arXiv subjects

So Takamoto

Publications and source records attributed to So Takamoto.

11 recordsLinked to original sources

arXiv2026

PFP/MM: A Hybrid Approach Combining a Universal Neural Network Potential with Classical Force Fields for Large-Scale Reactive Simulations

Universal machine-learning interatomic potentials (uMLIPs) enable reactive molecular simulations with near-DFT accuracy, yet applying them efficiently to large, realistic condensed-phase systems remains computationally demanding. Here we present PFP/MM, a hybrid approach that combines a uMLIP, PreFerred Potential (PFP), with molecular mechanics (MM) to enable both large-scale and long-time simulations that are challenging for uMLIP-only calculations. Using an alanine dipeptide in explicit water, we achieve multi-ns/day enhanced sampling and obtain a Ramachandran plot consistent with established basins. For an intramolecular nucleophilic addition reaction in a polar solvent environment, we reproduce the expected solvent-induced stabilization in the free-energy profile. We further apply the approach to a cytochrome P450 Compound I hydroxylation reaction and obtain a free-energy landscape consistent with the accepted reaction mechanism. These results demonstrate that uMLIP-based reactive simulations can be applied to diverse condensed-phase processes in large, realistic environments.

cond-mat.mtrl-sci↗

arXiv2026

Matlantis-PFP v8: Universal Machine Learning Interatomic Potential with Better Experimental Agreements via r2SCAN Functional

Universal Machine Learning Interatomic Potentials (uMLIPs) enable atomistic simulations and high-throughput screening at scales far beyond those accessible with density functional theory (DFT). However, most existing uMLIPs are trained on Perdew--Burke--Ernzerhof (PBE) generalized gradient approximation (GGA) data and are therefore fundamentally limited by PBE-level accuracy. In this paper, we argue that better zero-shot predictions versus experiments must be an explicit design target for uMLIPs and present PFP v8, a uMLIP available on the Matlantis service that overcomes the inherent limitations of the PBE functional by being trained to reproduce the regularized-restored strongly constrained and appropriately normed (r2SCAN) meta-GGA potential-energy surface across a wide range of chemical domains. Without requiring domain-specific fine-tuning, PFP v8 delivers systematically improved agreement with experimental data or high-accuracy references for crystals, molecules, and surfaces, outperforming PBE-based DFT calculations. Crucially, in long-time molecular dynamics simulations that are computationally impractical with DFT, PFP v8 predicts melting points with an average error of approximately 130 K, halving the error relative to PBE-trained models. These results establish that uMLIPs can move beyond the limitations of their training approximations and achieve substantially improved agreement with experiment across diverse chemical domains, further narrowing the gap between simulation and reality.

physics.chem-ph↗

arXiv2025

LightPFP: A Lightweight Route to Ab Initio Accuracy at Scale

Atomistic simulation methods have evolved through successive computational levels, each building upon more fundamental approaches: from quantum mechanics to density functional theory (DFT), and subsequently, to machine learning interatomic potentials (MLIPs). While universal MLIPs (u-MLIPs) offer broad transferability, their computational overhead limits large-scale applications. Task-specific MLIPs (ts-MLIPs) achieve superior efficiency but require prohibitively expensive DFT data generation for each material system. In this paper, we propose LightPFP, a data-efficient knowledge distillation framework. Instead of using costly DFT calculations, LightPFP generates a distilled ts-MLIP by leveraging u-MLIP to generate high-quality training data tailored for specific materials and utilizing a pre-trained light-weight MLIP to further enhance data efficiency. Across a broad spectrum of materials, including solid-state electrolytes, high-entropy alloys, and reactive ionic systems, LightPFP delivers three orders of magnitude faster model development than conventional DFT-based methods, while maintaining accuracy on par with first-principles predictions. Moreover, the distilled ts-MLIPs further sustain the computational efficiency essential for large-scale molecular dynamics, achieving 1-2 orders of magnitude faster inference than u-MLIPs. The framework further enables efficient precision transfer learning, where systematic errors from the u-MLIP can be corrected using as few as 10 high-accuracy DFT data points, as demonstrated for MgO melting point prediction. This u-MLIP-driven distillation approach enables rapid development of high-fidelity, efficient MLIPs for materials science applications.

cond-mat.mtrl-sci↗

arXiv2025

Efficient Crystal Structure Prediction Using Universal Neural Network Potential with Diversity Preservation in Genetic Algorithms

Crystal structure prediction (CSP) is crucial for identifying stable crystal structures in given systems and is a prerequisite for computational atomistic simulations. Recent advances in neural network potentials (NNPs) have reduced the computational cost of CSP. However, searching for stable crystal structures across the entire composition space in multicomponent systems remains a significant challenge. Here, we propose an improvement of genetic algorithm (GA) -based CSP method using a universal NNP. Our GA-based methods are designed to efficiently expand convex hull volumes while preserving the diversity of crystal structures. Our hull-informed filtering and elitist-selection procedures incorporate an aging mechanism that prioritizes recently improved compositions. We also employ niching to prevent convergence to a small set of stoichiometries, thereby preserving a diverse, high-quality population. Our evaluation shows that the present method outperforms the symmetry-aware random structure generation and existing CSP methods, achieving a larger convex hull with fewer trials. We demonstrated that our approach, combined with the developed universal NNP (PFP), can accurately reproduce and explore phase diagrams obtained through DFT calculations; this indicates the validity of PFP across a wide range of crystal structures and element combinations. This study, which integrates a universal NNP with a GA-based CSP method, highlights the promise of these methods in materials discovery.

cond-mat.mtrl-sci↗

arXiv2025

A practical guide to machine learning interatomic potentials -- Status and future

The rapid development and large body of literature on machine learning interatomic potentials (MLIPs) can make it difficult to know how to proceed for researchers who are not experts but wish to use these tools. The spirit of this review is to help such researchers by serving as a practical, accessible guide to the state-of-the-art in MLIPs. This review paper covers a broad range of topics related to MLIPs, including (i) central aspects of how and why MLIPs are enablers of many exciting advancements in molecular modeling, (ii) the main underpinnings of different types of MLIPs, including their basic structure and formalism, (iii) the potentially transformative impact of universal MLIPs for both organic and inorganic systems, including an overview of the most recent advances, capabilities, downsides, and potential applications of this nascent class of MLIPs, (iv) a practical guide for estimating and understanding the execution speed of MLIPs, including guidance for users based on hardware availability, type of MLIP used, and prospective simulation size and time, (v) a manual for what MLIP a user should choose for a given application by considering hardware resources, speed requirements, energy and force accuracy requirements, as well as guidance for choosing pre-trained potentials or fitting a new potential from scratch, (vi) discussion around MLIP infrastructure, including sources of training data, pre-trained potentials, and hardware resources for training, (vii) summary of some key limitations of present MLIPs and current approaches to mitigate such limitations, including methods of including long-range interactions, handling magnetic systems, and treatment of excited states, and finally (viii) we finish with some more speculative thoughts on what the future holds for the development and application of MLIPs over the next 3-10+ years.

cond-mat.mtrl-sci↗

arXiv2024

Generative Model for Constructing Reaction Path from Initial to Final States

Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths can be difficult for humans. This paper presents an innovative approach that utilizes neural networks to generate initial guesses for reaction pathways based on the initial state and learning from a database of low-energy transition paths. The proposed method is initiated by inputting the coordinates of the initial state, followed by progressive alterations to its structure. This iterative process culminates in the generation of the guess reaction path and the coordinates of the final state. The method does not require one-the-fly computation of the actual potential energy surface, and is therefore fast-acting. The application of this geometry-based method extends to complex reaction pathways illustrated by organic reactions. Training was executed on the Transition1x dataset of organic reaction pathways. The results revealed the generation of reactions that bore substantial similarities with the test set of chemical reaction paths. The method's flexibility allows for reactions to be generated either to conform to predetermined conditions or in a randomized manner.

physics.comp-ph↗

arXiv2022

Towards Universal Neural Network Potential for Material Discovery Applicable to Arbitrary Combination of 45 Elements

Computational material discovery is under intense study owing to its ability to explore the vast space of chemical systems. Neural network potentials (NNPs) have been shown to be particularly effective in conducting atomistic simulations for such purposes. However, existing NNPs are generally designed for narrow target materials, making them unsuitable for broader applications in material discovery. To overcome this issue, we have developed a universal NNP called PreFerred Potential (PFP), which is able to handle any combination of 45 elements. Particular emphasis is placed on the datasets, which include a diverse set of virtual structures used to attain the universality. We demonstrated the applicability of PFP in selected domains: lithium diffusion in LiFeSO${}_4$F, molecular adsorption in metal-organic frameworks, an order-disorder transition of Cu-Au alloys, and material discovery for a Fischer-Tropsch catalyst. They showcase the power of PFP, and this technology provides a highly useful tool for material discovery.

cond-mat.mtrl-sci↗

arXiv2021

TeaNet: universal neural network interatomic potential inspired by iterative electronic relaxations

A universal interatomic potential for an arbitrary set of chemical elements is urgently needed in computational materials science. Graph convolution neural network (GCN) has rich expressive power, but previously was mainly employed to transport scalars and vectors, not rank $\ge 2$ tensors. As classic interatomic potentials were inspired by tight-binding electronic relaxation framework, we want to represent this iterative propagation of rank $\ge 2$ tensor information by GCN. Here we propose an architecture called the tensor embedded atom network (TeaNet) where angular interaction is translated into graph convolution through the incorporation of Euclidean tensors, vectors and scalars. By applying the residual network (ResNet) architecture and training with recurrent GCN weights initialization, a much deeper (16 layers) GCN was constructed, whose flow is similar to an iterative electronic relaxation. Our traning dataset is generated by density functional theory calculation of mostly chemically and structurally randomized configurations. We demonstrate that arbitrary structures and reactions involving the first 18 elements on the periodic table (H to Ar) can be realized satisfactorily by TeaNet, including C-H molecular structures, metals, amorphous SiO${}_2$, and water, showing surprisingly good performance (energy mean absolute error 19 meV/atom) and robustness for arbitrary chemistries involving elements from H to Ar.

physics.comp-ph↗

arXiv2021

Calculations of Real-System Nanoparticles Using Universal Neural Network Potential PFP

It is essential to explore the stability and activity of real-system nanoparticles theoretically. While applications of theoretical methods for this purpose can be found in literature, the expensive computational costs of conventional theoretical methods hinder their massive applications to practical materials design. With the recent development of neural network algorithms along with the advancement of computer systems, neural network potentials have emerged as a promising candidate for the description of a wide range of materials, including metals and molecules, with a reasonable computational time. In this study, we successfully validate a universal neural network potential, PFP, for the description of monometallic Ru nanoparticles, PdRuCu ternary alloy nanoparticles, and the NO adsorption on Rh nanoparticles against first-principles calculations. We further conduct molecular dynamics simulations on the NO-Rh system and challenge the PFP to describe a large, supported Pt nanoparticle system.

cond-mat.mtrl-sci↗

arXiv2018

Elucidation of the atomic-scale mechanism of the anisotropic oxidation rate of 4H-SiC between the ($0001$) Si-face and ($000\overline{1}$) C-face by using a new Si-O-C interatomic potential

Silicon carbide (SiC) is an attractive semiconductor material for applications in power electronic devices. However, fabrication of a high-quality SiC/SiO${}_2$ interface has been a challenge. It is well-known that there is a great difference in oxidation rate between the Si-face and C-face, and that the quality of oxide on the Si-face is greater than that on the C-face. However, the atomistic mechanism of the thermal oxidation of SiC remains to be solved. In this paper, a new Si-C-O interatomic potential was developed to reproduce the kinetics of the thermal oxidation of SiC. Using this newly developed potential, large-scale SiC oxidation simulations at various temperature were performed. The results showed that the activation energy of the Si-face is much larger than that of the C-face. In the case of the Si-face, a flat and aligned interface structure including Si${}^{1+}$ was created. Based on the estimated activation energies of the intermediate oxide states, it is proposed that the stability of the flat interface structure is the origin of the high activation energy of the oxidation of the Si-face. In contrast, in the case of the C-face, it is found that the Si atom at the interface are easily pulled up by the O atoms. This process generates the disordered interface and decreases the activation energy of the oxidation. It is also proposed that many excess C atoms are created in the case of the C-face.

cond-mat.mtrl-sci↗

arXiv2018

Atomistic mechanism of graphene growth on SiC substrate: Large-scale molecular dynamics simulation based on a new charge-transfer bond-order type potential

Thermal decomposition of silicon carbide is a promising approach for the fabrication of graphene. However, the atomistic growth mechanism of graphene remains unclear. This paper describes the development of a new charge-transfer interatomic potential. Carbon bonds with a wide variety of characteristics can be reproduced by the proposed vectorized bond-order term. Large-scale thermal decomposition simulation enables us to observe the continuous growth process of the multi-ring carbon structure. The annealing simulation reveals the atomistic process by which the multi-ring carbon structure is transformed to flat graphene involving only 6-membered rings. Also, it is found that the surface atoms of the silicon carbide substrate enhance the homogeneous graphene formation.

cond-mat.mtrl-sci↗