arXiv subjects

Tsz Wai Ko

Publications and source records attributed to Tsz Wai Ko.

14 recordsLinked to original sources

arXiv2026

El Agente Potente: High-Throughput Agentic Atomistic Simulations

Foundational machine-learning interatomic potentials (MLIPs) are transforming atomistic simulations by achieving near-ab initio accuracy across large chemical spaces at a fraction of the computational cost. A central challenge in using these tools for high-throughput property calculations is translating high-level scientific intent into adaptive simulation campaigns without compromising workflow rigour. We introduce El Agente Potente, an agentic system that combines typed execution graphs with a complementary coding mode for MLIPs-driven atomistic simulations. Typed execution graphs provide structured and provenance-aware execution for standardized workflows, with large language models (LLMs) restricted to planning and routing while deterministic Python components perform scientific computation and validation. Complementing this structured execution, a coding agent constructs customized workflows for tasks requiring greater procedural flexibility while invoking existing Potente functions for supported calculations. We demonstrate El Agente Potente across computational materials discovery, molecular energy-landscape exploration, adsorption, and catalytic reaction workflows, together with systematic benchmarks of reproducibility and LLM token cost. These results establish typed execution graphs and code-based workflow construction as complementary mechanisms for agentic scientific computing, combining controlled, auditable execution with the flexibility required for customized atomistic simulations

cs.AI↗

arXiv2026

El Agente Quntur: A research collaborator agent for quantum chemistry

Quantum chemistry is a foundational enabling tool for the fields of chemistry, materials science, computational biology and others. Despite of its power, the practical application of quantum chemistry simulations remains in the hands of qualified experts due to methodological complexity, software heterogeneity, and the need for informed interpretation of results. To bridge the accessibility gap for these tools and expand their reach to chemists with broader backgrounds, we introduce El Agente Quntur, a hierarchical, multi-agent AI system designed to operate not merely as an automation tool but as a research collaborator for computational quantum chemistry. Quntur was designed following three main strategies: i) elimination of hard-coded procedural policies in favour of reasoning-driven decisions, ii) construction of general and composable actions that facilitate generalization and efficiency, and iii) implementation of guided deep research to integrate abstract quantum-chemical reasoning across subdisciplines and a detailed understanding of the software's internal logic and syntax. Although instantiated in ORCA, these design principles are applicable to research agents more generally and easily expandable to additional quantum chemistry packages and beyond. Quntur supports the full range of calculations available in ORCA 6.0 and reasons over software documentation and scientific literature to plan, execute, adapt, and analyze in silico chemistry experiments following best practices. We discuss the advances and current bottlenecks in agentic systems operating at the research level in computational chemistry, and outline a roadmap toward a fully autonomous end-to-end computational chemistry research agent.

physics.chem-ph↗

arXiv2026

A Linear-Scaling, Charge-Aware Foundation Potential for Atomistic Simulations

Electrostatics govern charge transfer and reactivity in materials. However, most foundation potentials (FPs) either neglect explicit electrostatic interactions or come at prohibitive computational cost. Here, we introduce charge-equilibrated TensorNet (QET), an equivariant, charge-aware architecture that achieves linear scaling with system size via an analytically solvable charge-equilibration scheme. We demonstrate that a trained QET FP matches state-of-the-art FPs on materials property benchmarks but delivers qualitatively different predictions in systems dominated by electrostatic interactions. The QET FP reproduces the correct structure and density of the NaCl-CaCl2 ionic liquid and the crystallization of Ge1Sb2Te4 phase change memory, which charge-agnostic FPs miss. We further show that a fine-tuned QET captures reactive processes at the Li/Li6PS5Cl solid-electrolyte interface and supports simulations under applied electrochemical potentials. These results remove a fundamental constraint in large-scale atomistic simulations of electrostatics and establish a general, data-driven framework for charge-aware FPs with transformative applications in energy storage, catalysis, and beyond.

cond-mat.mtrl-sci↗

arXiv2026

El Agente Gráfico: A Semantic Execution Runtime for Scientific Agents

Large language models (LLMs) can plan scientific workflows and generate code, but these capabilities do not specify how scientific state is validated, transferred and recorded across heterogeneous computational and experimental operations. Here we present El Agente Gráfico, a semantic execution runtime for scientific agents that uses typed execution graphs to enforce admissible scientific state transitions, record provenance and confine model judgement to explicit decision points. Using the same top-level LLM and task-specific rubrics on six university-level quantum chemistry exercises, El Agente Gráfico improved performance while reducing model cost by approximately 80% and wall-clock time by more than fourfold relative to our previous multi-agent architecture. Across ensemble spectroscopy and metal-organic framework (MOF) design, the runtime supported typed-state transfer, parallel execution and cross-session persistence. Open-ended studies of a disulfide redox mechanism and the vibrational hypothesis of olfaction required the agent to define the chemical scope and computational pathway of each investigation. A graph-construction skill distilled from these studies then enabled coding agents to author typed execution graphs for MOF literature mining. Together, these results show how typed execution graphs turn reusable procedural knowledge into scientific protocols that can be inspected, revised and transferred across computational and physical systems.

cs.AI↗

arXiv2026

El Agente Sólido: A New Age(nt) for Solid State Simulations

Quantum chemistry calculations are a key component of the materials discovery process. The results from first-principles explorations enable the prediction of material properties prior to experimental validation. Despite their impact, the practical use of first-principles methods remains limited by the expertise required to design, execute, and troubleshoot complex computational workflows. Even when workflows are successfully built, they are sometimes rigid and not adaptable to different use cases. Recent advances in large language models (LLMs) and agentic systems offer a pathway to flexibly automate these processes and lower barriers to entry. Here, we introduce El Agente Sólido, a hierarchical multi-agent framework for automating solid-state quantum chemistry workflows using the open-source Quantum ESPRESSO simulation package. The framework translates high-level scientific objectives expressed in natural language into end-to-end computational pipelines that include structure generation, input file construction, workflow execution, and post-processing analysis. El Agente Sólido integrates density functional theory with phonon calculations and machine-learning interatomic potentials to enable efficient and physically consistent simulations. Extensive benchmarking and case studies demonstrate that El Agente Sólido reliably executes a wide range of solid-state calculations, highlighting its potential to improve reproducibility and accelerate computational materials discovery

cond-mat.mtrl-sci↗

arXiv2025

Iterative charge equilibration for fourth-generation high-dimensional neural network potentials

Machine learning potentials (MLP) allow to perform large-scale molecular dynamics simulations with about the same accuracy as electronic structure calculations provided that the selected model is able to capture the relevant physics of the system. For systems exhibiting long-range charge transfer, fourth-generation MLPs need to be used, which take global information about the system and electrostatic interactions into account. This can be achieved in a charge equilibration (QEq) step, but the direct solution (dQEq) of the set of linear equations results in an unfavorable cubic scaling with system size making this step computationally demanding for large systems. In this work, we propose an alternative approach that is based on the iterative solution of the charge equilibration problem (iQEq) to determine the atomic partial charges. We have implemented the iQEq method, which scales quadratically with system size, in the parallel molecular dynamics software LAMMPS for the example of a fourth-generation high-dimensional neural network potential (4G-HDNNP) intended to be used in combination with the n2p2 library. The method itself is general and applicable to many different types of fourth-generation MLPs. An assessment of the accuracy and the efficiency is presented for a benchmark system of FeCl$_3$ in water.

cond-mat.mtrl-sci↗

arXiv2025

A Foundational Potential Energy Surface Dataset for Materials

Accurate potential energy surface (PES) descriptions are essential for atomistic simulations of materials. Universal machine learning interatomic potentials (UMLIPs)$^{1-3}$ offer a computationally efficient alternative to density functional theory (DFT)$^4$ for PES modeling across the periodic table. However, their accuracy today is fundamentally constrained due to a reliance on DFT relaxation data.$^{5,6}$ Here, we introduce MatPES, a foundational PES dataset comprising $\sim 400,000$ structures carefully sampled from 281 million molecular dynamics snapshots that span 16 billion atomic environments. We demonstrate that UMLIPs trained on the modestly sized MatPES dataset can rival, or even outperform, prior models trained on much larger datasets across a broad range of equilibrium, near-equilibrium, and molecular dynamics property benchmarks. We also introduce the first high-fidelity PES dataset based on the revised regularized strongly constrained and appropriately normed (r$^2$SCAN) functional$^7$ with greatly improved descriptions of interatomic bonding. The open source MatPES initiative emphasizes the importance of data quality over quantity in materials science and enables broad community-driven advancements toward more reliable, generalizable, and efficient UMLIPs for large-scale materials discovery and design.

cond-mat.mtrl-sci↗

arXiv2025

Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry

Graph deep learning models, which incorporate a natural inductive bias for a collection of atoms, are of immense interest in materials science and chemistry. Here, we introduce the Materials Graph Library (MatGL), an open-source graph deep learning library for materials science and chemistry. Built on top of the popular Deep Graph Library (DGL) and Python Materials Genomics (Pymatgen) packages, our intention is for MatGL to be an extensible ``batteries-included'' library for the development of advanced graph deep learning models for materials property predictions and interatomic potentials. At present, MatGL has efficient implementations for both invariant and equivariant graph deep learning models, including the Materials 3-body Graph Network (M3GNet), MatErials Graph Network (MEGNet), Crystal Hamiltonian Graph Network (CHGNet), TensorNet and SO3Net architectures. MatGL also includes a variety of pre-trained universal interatomic potentials (aka ``foundational materials models (FMM)'') and property prediction models are also included for out-of-box usage, benchmarking and fine-tuning. Finally, MatGL includes support for Pytorch Lightning for rapid training of models.

cond-mat.mtrl-sci↗

arXiv2024

Data-Efficient Construction of High-Fidelity Graph Deep Learning Interatomic Potentials

Machine learning potentials (MLPs) have become an indispensable tool in large-scale atomistic simulations because of their ability to reproduce ab initio potential energy surfaces (PESs) very accurately at a fraction of computational cost. For computational efficiency, the training data for most MLPs today are computed using relatively cheap density functional theory (DFT) methods such as the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) functional. Meta-GGAs such as the recently developed strongly constrained and appropriately normed (SCAN) functional have been shown to yield significantly improved descriptions of atomic interactions for diversely bonded systems, but their higher computational cost remains an impediment to their use in MLP development. In this work, we outline a data-efficient multi-fidelity approach to constructing Materials 3-body Graph Network (M3GNet) interatomic potentials that integrate different levels of theory within a single model. Using silicon and water as examples, we show that a multi-fidelity M3GNet model trained on a combined dataset of low-fidelity GGA calculations with 10% of high-fidelity SCAN calculations can achieve accuracies comparable to a single-fidelity M3GNet model trained on a dataset comprising 8x the number of SCAN calculations. This work paves the way for the development of high-fidelity MLPs in a cost-effective manner by leveraging existing low-fidelity datasets.

physics.comp-ph↗

arXiv2024

Superionic surface Li-ion transport in carbonaceous materials

Unlike Li-ion transport in the bulk of carbonaceous materials, little is known about Li-ion diffusion on their surface. In this study, we have discovered an ultra-fast Li-ion transport phenomenon on the surface of carbonaceous materials, particularly when they have limited Li insertion capacity along with a high surface area. This is exemplified by a carbon black, Ketjen Black (KB). An ionic conductivity of 18.1 mS cm-1 at room temperature is observed, far exceeding most solid-state ion conductors. Theoretical calculations reveal a low diffusion barrier for the surface Li species. The species is also identified as Li*, which features a partial positive charge. As a result, lithiated KB functions effectively as an interlayer between Li and solid-state electrolytes (SSE) to mitigate dendrite growth and cell shorting. This function is found to be electrolyte agnostic, effective for both sulfide and halide SSEs. Further, lithiated KB can act as a high-performance mixed ion/electron conductor that is thermodynamically stable at potentials near Li metal. A graphite anode mixed with KB instead of a solid electrolyte demonstrates full utilization with a capacity retention of ~85% over 300 cycles. The discovery of this surface-mediated ultra-fast Li-ion transport mechanism provides new directions for the design of solid-state ion conductors and solid-state batteries.

cond-mat.mtrl-sci↗

arXiv2023

Robust Training of Machine Learning Interatomic Potentials with Dimensionality Reduction and Stratified Sampling

Machine learning interatomic potentials (MLIPs) enable the accurate simulation of materials at larger sizes and time scales, and play increasingly important roles in the computational understanding and design of materials. However, MLIPs are only as accurate and robust as the data they are trained on. In this work, we present DImensionality-Reduced Encoded Clusters with sTratified (DIRECT) sampling as an approach to select a robust training set of structures from a large and complex configuration space. By applying DIRECT sampling on the Materials Project relaxation trajectories dataset with over one million structures and 89 elements, we develop an improved materials 3-body graph network (M3GNet) universal potential that extrapolate more reliably to unseen structures. We further show that molecular dynamics (MD) simulations with universal potentials such as M3GNet can be used in place of expensive \textit{ab initio} MD to rapidly create a large configuration space for target materials systems. Combined with DIRECT sampling, we develop a highly reliable moment tensor potential for Ti-H system without the need for iterative optimization. This work paves the way towards robust high throughput development of MLIPs across any compositional complexity.

cond-mat.mtrl-sci↗

arXiv2023

Accurate Fourth-Generation Machine Learning Potentials by Electrostatic Embedding

In recent years, significant progress has been made in the development of machine learning potentials (MLPs) for atomistic simulations with applications in many fields from chemistry to materials science. While most current MLPs are based on environment-dependent atomic energies, the limitations of this locality approximation can be overcome, e.g., in fourth-generation MLPs, which incorporate long-range electrostatic interactions based on an equilibrated global charge distribution. Apart from the considered interactions, the quality of MLPs crucially depends on the information available about the system, i.e., the descriptors. In this work we show that including -- in addition to structural information -- the electrostatic potential arising from the charge distribution in the atomic environments significantly improves the quality and transferability of the potentials. Moreover, the extended descriptor allows to overcome current limitations of two- and three-body based feature vectors regarding artificially degenerate atomic environments. The capabilities of such an electrostatically embedded fourth-generation high-dimensional neural network potential (ee4G-HDNNP), which is further augmented by pairwise interactions, are demonstrated for NaCl as a benchmark system. Employing a data set containing only neutral and negatively charged NaCl clusters, even small energy differences between different cluster geometries can be resolved, and the potential shows an impressive transferability to positively charged clusters as well as the melt.

physics.chem-ph↗

arXiv2021

Neural Network Potentials: A Concise Overview of Methods

In the past two decades, machine learning potentials (MLP) have reached a level of maturity that now enables applications to large-scale atomistic simulations of a wide range of systems in chemistry, physics and materials science. Different machine learning algorithms have been used with great success in the construction of these MLPs. In this review, we discuss an important group of MLPs relying on artificial neural networks to establish a mapping from the atomic structure to the potential energy. In spite of this common feature, there are important conceptual differences, which concern the dimensionality of the systems, the inclusion of long-range electrostatic interactions, global phenomena like non-local charge transfer, and the type of descriptor used to represent the atomic structure, which can either be predefined or learnable. A concise overview is given along with a discussion of the open challenges in the field.

physics.chem-ph↗

arXiv2020

A Fourth-Generation High-Dimensional Neural Network Potential with Accurate Electrostatics Including Non-local Charge Transfer

Machine learning potentials have become an important tool for atomistic simulations in many fields, from chemistry via molecular biology to materials science. Most of the established methods, however, rely on local properties and are thus unable to take global changes in the electronic structure into account, which result from long-range charge transfer or different charge states. In this work we overcome this limitation by introducing a fourth-generation high-dimensional neural network potential that combines a charge equilibration scheme employing environment-dependent atomic electronegativities with accurate atomic energies. The method, which is able to correctly describe global charge distributions in arbitrary systems, yields much improved energies and substantially extends the applicability of modern machine learning potentials. This is demonstrated for a series of systems representing typical scenarios in chemistry and materials science that are incorrectly described by current methods, while the fourth-generation neural network potential is in excellent agreement with electronic structure calculations.

cond-mat.mtrl-sci↗