zeolite
Towards Fully Automated Molecular Simulations: Multi-Agent Framework for Simulation Setup and Force Field Extraction
Petković, Marko, Menkovski, Vlado, Calero, Sofía
Automated characterization of porous materials has the potential to accelerate materials discovery, but it remains limited by the complexity of simulation setup and force field selection. We propose a multi-agent framework in which LLM-based agents can autonomously understand a characterization task, plan appropriate simulations, assemble relevant force fields, execute them and interpret their results to guide subsequent steps. As a first step toward this vision, we present a multi-agent system for literature-informed force field extraction and automated RASPA simulation setup. Initial evaluations demonstrate high correctness and reproducibility, highlighting this approach's potential to enable fully autonomous, scalable materials characterization.
Benchmarking Universal Interatomic Potentials on Zeolite Structures
Ito, Shusuke, Muraoka, Koki, Nakayama, Akira
Interatomic potentials (IPs) with wide elemental coverage and high accuracy are powerful tools for high-throughput materials discovery. While the past few years witnessed the development of multiple new universal IPs that cover wide ranges of the periodic table, their applicability to target chemical systems should be carefully investigated. We benchmark several universal IPs using equilibrium zeolite structures as testbeds. We select a diverse set of universal IPs encompassing two major categories: (i) universal analytic IPs, including GFN-FF, UFF, and Dreiding; (ii) pretrained universal machine learning IPs (MLIPs), comprising CHGNet, ORB-v3, MatterSim, eSEN-30M-OAM, PFP-v7, and EquiformerV2-lE4-lF100-S2EFS-OC22. We compare them with established tailor-made IPs, SLC, ClayFF, and BSFF using experimental data and density functional theory (DFT) calculations with dispersion correction as the reference. The tested zeolite structures comprise pure silica frameworks and aluminosilicates containing copper species, potassium, and organic cations. We found that GFN-FF is the best among the tested universal analytic IPs, but it does not achieve satisfactory accuracy for highly strained silica rings and aluminosilicate systems. All MLIPs can well reproduce experimental or DFT-level geometries and energetics. Among the universal MLIPs, the eSEN-30M-OAM model shows the most consistent performance across all zeolite structures studied. These findings show that the modern pretrained universal MLIPs are practical tools in zeolite screening workflows involving various compositions.
Symmetry-Informed Graph Neural Networks for Carbon Dioxide Isotherm and Adsorption Prediction in Aluminum-Substituted Zeolites
Petković, Marko, Luna, José-Manuel Vicent, Dinne, Elīza Beate, Menkovski, Vlado, Calero, Sofía
Accurately predicting adsorption properties in nanoporous materials using Deep Learning models remains a challenging task. This challenge becomes even more pronounced when attempting to generalize to structures that were not part of the training data.. In this work, we introduce SymGNN, a graph neural network architecture that leverages material symmetries to improve adsorption property prediction. By incorporating symmetry operations into the message-passing mechanism, our model enhances parameter sharing across different zeolite topologies, leading to improved generalization. We evaluate SymGNN on both interpolation and generalization tasks, demonstrating that it successfully captures key adsorption trends, including the influence of both the framework and aluminium distribution on CO$_2$ adsorption. Furthermore, we apply our model to the characterization of experimental adsorption isotherms, using a genetic algorithm to infer likely aluminium distributions. Our results highlight the effectiveness of machine learning models trained on simulations for studying real materials and suggest promising directions for fine-tuning with experimental data and generative approaches for the inverse design of multifunctional nanomaterials.
Graph Neural Networks for Carbon Dioxide Adsorption Prediction in Aluminium-Exchanged Zeolites
Petković, Marko, Vicent-Luna, José Manuel, Menkovski, Vlado, Calero, Sofía
The ability to efficiently predict adsorption properties of zeolites can be of large benefit in accelerating the design process of novel materials. The existing configuration space for these materials is wide, while existing molecular simulation methods are computationally expensive. In this work, we propose a model which is 4 to 5 orders of magnitude faster at adsorption properties compared to molecular simulations. To validate the model, we generated datasets containing various aluminium configurations for the MOR, MFI, RHO and ITW zeolites along with their heat of adsorptions and Henry coefficients for CO$_2$, obtained from Monte Carlo simulations. The predictions obtained from the Machine Learning model are in agreement with the values obtained from the Monte Carlo simulations, confirming that the model can be used for property prediction. Furthermore, we show that the model can be used for identifying adsorption sites. Finally, we evaluate the capability of our model for generating novel zeolite configurations by using it in combination with a genetic algorithm.
Equivariant Parameter Sharing for Porous Crystalline Materials
Petković, Marko, Romero-Marimon, Pablo, Menkovski, Vlado, Calero, Sofia
Efficiently predicting properties of porous crystalline materials has great potential to accelerate the high throughput screening process for developing new materials, as simulations carried out using first principles model are often computationally expensive. To effectively make use of Deep Learning methods to model these materials, we need to utilize the symmetries present in the crystals, which are defined by their space group. Existing methods for crystal property prediction either have symmetry constraints that are too restrictive or only incorporate symmetries between unit cells. In addition, these models do not explicitly model the porous structure of the crystal. In this paper, we develop a model which incorporates the symmetries of the unit cell of a crystal in its architecture and explicitly models the porous structure. We evaluate our model by predicting the heat of adsorption of CO$_2$ for different configurations of the mordenite zeolite. Our results confirm that our method performs better than existing methods for crystal property prediction and that the inclusion of pores results in a more efficient model.
Inorganic synthesis-structure maps in zeolites with machine learning and crystallographic distances
Schwalbe-Koda, Daniel, Widdowson, Daniel E., Pham, Tuan Anh, Kurlin, Vitaliy A.
Zeolites are inorganic materials known for their diversity of applications, synthesis conditions, and resulting polymorphs. Although their synthesis is controlled both by inorganic and organic synthesis conditions, computational studies of zeolite synthesis have focused mostly on organic template design. In this work, we use a strong distance metric between crystal structures and machine learning (ML) to create inorganic synthesis maps in zeolites. Starting with 253 known zeolites, we show how the continuous distances between frameworks reproduce inorganic synthesis conditions from the literature without using labels such as building units. An unsupervised learning analysis shows that neighboring zeolites according to our metric often share similar inorganic synthesis conditions, even in template-based routes. In combination with ML classifiers, we find synthesis-structure relationships for 14 common inorganic conditions in zeolites, namely Al, B, Be, Ca, Co, F, Ga, Ge, K, Mg, Na, P, Si, and Zn. By explaining the model predictions, we demonstrate how (dis)similarities towards known structures can be used as features for the synthesis space. Finally, we show how these methods can be used to predict inorganic synthesis conditions for unrealized frameworks in hypothetical databases and interpret the outcomes by extracting local structural patterns from zeolites. In combination with template design, this work can accelerate the exploration of the space of synthesis conditions for zeolites.
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How AI could help bring a sustainable reckoning to hydropower
Hydropower has been stirring up controversies since the early 2000s. Despite being promoted as a solution to mitigate climate change, the hydropower bubble burst when researchers discovered in 2005 that hydropower dams are responsible for huge amounts of greenhouse gas emissions. Hydropower dams' walls restrict the flow of rivers and turn them into pools of stagnant water. Reservoir surfaces and turbines then release methane into the atmosphere. Methane makes up approximately 80 percent of the greenhouse gases emitted from hydropower dams, peaking in the first decade of the dams lifecycle.
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Using adversarial attacks to refine molecular energy predictions
Neural networks (NNs) are increasingly being used to predict new materials, the rate and yield of chemical reactions, and drug-target interactions, among others. For these applications, they are orders of magnitude faster than traditional methods such as quantum mechanical simulations. The price for this agility, however, is reliability. Because machine learning models only interpolate, they may fail when used outside the domain of training data. But the part that worried Rafael Gómez-Bombarelli, the Jeffrey Cheah Career Development Professor in the MIT Department of Materials Science and Engineering, and graduate students Daniel Schwalbe-Koda and Aik Rui Tan was that establishing the limits of these machine learning (ML) models is tedious and labor-intensive.
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