Publications

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Preprints

1. Maximizing Efficiency of Dataset Compression for Machine Learning Potentials With Information Theory

   Benjamin Yu, Vincenzo Lordi, Daniel Schwalbe-Koda

   arXiv:2511.10561

    

   (2025)

   [DOI] [preprint] [code] [data]
2. A Generative Diffusion Model for Amorphous Materials

   Kai Yang, Daniel Schwalbe-Koda

   arXiv:2507.05024

    

   (2025)

   [DOI] [preprint] [code] [data] [blog post]
3. MatLLMSearch: Crystal Structure Discovery with Evolution-Guided Large Language Models

   Jingru Gan, Peichen Zhong, Yuanqi Du, Yanqiao Zhu, Chenru Duan, Haorui Wang, Daniel Schwalbe-Koda, Carla P Gomes, Kristin A Persson, Wei Wang

   arXiv:2502.20933

    

   (2025)

   [DOI] [preprint]

Journal publications

1. An exhaustive mapping of zeolite-template chemical space

   Mingrou Xie, Daniel Schwalbe-Koda, Yolanda M. Semanate-Esquivel, Alexander Bello-Jurado, Omar Santiago-Reyes, Cecilia Paris, Manuel Moliner, Rafael Gómez-Bombarelli

   Nature Computational Science

    

   (2025)

   [DOI] [preprint] [data]
2. Model-free estimation of completeness, uncertainties, and outliers in atomistic machine learning using information theory

   Daniel Schwalbe-Koda, Sebastien Hamel, Babak Sadigh, Fei Zhou, Vincenzo Lordi

   Nature Communications

    

   (2025)

   [DOI] [preprint] [code] [data]
3. Comprehensive sampling of coverage effects in catalysis by leveraging generalization in neural network models

   Daniel Schwalbe-Koda, Nitish Govindarajan, Joel Varley

   Digital Discovery

    

   (2025)

   [DOI] [preprint] [code] [data]
4. One-Pot Synthesis of CHA/ERI-Type Zeolite Intergrowth from a Single Multiselective Organic Structure-Directing Agent

   Soonhyoung Kwon, Estefanı́a Bello-Jurado, Evgeniia Ikonnikova, Hwajun Lee, Daniel Schwalbe-Koda, Avelino Corma, Tom Willhammar, Elsa A Olivetti, Rafael Gomez-Bombarelli, Manuel Moliner, Yuriy Román-Leshkov

   ACS Applied Materials & Interfaces

    

   (2024)

   [DOI]
5. Thermodynamics and electronic structure of adsorbed and intercalated plumbene in graphene/hexagonal SiC heterostructures

   Simone Brozzesi, Paola Gori, Daniel S Koda, Friedhelm Bechstedt, Olivia Pulci

   Scientific Reports

    

   (2024)

   [DOI]
6. Inorganic synthesis-structure maps in zeolites with machine learning and crystallographic distances

   Daniel Schwalbe-Koda, Daniel E Widdowson, Tuan Anh Pham, Vitaliy A Kurlin

   Digital Discovery

    

   (2023)

   [DOI] [preprint] [code] [data]
7. Data efficiency and extrapolation trends in neural network interatomic potentials

   Joshua A. Vita, Daniel Schwalbe-Koda

   Machine Learning: Science and Technology

    

   (2023)

   [DOI] [preprint] [code] [data]
8. mkite: A distributed computing platform for high-throughput materials simulations

   Daniel Schwalbe-Koda

   Computational Materials Science

    

   (2023)

   [DOI] [preprint] [code]
9. Mechanistic Insights on Permeation of Water over Iron Cations in Nanoporous Silicon Oxide Films for Selective H2 and O2 Evolution

   Fikret Aydin, Marcos F. Calegari Andrade, Robert S. Stinson, Alexandra Zagalskaya, Daniel Schwalbe-Koda, Zejie Chen, Shubham Sharma, Amitesh Maiti, Daniel V. Esposito, Shane Ardo, Tuan Anh Pham, Tadashi Ogitsu

   ACS Applied Materials & Interfaces

    

   (2023)

   [DOI]
10. Approaching enzymatic catalysis with zeolites or how to select one reaction mechanism competing with others

    Pau Ferri, Chengeng Li, Daniel Schwalbe-Koda, Mingrou Xie, Manuel Moliner, Rafael Gómez-Bombarelli, Mercedes Boronat, Avelino Corma

    Nature Communications

     

    (2023)

    [DOI]
11. Human- and Machine-Centred Designs of Molecules and Materials for Sustainability and Decarbonization

    Jiayu Peng, Daniel Schwalbe-Koda, Karthik Akkiraju, Tian Xie, Livia Giordano, Yang Yu, C. John Eom, Jaclyn R. Lunger, Daniel J. Zheng, Reshma R. Rao, Sokseiha Muy, Jeffrey C. Grossman, Karsten Reuter, Rafael Gómez-Bombarelli, Yang Shao-Horn

    Nature Reviews Materials

     

    (2022)

    [DOI]
12. Repurposing Templates for Zeolite Synthesis from Simulations and Data Mining

    Daniel Schwalbe-Koda, Omar A Santiago-Reyes, Avelino Corma, Yuriy Román-Leshkov, Manuel Moliner, Rafael Gómez-Bombarelli

    Chemistry of Materials

     

    (2022)

    [DOI]
13. Tunable CHA/AEI Zeolite Intergrowths with A Priori Biselective Organic Structure-Directing Agents: Controlling Enrichment and Implications for Selective Catalytic Reduction of NOx

    Estefanı́a Bello-Jurado, Daniel Schwalbe-Koda, Mathias Nero, Cecilia Paris, Toni Uusimäki, Yuriy Román-Leshkov, Avelino Corma, Tom Willhammar, Rafael Gómez-Bombarelli, Manuel Moliner

    Angewandte Chemie International Edition

     

    (2022)

    [DOI]
14. Sampling Lattices in Semi-Grand Canonical Ensemble with Autoregressive Machine Learning

    James Damewood, Daniel Schwalbe-Koda, Rafael Gómez-Bombarelli

    npj Computational Materials

     

    (2022)

    [DOI] [preprint] [code]
15. Learning Matter: Materials Design with Machine Learning and Atomistic Simulations

    Simon Axelrod, Daniel Schwalbe-Koda, Somesh Mohapatra, James Damewood, Kevin P Greenman, Rafael Gómez-Bombarelli

    Accounts of Materials Research

     

    (2022)

    [DOI]
16. A priori control of zeolite phase competition and intergrowth with high-throughput simulations

    Daniel Schwalbe-Koda, Soonhyoung Kwon, Cecilia Paris, Estefania Bello-Jurado, Zach Jensen, Elsa Olivetti, Tom Willhammar, Avelino Corma, Yuriy Román-Leshkov, Manuel Moliner, Rafael Gómez-Bombarelli

    Science

     

    (2021)

    [DOI] [code] [data]
17. Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks

    Daniel Schwalbe-Koda*, Aik Rui Tan*, Rafael Gómez-Bombarelli

    Nature Communications

     

    (2021)

    [DOI] [preprint] [code] [data]
18. Data-Driven Design of Biselective Templates for Intergrowth Zeolites

    Daniel Schwalbe-Koda, Avelino Corma, Yuriy Román-Leshkov, Manuel Moliner, Rafael Gómez-Bombarelli

    The Journal of Physical Chemistry Letters

     

    (2021)

    [DOI] [preprint] [data]
19. Supramolecular Recognition in Crystalline Nanocavities Through Monte Carlo and Voronoi Network Algorithms

    Daniel Schwalbe-Koda, Rafael Gómez-Bombarelli

    The Journal of Physical Chemistry C

     

    (2021)

    [DOI] [preprint] [code]
20. Benchmarking binding energy calculations for organic structure-directing agents in pure-silica zeolites

    Daniel Schwalbe-Koda, Rafael Gómez-Bombarelli

    The Journal of Chemical Physics

     

    (2021)

    [DOI] [preprint] [code] [data]
21. Discovering relationships between OSDAs and zeolites through data mining and generative neural networks

    Zach Jensen, Soonhyoung Kwon, Daniel Schwalbe-Koda, Cecilia Paris, Rafael Gómez-Bombarelli, Yuriy Román-Leshkov, Avelino Corma, Manuel Moliner, Elsa A Olivetti

    ACS Central Science

     

    (2021)

    [DOI] [code]
22. Active learning accelerates ab initio molecular dynamics on reactive energy surfaces

    Shi Jun Ang, Wujie Wang, Daniel Schwalbe-Koda, Simon Axelrod, Rafael Gómez-Bombarelli

    Chem

     

    (2021)

    [DOI] [code]
23. Temperature-transferable coarse-graining of ionic liquids with dual graph convolutional neural networks

    Jurgis Ruza, Wujie Wang, Daniel Schwalbe-Koda, Simon Axelrod, William H Harris, Rafael Gómez-Bombarelli

    The Journal of Chemical Physics

     

    (2020)

    [DOI] [preprint]
24. Graph similarity drives zeolite diffusionless transformations and intergrowth

    Daniel Schwalbe-Koda, Zach Jensen, Elsa Olivetti, Rafael Gómez-Bombarelli

    Nature Materials

     

    (2019)

    [DOI] [preprint] [data]
25. Charge qubit in van der Waals heterostructures

    Bruno Lucatto, Daniel S. Koda, Friedhelm Bechstedt, Marcelo Marques, Lara K. Teles

    Physical Review B

     

    (2019)

    [DOI]
26. Approximate quasiparticle correction for calculations of the energy gap in two-dimensional materials

    Ivan Guilhon, Daniel S. Koda, Luis G. Ferreira, Marcelo Marques, Lara K. Teles

    Physical Review B

     

    (2018)

    [DOI]
27. Trends on band alignments: Validity of Anderson’s rule in SnS2- and SnSe2-based van der Waals heterostructures

    Daniel S. Koda, Friedhelm Bechstedt, Marcelo Marques, Lara K. Teles

    Physical Review B

     

    (2018)

    [DOI]
28. Tuning Electronic Properties and Band Alignments of Phosphorene Combined With MoSe2 and WSe2

    Daniel S. Koda, Friedhelm Bechstedt, Marcelo Marques, Lara Kühl Teles

    The Journal of Physical Chemistry C

     

    (2017)

    [DOI]
29. Deposition of topological silicene, germanene and stanene on graphene-covered SiC substrates

    Filipe Matusalem, Daniel S. Koda, Friedhelm Bechstedt, Marcelo Marques, Lara K. Teles

    Scientific Reports

     

    (2017)

    [DOI]
30. Coincidence Lattices and Interlayer Twist in van der Waals Heterostructures: Application of the Coincidence Lattice Method on hBN/MoSe2 Heterobilayer Systems

    Daniel S. Koda, Friedhelm Bechstedt, Marcelo Marques, Lara K. Teles

    Journal of Electronic Materials

     

    (2017)

    [DOI]
31. Coincidence lattices of 2D crystals: Heterostructure predictions and applications

    Daniel S. Koda, Friedhelm Bechstedt, Marcelo Marques, Lara K. Teles

    The Journal of Physical Chemistry C

     

    (2016)

    [DOI] [code]

Book chapters

1. Generating, Managing, and Mining Big Data in Zeolite Simulations

   Daniel Schwalbe-Koda, Rafael Gómez-Bombarelli

   In: AI‐Guided Design and Property Prediction for Zeolites and Nanoporous Materials

    

   (2023)

   [DOI]
2. Generative models for automatic chemical design

   Daniel Schwalbe-Koda, Rafael Gómez-Bombarelli

   In: Machine Learning Meets Quantum Physics

    

   (2020)

   [DOI] [preprint]

Patents

1. Molecule Selection Using Simulation and Ranking Based on Binding Matrices

   Rafael Gomez-Bombarelli, Daniel Schwalbe-Koda

   Patent US20230360738A1

    

   (2023)
2. Synthesis of the CHA/AEI intergrowth, synthesis procedure and its use in catalytic applications

   Estefania Bello, Cecilia Paris Carrizo, Daniel Schwalbe-Koda, Yuriy Román-Leshkov, Avelino Corma, Rafael Gómez-Bombarelli, Manuel Moliner Marín

   Patent ES2829385 B2

    

   (2021)