgh May 2015 - August 2015
  • Researched the stability and adsorption properties of metal oxide surfaces, leading to 1 publication.
  • Leveraged the Unix-based HPC Facilities operated by the University of Pittsburgh Center for Simulation and Modeling.
  • Revealed fundamental structural trends in tin oxide catalysts.
  • Developed Python code to automate the submission, output processing, and analysis of calculations.

Undergraduate Researcher

Hartel Lab, Winthrop University January 2013 - May 2016
  • Performed part-time research during the academic year, and full-time research during the Summer of 2014.
  • Implemented novel synthetic procedures for the improved synthesis of aldol products.
  • Leveraged an array of analytical chemistry instrumentation including NMR, Mass Spectrometry, and IR Spectroscopy.
  • Successfully prepared and defended an honors program thesis based upon organic chemistry research.

Education

PhD in Chemical Engineering

University of Pittsburgh (Pittsburgh, PA) September 2016 - January 2021
  • GPA: 3.65 / 4.00
  • PhD Thesis: Computational Design of Optimal Bimetallic Nanoparticles: Bridging Stability with Adsorption

BS in Chemistry (Cum Laude)

Winthrop University (Rock Hill, SC) August 2012 - May 2016
  • GPA: 3.51 / 4.00
  • Concentration in Engineering-Physics
  • Minor in Applied Thesis
  • Honors Thesis: Reaction of Protected Cyanohydrins with Epoxides as an Alternative for the Enantio- and Diastereoselective Production of Aldols

Publications

  1. Dean, J.; Scheffler, M.; Purcell, T. A. R.; Barabash, S. V.; Bhowmik, R.; Bazhirov, T. Interpretable Machine Learning for Materials Design. Journal of Materials Research 2023. 38, 4477-4496. DOI: 10.1557/s43578-023-01164-w arXiv DOI: 10.48550/arXiv.2112.00239
  2. Dean, J.; Yang, Y.; Veser, G.; Mpourmpakis, G. CuZrO3: If it Exists it Should be a Sandwich. Physical Chemistry Chemical Physics 2021. 23, 23748-23757. DOI: 10.1039/D1CP02245H .
  3. Yin, X.; Isenberg, N. M.; Hanselman, C. L.; Dean, J. Mpourmpakis, G. Gounaris, C. E Designing Stable Bimetallic Nanoclusters via an Iterative Two-Step Optimization Approach. Molecular Systems Design & Engineering 2021. 6, 545-557. DOI: 10.1039/D1ME00027F
  4. Abdelgaid, M.; Dean, J.; Mpourmpakis, G. Improving Alkane Dehydrogenation on γ-Al2O3 through Ga Doping. Catalysis Science and Technology 2020. 10, 7194-7202. DOI: 10.1039/D0CY01474E
  5. Dean, J.; Cowan, M.; Estes, J.; Ramadan, M.; Mpourmpakis, G. Rapid Prediction of Bimetallic Mixing Behavior at the Nano Scale. ACS Nano 2019. 14 (7), 8171-8180. DOI: 10.1021/acsnano.0c01586
  6. Tan, K.; Dixit, M.; Dean, J.; Mpourmpakis, G. Predicting Metal-Support Interactions in Oxide-Supported Single-Atom Catalysts. Industry Engineering Chemistry Research 2019. 58 (44), 20236-20246. DOI: 10.1021/acs.iecr.9b04068
  7. Dean, J.; Taylor, M. G.; Mpourmpakis, G. Unfolding Adsorption on Metal Nanoparticles: Connecting Stability with Catalysis. Science Advances 2019. 5 (9), eaax5101. DOI: 10.1126/sciadv.aax5101
  8. Dean, J.; Yang, Y.; Austin, N.; Veser, G.; Mpourmpakis, G. Design of Copper-based Bimetallic Nanoparticles for Carbon Dioxide Adsorption and Activation. ChemSusChem 2018. 11 (7), 1169-1178. Cover Feature of ChemSusChem July 2018 issue). DOI: 10.1002/cssc.201702342
  9. Saravanan, K.; Basdogan, Y.; Dean, J.; Keith, J. A. Computational Investigation of CO2 Electroreduction on Tin Oxide and Predictions of Ti, V, Nb, and Zr Dopants for Improved Catalysis. Journal of Materials Chemistry A 2017. 5, 11756-11763. DOI: 10.1039/C7TA00405B

Conference Presentations

  1. Orienteering in an Uncharted Chemical Space: Searching for an Optimal Bimetallic Nanocatalyst, 2020 AiChE Annual Meeting (Oral Presentation, Virtual)
  2. Generalized Adsorption Models on Metal Nanoparticles, 2020 University of Pittsburgh Department of Chemical and Petroleum Engineering Research Day (Poster Presentation)
  3. Generalized Adsorption Models on Metal Nanoparticles, 2019 AIChE Annual Meeting (Poster Presentation)
  4. Rapid Prediction of Adsorption at the Nano Scale, Pittsburgh Quantum Institute Science2019 Meeting (Poster Presentation)
  5. Size, Shape, and Composition Dependent Adsorption Model on Metal Nanoparticles, 2019 Pittsburgh-Cleveland Catalysis Society Annual Meeting (Poster Presentation)
  6. Computational Prediction of the Structure and Catalytic Properties of Copper Zirconium Oxide, 2019 University of Pittsburgh Department of Chemical and Petroleum Engineering Research Day (Oral Presentation)
  7. The Computational Prediction of the Structure and Catalytic Properties of Copper Zirconium Oxide, 2018 AIChE Annual Meeting (Oral Presentation)
  8. Computer-Aided bimetallic Nanoparticle Design for Carbon Dioxide Adsorption and Activation, Fall 2018 ACS National Meeting (Oral Presentation)
  9. Computational Prediction of the Structure and Catalytic Properties of Copper Zirconium Oxide, 2018 Pittsburgh-Cleveland Catalysis Society Annual Meeting (Poster Presentation)
  10. Designing Cu-based Bimetallic Nanoparticles for CO2 Adsorption and Activation, Pittsburgh Quantum Institute Science2018 Annual Meeting (Poster Presentation)
  11. Designing Cu-based Bimetallic Nanoparticles for CO2 Adsorption and Activation, 2018 University of Pittsburgh Department of Chemical and Petroleum Engineering Research Day (Poster Presentation)
  12. Designing Cu-based Bimetallic Nanoparticles for CO2 Activation, 2017 AIChE Annual Meeting (Oral Presentation)
  13. CO2 Activation on Cu-based Bimetallic Nanoparticles, 2017 Pittsburgh-Cleveland Catalysis Society Annual Meeting (Poster Presentation)
  14. Designing Cu-based Bimetallic Nanoparticles for CO2 Activation, 2017 Simulators Meeting at Carnegie Melon University (Oral Presentation)
  15. The Reaction of Protected Cyanohydrins with Epoxides as an Alternative for the Enantio- and Diastereoselective Preparation of Aldols, 2016 Winthrop University Showcase of Undergraduate Research and Creative Endeavors Meeting (Poster Presentation)
  16. Toward ab initio Modeling of CO2 Electroreduction on α-Sn, β-Sn, and SnO2 Particles, 2015 Duquesne University Summer Undergraduate Research Symposium (Poster Presentation)
  17. The Reaction of Protected Cyanohydrins with Epoxides as an Alternative for the Enantio- and Diaseteroselective Preparation of Aldols: Studies with Lactronitrile, 2015 Winthrop University Showcase of Undergraduate Research and Creative Endeavors meeting (Poster Presentation)
  18. The Reaction of Protected Cyanohydrins with Epoxides as an Alternative for the Enantio- and Diastereoselective Preparation of Aldols, 2014 Winthrop University Showcase of Undergraduate Research and Creative Endeavors Meeting (Poster Presentation)
  19. The Reaction of O-Silylated Alkyl Cyanohydrins with Epoxides for the Enantio- and Diastereoselective Preparation of Aldols, 2014 Winthrop University Summer Undergraduate Research Experience Meeting, Summer Session (Oral Presentation)

Grants

  1. Led the preparation of a successfully-funded 2.00-million CPU-hour allocation for the CANELa research group from the National Science Foundation's Extreme Science and Engineering Discovery Environment for 2020.
  2. Assisted in the preparation of a successfully-funded 4.5-million CPU-hour allocation for the CANELa research group from the University of Pittsburgh Center for Research Computing for 2020.
  3. Led the preparation of a successfully-funded 4.5-million CPU-hour allocation for the CANELa research group from the University of Pittsburgh Center for Research Computing for 2019.
  4. Assisted in the preparation of a successfully-funded 1.2 million CPU-hour allocation for the CANELa research group from the National Science Foundation's Extreme Science and Engineering Discovery Environment for 2017.

Awards and Accomplishments

  • Catalysis and Reaction Engineering Division Student Conference Award, Fall 2020 AIChE Annual Meeting.
  • Fall 2019 Outstanding PhD Paper Award, University of Pittsburgh Chemical Engineering Department.
  • 1st-Place Poster Award, 2018 Pittsburgh-Cleveland Catalysis Society Annual Meeting.
  • 2nd-Place Poster Award, 2017 Pittsburgh-Cleveland Catalysis Society Annual Meeting.
  • Dean's List Fall 2013, Fall 2014, Fall 2015, and Spring 2016 at Winthrop University.
  • Winthrop University Eagle STEM Scholarship, 2012-2016.
  • South Carolina Palmetto Fellows Scholarship, 2012-2016.