arXiv subjects

Yanzhou Wang

Publications and source records attributed to Yanzhou Wang.

At least 19 recordsLinked to original sources

arXiv2026

GPUMDkit: A User-Friendly Toolkit for GPUMD and NEP

Machine-learned interatomic potentials have revolutionized molecular dynamics simulations by providing quantum-mechanical accuracy at empirical-potential speeds. The graphics processing unit molecular dynamics (GPUMD) package, featuring the highly efficient neuroevolution potential (NEP) framework, has emerged as a powerful tool in this domain. However, the complexity of force field development, active learning, and trajectory post-processing often requires extensive manual scripting, imposing a steep learning curve on new users. To address this, we present GPUMDkit, a comprehensive and user-friendly toolkit that streamlines the entire simulation workflow for GPUMD and NEP. GPUMDkit integrates a suite of essential functionalities, including format conversion, structure sampling, property calculation, and data visualization, accessible through both interactive and command-line interfaces. Its modular, extensible architecture ensures accessibility for users of all experience levels while allowing seamless integration of new features. By automating complex tasks and enhancing productivity, GPUMDkit substantially lowers the barrier to using GPUMD and NEP programs. This article describes the program architecture and demonstrates its capabilities through practical applications.

cond-mat.mtrl-sci↗

arXiv2025

Thermal conductivities of monolayer graphene oxide from machine learning molecular dynamics simulations

Graphene oxide (GO) exhibits rich chemical heterogeneity that strongly influences its structural, thermal, and mechanical properties, yet quantitatively linking reduction chemistry to heat transport remains challenging. In this work, we develop a machine-learned neuroevolution potential (NEP) trained on an existing density functional theory dataset (\textit{Angew.\ Chem.\ Int.\ Ed.}, \textbf{63} , e202410088 (2024)), achieving reasonable accuracy at a computational cost much lower than the existing machine-learned and empirical potentials. Leveraging this potential, we perform large-scale molecular dynamics (MD) simulations to model the thermal reduction of GO across realistic structural domains. Using the homogeneous nonequilibrium MD method with a proper quantum-statistical correction scheme, we find that reduced GO exhibits strongly suppressed thermal conductivities, ranging from a few to tens of Wm$^{-1}$K$^{-1}$, substantially lower than pristine GO without defects and far below graphene. Moreover, the thermal conductivity of reduced GO increases moderately with increasing OH/O ratio, except at the highest oxidation level (O/C=0.5) where this trend inverts, while decreasing significantly with increasing O/C ratio, a trend strongly correlated with the fraction of recovered graphene-like structures. Our work provides a computationally tractable and predictive atomistic machine learning framework for exploring how chemical structure governs heat transport in heterogeneous carbon materials.

physics.chem-ph↗

arXiv2025

Stabilisation of hBN/SiC Heterostructures with Vacancies and Transition-Metal Atoms

When two-dimensional atomic layers of different materials are brought into close proximity to form van der Waals (vdW) heterostructures, interactions between adjacent layers significantly influence their physicochemical properties. These effects seem particularly pronounced when the interface exhibits local order and near-perfect structural alignment, leading to the emergence of Moiré patterns. Using quantum mechanical density functional theory calculations, we propose a prototypical bilayer heterostructure composed of hexagonal boron nitride (hBN) and silicon carbide (SiC), characterized by a lattice mismatch of 18.77\% between their primitive unit cells. We find that the removal of boron atoms from specific lattice sites can convert the interlayer interaction from weak vdW coupling to robust localized silicon-nitrogen covalent bonding. Motivated by this, we study the binding of transition-metal adatoms and formulate design guidelines to enhance surface reactivity, thereby enabling the controlled isolation of single-metal atoms. Our machine-learning-assisted molecular dynamics simulations confirm both dynamical stability and metal anchoring feasibility at finite temperatures. Our results suggest the hBN/SiC heterostructure as a versatile platform for atomically precise transition-metal functionalization, having potential for next-generation catalytic energy-conversion technologies.

cond-mat.mtrl-sci↗

arXiv2025

Atomistic understanding of hydrogen bubble-induced embrittlement in tungsten enabled by machine learning molecular dynamics

Hydrogen bubble formation within nanoscale voids is a critical mechanism underlying the embrittlement of metallic materials, yet its atomistic origins remains elusive. Here, we present an accurate and transferable machine-learned potential (MLP) for the tungsten-hydrogen binary system within the neuroevolution potential (NEP) framework, trained through active learning on extensive density functional theory data. The developed NEP-WH model reproduces a wide range of lattice and defect properties in tungsten systems, as well as hydrogen solubility, with near first-principles accuracy, while retaining the efficiency of empirical potentials. Crucially, it is the first MLP capable of capturing hydrogen trapping and H\textsubscript{2} formation in nanovoids, with quantitative fidelity. Large-scale machine-learning molecular dynamics simulations reveal a distinct aggregation pathway where planar hydrogen clusters nucleate and grow along \{100\} planes near voids, with hexagonal close-packed structures emerging at their intersections. Under uniaxial tension, these aggregates promote bubble fracture and the development of regular \{100\} cracks, suppressing dislocation activity and resulting in brittle fracture behavior. This work provides detailed atomistic insights into hydrogen bubble evolution and fracture in nanovoids, enables predictive modeling of structural degradation in extreme environments, and advances fundamental understanding of hydrogen-induced damage in structural metals.

cond-mat.mtrl-sci↗

arXiv2025

Revealing the impact of chemical short-range order on radiation damage in MoNbTaVW high-entropy alloys using a machine-learning potential

The effect of chemical short-range order (CSRO) on primary radiation damage in MoNbTaVW high-entropy alloys is investigated using hybrid Monte Carlo/molecular dynamics simulations with a machine-learned potential. We show that CSRO enhances radiation tolerance by promoting interstitial diffusion while suppressing vacancy migration, thereby increasing defect recombination efficiency during recovery stage. However, CSRO is rapidly degraded under cumulative irradiation, with Warren-Cowley parameters dropping below 0.3 at a dose of only 0.03~dpa. This loss of ordering reduces the long-term enhancement of CSRO on radiation resistance. Our results highlight that while CSRO can effectively improve the radiation tolerance of MoNbTaVW, its stability under irradiation is critical to realizing and sustaining this benefit.

cond-mat.mtrl-sci↗

arXiv2025

NEP89: Universal neuroevolution potential for inorganic and organic materials across 89 elements

While machine-learned interatomic potentials offer near-quantum-mechanical accuracy for atomistic simulations, many are material-specific or computationally intensive, limiting their broader use. Here, we introduce NEP89, a foundation model based on neuroevolution potential architecture, delivering near-empirical-potential speed and high accuracy across 89 elements. A compact yet comprehensive training dataset covering inorganic and organic materials was curated through descriptor-space subsampling and iterative refinement across multiple datasets. NEP89 achieves competitive accuracy compared to representative foundation models while being three to four orders of magnitude more computationally efficient, enabling previously impractical large-scale atomistic simulations of inorganic and organic systems. In addition to its out-of-the-box applicability to diverse scenarios, including million-atom-scale compression of compositionally complex alloys, ion diffusion in solid-state electrolytes and water, rocksalt dissolution, methane combustion, and protein-ligand dynamics, NEP89 also supports fine-tuning for rapid adaptation to user-specific applications, such as mechanical, thermal, structural, and spectral properties of two-dimensional materials, metallic glasses, and organic crystals.

cond-mat.mtrl-sci↗

arXiv2025

Structural and transport properties of LiTFSI/G3 electrolyte with machine-learned molecular dynamics

The lithium bis(trifluoromethylsulfonyl)azanide-triglyme electrolyte plays a critical role in the performance of lithium-ion batteries. However, its solvation structure and transport properties at the atomic scale remain incompletely understood. In this study, we develop an efficient and accurate neuroevolution potential (NEP) model by integrating bootstrap and active learning strategies. Using machine-learned NEP-driven molecular dynamics simulations, we explore the structural and diffusion properties of LiTFSI/G3 across a wide range of the solute-to-solvent ratios, systematically analyzing electrolyte density, ion coordination, viscosity, and lithium self-diffusion. The computed densities show excellent agreement with experimental data, and pair correlation analysis reveals significant interactions between lithium ions and surrounding oxygen atoms, which strongly impacts Li$^+$ mobility. Viscosity and diffusion calculations further demonstrate that increasing LiTFSI concentration enhances Li-O interactions, resulting in higher viscosity and reduced lithium diffusion. Additionally, machine learning-based path integral molecular dynamics (PIMD) simulations confirm the negligible impact of quantum effects on Li$^+$ transport. The electrolyte-specific protocol developed in this work provides a systematic framework for constructing high-fidelity machine learning potentials for complex systems.

cond-mat.mtrl-sci↗

arXiv2025

Softening of Vibrational Modes and Anharmonicity Induced Thermal Conductivity Reduction in a-Si:H at High Temperatures

Hydrogenated amorphous silicon (a-Si:H) has garnered considerable attention in the semiconductor industry, particularly for its use in solar cells and passivation layers for high performance silicon solar cells, owing to its exceptional photoelectric properties and scalable manufacturing processes. A comprehensive understanding of thermal transport mechanism in a-Si:H is essential for optimizing thermal management and ensuring the reliable operation of these devices. In this study, we developed a neuroevolution machine learning potential based on first-principles calculations of energy, forces, and virial, which enables accurate modeling of interatomic interactions in both a-Si:H and a-Si systems. Using the homogeneous nonequilibrium molecular dynamics (HNEMD) method, we systematically investigated the thermal conductivity of a-Si:H and a-Si across a temperature range of 300-1000 K and hydrogen concentrations ranging from 6 to 12 at%. Our simulation results found that thermal conductivity of a-Si:H with 12 at% hydrogen was significantly reduced by 12% compared to that of a-Si at 300 K. We analyzed the spectral thermal conductivity, vibrational density of states and lifetimes of vibrational modes, and revealed the softening of vibrational modes and anharmonicity effects contribute to the reduction of thermal conductivity as temperature and hydrogen concentration increase. Furthermore, the influence of hydrogen concentration and temperature on diffuson and propagon contribution to thermal conductivity of a-Si:H was revealed. This study provides valuable insights for developing thermal management strategies in silicon-based semiconducting devices and advances the understanding of thermal transport in amorphous systems.

cond-mat.mtrl-sci↗

arXiv2025

Advances in modeling complex materials: The rise of neuroevolution potentials

Interatomic potentials are essential for driving molecular dynamics (MD) simulations, directly impacting the reliability of predictions regarding the physical and chemical properties of materials. In recent years, machine-learned potentials (MLPs), trained against first-principles calculations, have become a new paradigm in materials modeling as they provide a desirable balance between accuracy and computational cost. The neuroevolution potential (NEP) approach, implemented in the open-source GPUMD software, has emerged as a promising machine-learned potential, exhibiting impressive accuracy and exceptional computational efficiency. This review provides a comprehensive discussion on the methodological and practical aspects of the NEP approach, along with a detailed comparison with other representative state-of-the-art MLP approaches in terms of training accuracy, property prediction, and computational efficiency. We also demonstrate the application of the NEP approach to perform accurate and efficient MD simulations, addressing complex challenges that traditional force fields typically can not tackle. Key examples include structural properties of liquid and amorphous materials, chemical order in complex alloy systems, phase transitions, surface reconstruction, material growth, primary radiation damage, fracture in two-dimensional materials, nanoscale tribology, and mechanical behavior of compositionally complex alloys under various mechanical loadings. This review concludes with a summary and perspectives on future extensions to further advance this rapidly evolving field.

cond-mat.mtrl-sci↗

arXiv2024

Density dependence of thermal conductivity in nanoporous and amorphous carbon with machine-learned molecular dynamics

Disordered forms of carbon are an important class of materials for applications such as thermal management. However, a comprehensive theoretical understanding of the structural dependence of thermal transport and the underlying microscopic mechanisms is lacking. Here we study the structure-dependent thermal conductivity of disordered carbon by employing molecular dynamics (MD) simulations driven by a machine-learned interatomic potential based on the efficient neuroevolution potential approach. Using large-scale MD simulations, we generate realistic nanoporous carbon (NP-C) samples with density varying from $0.3$ to $1.5$ g cm$^{-3}$ dominated by sp$^2$ motifs, and amorphous carbon (a-C) samples with density varying from $1.5$ to $3.5$ g cm$^{-3}$ exhibiting mixed sp$^2$ and sp$^3$ motifs. Structural properties including short- and medium-range order are characterized by atomic coordination, pair correlation function, angular distribution function and structure factor. Using the homogeneous nonequilibrium MD method and the associated quantum-statistical correction scheme, we predict a linear and a superlinear density dependence of thermal conductivity for NP-C and a-C, respectively, in good agreement with relevant experiments. The distinct density dependences are attributed to the different impacts of the sp$^2$ and sp$^3$ motifs on the spectral heat capacity, vibrational mean free paths and group velocity. We additionally highlight the significant role of structural order in regulating the thermal conductivity of disordered carbon.

cond-mat.mtrl-sci↗

arXiv2024

Minimally Invasive Flexible Needle Manipulation Based on Finite Element Simulation and Cross Entropy Method

We present a novel approach for minimally invasive flexible needle manipulations by pairing a real-time finite element simulator with the cross-entropy method. Additionally, we demonstrate how a kinematic-driven bang-bang controller can complement the control framework for better tracking performance. We show how electromagnetic (EM) tracking can be readily incorporated into the framework to provide controller feedback. Tissue phantom experiment with EM tracking shows the average targeting error is $0.16 \pm 0.29mm$.

cs.RO↗

arXiv2024

General-purpose machine-learned potential for 16 elemental metals and their alloys

Machine-learned potentials (MLPs) have exhibited remarkable accuracy, yet the lack of general-purpose MLPs for a broad spectrum of elements and their alloys limits their applicability. Here, we present a feasible approach for constructing a unified general-purpose MLP for numerous elements, demonstrated through a model (UNEP-v1) for 16 elemental metals and their alloys. To achieve a complete representation of the chemical space, we show, via principal component analysis and diverse test datasets, that employing one-component and two-component systems suffices. Our unified UNEP-v1 model exhibits superior performance across various physical properties compared to a widely used embedded-atom method potential, while maintaining remarkable efficiency. We demonstrate our approach's effectiveness through reproducing experimentally observed chemical order and stable phases, and large-scale simulations of plasticity and primary radiation damage in MoTaVW alloys. This work represents a significant leap towards a unified general-purpose MLP encompassing the periodic table, with profound implications for materials science.

cond-mat.mtrl-sci↗

arXiv2024

Correcting force error-induced underestimation of lattice thermal conductivity in machine learning molecular dynamics

Machine learned potentials (MLPs) have been widely employed in molecular dynamics (MD) simulations to study thermal transport. However, literature results indicate that MLPs generally underestimate the lattice thermal conductivity (LTC) of typical solids. Here, we quantitatively analyze this underestimation in the context of the neuroevolution potential (NEP), which is a representative MLP that balances efficiency and accuracy. Taking crystalline silicon, GaAs, graphene, and PbTe as examples, we reveal that the fitting errors in the machine-learned forces against the reference ones are responsible for the underestimated LTC as they constitute external perturbations to the interatomic forces. Since the force errors of a NEP model and the random forces in the Langevin thermostat both follow a Gaussian distribution, we propose an approach to correcting the LTC by intentionally introducing different levels of force noises via the Langevin thermostat and then extrapolating to the limit of zero force error. Excellent agreement with experiments is obtained by using this correction for all the prototypical materials over a wide range of temperatures. Based on spectral analyses, we find that the LTC underestimation mainly arises from increased phonon scatterings in the low-frequency region caused by the random force errors.

cond-mat.mtrl-sci↗

arXiv2024

Molecular dynamics simulations of heat transport using machine-learned potentials: A mini review and tutorial on GPUMD with neuroevolution potentials

Molecular dynamics (MD) simulations play an important role in understanding and engineering heat transport properties of complex materials. An essential requirement for reliably predicting heat transport properties is the use of accurate and efficient interatomic potentials. Recently, machine-learned potentials (MLPs) have shown great promise in providing the required accuracy for a broad range of materials. In this mini review and tutorial, we delve into the fundamentals of heat transport, explore pertinent MD simulation methods, and survey the applications of MLPs in MD simulations of heat transport. Furthermore, we provide a step-by-step tutorial on developing MLPs for highly efficient and predictive heat transport simulations, utilizing the neuroevolution potentials (NEPs) as implemented in the GPUMD package. Our aim with this mini review and tutorial is to empower researchers with valuable insights into cutting-edge methodologies that can significantly enhance the accuracy and efficiency of MD simulations for heat transport studies.

cond-mat.mtrl-sci↗

arXiv2024

Shape Manipulation of Bevel-Tip Needles for Prostate Biopsy Procedures: A Comparison of Two Resolved-Rate Controllers

Prostate cancer diagnosis continues to encounter challenges, often due to imprecise needle placement in standard biopsies. Several control strategies have been developed to compensate for needle tip prediction inaccuracies, however none were compared against each other, and it is unclear whether any of them can be safely and universally applied in clinical settings. This paper compares the performance of two resolved-rate controllers, derived from a mechanics-based and a data-driven approach, for bevel-tip needle control using needle shape manipulation through a template. We demonstrate for a simulated 12-core biopsy procedure under model parameter uncertainty that the mechanics-based controller can better reach desired targets when only the final goal configuration is presented even with uncertainty on model parameters estimation, and that providing a feasible needle path is crucial in ensuring safe surgical outcomes when either controller is used for needle shape manipulation.

cs.RO↗

arXiv2023

Bevel-Tip Needle Deflection Modeling, Simulation, and Validation in Multi-Layer Tissues

Percutaneous needle insertions are commonly performed for diagnostic and therapeutic purposes as an effective alternative to more invasive surgical procedures. However, the outcome of needle-based approaches relies heavily on the accuracy of needle placement, which remains a challenge even with robot assistance and medical imaging guidance due to needle deflection caused by contact with soft tissues. In this paper, we present a novel mechanics-based 2D bevel-tip needle model that can account for the effect of nonlinear strain-dependent behavior of biological soft tissues under compression. Real-time finite element simulation allows multiple control inputs along the length of the needle with full three-degree-of-freedom (DOF) planar needle motions. Cross-validation studies using custom-designed multi-layer tissue phantoms as well as heterogeneous chicken breast tissues result in less than 1mm in-plane errors for insertions reaching depths of up to 61 mm, demonstrating the validity and generalizability of the proposed method.

cs.RO↗

arXiv2023

Combining linear-scaling quantum transport and machine-learning molecular dynamics to study thermal and electronic transports in complex materials

We propose an efficient approach for simultaneous prediction of thermal and electronic transport properties in complex materials. Firstly, a highly efficient machine-learned neuroevolution potential is trained using reference data from quantum-mechanical density-functional theory calculations. This trained potential is then applied in large-scale molecular dynamics simulations, enabling the generation of realistic structures and accurate characterization of thermal transport properties. In addition, molecular dynamics simulations of atoms and linear-scaling quantum transport calculations of electrons are coupled to account for the electron-phonon scattering and other disorders that affect the charge carriers governing the electronic transport properties. We demonstrate the usefulness of this unified approach by studying thermoelectric transport properties of a graphene antidot lattice.

cond-mat.mtrl-sci↗

arXiv2023

Quantum-corrected thickness-dependent thermal conductivity in amorphous silicon predicted by machine-learning molecular dynamics simulations

Amorphous silicon (a-Si) is an important thermal-management material and also serves as an ideal playground for studying heat transport in strongly disordered materials. Theoretical prediction of the thermal conductivity of a-Si in a wide range of temperatures and sample sizes is still a challenge. Herein we present a systematic investigation of the thermal transport properties of a-Si by employing large-scale molecular dynamics (MD) simulations with an accurate and efficient machine-learned neuroevolution potential (NEP) trained against abundant reference data calculated at the quantum-mechanical density-functional-theory level. The high efficiency of NEP allows us to study the effects of finite size and quenching rate in the formation of a-Si in great detail. We find that it requires a simulation cell up to $64,000$ atoms (a cubic cell with a linear size of 11 nm) and a quenching rate down to $10^{11}$ K s$^{-1}$ for fully convergent thermal conductivity. Structural properties, including short- and medium-range order as characterized by the pair correlation function, angular distribution function, coordination number, ring statistics and structure factor are studied to demonstrate the accuracy of NEP and to further evaluate the role of quenching rate. Using both the heterogeneous and the homogeneous nonequilibrium MD methods and the related spectral decomposition techniques, we calculate the temperature- and thickness-dependent thermal conductivity values of a-Si and show that they agree well with available experimental results from 10 K to room temperature. Our results also highlight the importance of quantum effects in the calculated thermal conductivity and support the quantum correction method based on the spectral thermal conductivity.

cond-mat.mtrl-sci↗