arXiv subjects

Sheng Gong

Publications and source records attributed to Sheng Gong.

16 recordsLinked to original sources

arXiv2025

Accelerated Machine Learning Force Field for Predicting Thermal Conductivity of Organic Liquids

The thermal conductivity of organic liquids is a vital parameter influencing various industrial and environmental applications, including energy conversion, electronics cooling, and chemical processing. However, atomistic simulation of thermal conductivity of organic liquids has been hindered by the limited accuracy of classical force fields and the huge computational demand of ab initio methods. In this work, we present a machine learning force field (MLFF)-based molecular dynamics simulation workflow to predict the thermal conductivity of 20 organic liquids. Here, we introduce the concept of differential attention into the MLFF architecture for enhanced learning ability, and we use density of the liquids to align the MLFF with experiments. As a result, this workflow achieves a mean absolute percentage error of 14% for the thermal conductivity of various organic liquids, significantly lower than that of the current off-the-shelf classical force field (78%). Furthermore, the MLFF is rewritten using Triton language to maximize simulation speed, enabling rapid prediction of thermal conductivity.

physics.chem-ph↗

arXiv2025

Artificial Intelligence Driven Workflow for Accelerating Design of Novel Photosensitizers

The discovery of high-performance photosensitizers has long been hindered by the time-consuming and resource-intensive nature of traditional trial-and-error approaches. Here, we present \textbf{A}I-\textbf{A}ccelerated \textbf{P}hoto\textbf{S}ensitizer \textbf{I}nnovation (AAPSI), a closed-loop workflow that integrates expert knowledge, scaffold-based molecule generation, and Bayesian optimization to accelerate the design of novel photosensitizers. The scaffold-driven generation in AAPSI ensures structural novelty and synthetic feasibility, while the iterative AI-experiment loop accelerates the discovery of novel photosensitizers. AAPSI leverages a curated database of 102,534 photosensitizer-solvent pairs and generate 6,148 synthetically accessible candidates. These candidates are screened via graph transformers trained to predict singlet oxygen quantum yield ($\phi_\Delta$) and absorption maxima ($\lambda_{max}$), following experimental validation. This work generates several novel candidates for photodynamic therapy (PDT), among which the hypocrellin-based candidate HB4Ph exhibits exceptional performance at the Pareto frontier of high quantum yield of singlet oxygen and long absorption maxima among current photosensitizers ($\phi_\Delta$=0.85, $\lambda_{max}$=650nm).

cond-mat.mtrl-sci↗

arXiv2025

Bridging Quantum Mechanics to Liquid Properties via a Universal Organic Force Field

Molecular dynamics simulations are essential tools for unraveling atomic-level insights into the structure and behavior of condensed-phase systems. However, the universal and accurate prediction of macroscopic properties based on quantum mechanical calculations remains a significant challenge, often hindered by the trade-off between computational cost and simulation accuracy. Here we present ByteFF-Pol, a polarizable force field parameterized by a graph neural network and trained exclusively on high-level quantum mechanical data. By leveraging physically-motivated force field forms and training strategies, ByteFF-Pol predicts thermodynamic and transport properties for a wide range of small-molecule liquids and electrolytes with high accuracy, surpassing current classical and machine learning force fields. This ability to make predictions without system-specific training bridges the gap between microscopic calculations and macroscopic liquid properties, enabling the exploration of previously intractable chemical spaces. This advancement enables the precise design of new electrolytes and custom-tailored solvents, establishing a robust foundation for data-driven materials discovery.

physics.comp-ph↗

arXiv2025

A Unified Predictive and Generative Solution for Liquid Electrolyte Formulation

Liquid electrolytes are critical components of next-generation energy storage systems, enabling fast ion transport, minimizing interfacial resistance, and ensuring electrochemical stability for long-term battery performance. However, measuring electrolyte properties and designing formulations remain experimentally and computationally expensive. In this work, we present a unified framework for designing liquid electrolyte formulation, integrating a forward predictive model with an inverse generative approach. Leveraging both computational and experimental data collected from literature and extensive molecular simulations, we train a predictive model capable of accurately estimating electrolyte properties from ionic conductivity to solvation structure. Our physics-informed architecture preserves permutation invariance and incorporates empirical dependencies on temperature and salt concentration, making it broadly applicable to property prediction tasks across molecular mixtures. Furthermore, we introduce -- to the best of our knowledge -- the first generative machine learning framework for molecular mixture design, demonstrated on electrolyte systems. This framework supports multi-condition-constrained generation, addressing the inherently multi-objective nature of materials design. As a proof of concept, we experimentally identified three liquid electrolytes with both high ionic conductivity and anion-concentrated solvation structure. This unified framework advances data-driven electrolyte design and can be readily extended to other complex chemical systems beyond electrolytes.

cond-mat.mtrl-sci↗

arXiv2024

Data-Driven Parametrization of Molecular Mechanics Force Fields for Expansive Chemical Space Coverage

A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high computational efficiency. With the rapid expansion of synthetically accessible chemical space, traditional look-up table approaches face significant challenges. In this study, we address this issue using a modern data-driven approach, developing ByteFF, an Amber-compatible force field for drug-like molecules. To create ByteFF, we generated an expansive and highly diverse molecular dataset at the B3LYP-D3(BJ)/DZVP level of theory. This dataset includes 2.4 million optimized molecular fragment geometries with analytical Hessian matrices, along with 3.2 million torsion profiles. We then trained an edge-augmented, symmetry-preserving molecular graph neural network (GNN) on this dataset, employing a carefully optimized training strategy. Our model predicts all bonded and non-bonded MM force field parameters for drug-like molecules simultaneously across a broad chemical space. ByteFF demonstrates state-of-the-art performance on various benchmark datasets, excelling in predicting relaxed geometries, torsional energy profiles, and conformational energies and forces. Its exceptional accuracy and expansive chemical space coverage make ByteFF a valuable tool for multiple stages of computational drug discovery.

cs.LG↗

arXiv2024

CrysToGraph: A Comprehensive Predictive Model for Crystal Materials Properties and the Benchmark

The ionic bonding across the lattice and ordered microscopic structures endow crystals with unique symmetry and determine their macroscopic properties. Unconventional crystals, in particular, exhibit non-traditional lattice structures or possess exotic physical properties, making them intriguing subjects for investigation. Therefore, to accurately predict the physical and chemical properties of crystals, it is crucial to consider long-range orders. While GNN excels at capturing the local environment of atoms in crystals, they often face challenges in effectively capturing longer-ranged interactions due to their limited depth. In this paper, we propose CrysToGraph ($\textbf{Crys}$tals with $\textbf{T}$ransformers $\textbf{o}$n $\textbf{Graph}$s), a novel transformer-based geometric graph network designed specifically for unconventional crystalline systems, and UnconvBench, a comprehensive benchmark to evaluate models' predictive performance on unconventional crystal materials such as defected crystals, low-dimension crystals and MOF. CrysToGraph effectively captures short-range interactions with transformer-based graph convolution blocks as well as long-range interactions with graph-wise transformer blocks. CrysToGraph proofs its effectiveness in modelling unconventional crystal materials in multiple tasks, and moreover, it outperforms most existing methods, achieving new state-of-the-art results on the benchmarks of both unconventional crystals and traditional crystals.

cond-mat.mtrl-sci↗

arXiv2024

Enhancing GPU-acceleration in the Python-based Simulations of Chemistry Framework

We describe our contribution as industrial stakeholders to the existing open-source GPU4PySCF project (https: //github.com/pyscf/gpu4pyscf), a GPU-accelerated Python quantum chemistry package. We have integrated GPU acceleration into other PySCF functionality including Density Functional Theory (DFT), geometry optimization, frequency analysis, solvent models, and density fitting technique. Through these contributions, GPU4PySCF v1.0 can now be regarded as a fully functional and industrially relevant platform which we demonstrate in this work through a range of tests. When performing DFT calculations on modern GPU platforms, GPU4PySCF delivers 30 times speedup over a 32-core CPU node, resulting in approximately 90% cost savings for most DFT tasks. The performance advantages and productivity improvements have been found in multiple industrial applications, such as generating potential energy surfaces, analyzing molecular properties, calculating solvation free energy, identifying chemical reactions in lithium-ion batteries, and accelerating neural-network methods. With the improved design that makes it easy to integrate with the Python and PySCF ecosystem, GPU4PySCF is natural choice that we can now recommend for many industrial quantum chemistry applications.

physics.comp-ph↗

arXiv2024

A predictive machine learning force field framework for liquid electrolyte development

Despite the widespread applications of machine learning force fields (MLFF) in solids and small molecules, there is a notable gap in applying MLFF to simulate liquid electrolyte, a critical component of the current commercial lithium-ion battery. In this work, we introduce BAMBOO (\textbf{B}yteDance \textbf{A}I \textbf{M}olecular Simulation \textbf{Boo}ster), a predictive framework for molecular dynamics (MD) simulations, with a demonstration of its capability in the context of liquid electrolyte for lithium batteries. We design a physics-inspired graph equivariant transformer architecture as the backbone of BAMBOO to learn from quantum mechanical simulations. Additionally, we introduce an ensemble knowledge distillation approach and apply it to MLFFs to reduce the fluctuation of observations from MD simulations. Finally, we propose a density alignment algorithm to align BAMBOO with experimental measurements. BAMBOO demonstrates state-of-the-art accuracy in predicting key electrolyte properties such as density, viscosity, and ionic conductivity across various solvents and salt combinations. The current model, trained on more than 15 chemical species, achieves the average density error of 0.01 g/cm$^3$ on various compositions compared with experiment.

cond-mat.mtrl-sci↗

arXiv2023

Multimodal machine learning for materials science: composition-structure bimodal learning for experimentally measured properties

The widespread application of multimodal machine learning models like GPT-4 has revolutionized various research fields including computer vision and natural language processing. However, its implementation in materials informatics remains underexplored, despite the presence of materials data across diverse modalities, such as composition and structure. The effectiveness of machine learning models trained on large calculated datasets depends on the accuracy of calculations, while experimental datasets often have limited data availability and incomplete information. This paper introduces a novel approach to multimodal machine learning in materials science via composition-structure bimodal learning. The proposed COmposition-Structure Bimodal Network (COSNet) is designed to enhance learning and predictions of experimentally measured materials properties that have incomplete structure information. Bimodal learning significantly reduces prediction errors across distinct materials properties including Li conductivity in solid electrolyte, band gap, refractive index, dielectric constant, energy, and magnetic moment, surpassing composition-only learning methods. Furthermore, we identified that data augmentation based on modal availability plays a pivotal role in the success of bimodal learning.

cond-mat.mtrl-sci↗

arXiv2023

Examining graph neural networks for crystal structures: limitations and opportunities for capturing periodicity

Historically, materials informatics has relied on human-designed descriptors of materials structures. In recent years, graph neural networks (GNNs) have been proposed for learning representations of crystal structures from data end-to-end producing vectorial embeddings that are optimized for downstream prediction tasks. However, a systematic scheme is lacking to analyze and understand the limits of GNNs for capturing crystal structures. In this work, we propose to use human-designed descriptors as a bank of human knowledge to test whether black-box GNNs can capture the knowledge of crystal structures. We find that current state-of-the-art GNNs cannot capture the periodicity of crystal structures well, and we analyze the limitations of the GNN models that result in this failure from three aspects: local expressive power, long-range information, and readout function. We propose an initial solution, hybridizing descriptors with GNNs, to improve the prediction of GNNs for materials properties, especially phonon internal energy and heat capacity with 90% lower errors, and we analyze the mechanisms for the improved prediction. All the analysis can be extended easily to other deep representation learning models, human-designed descriptors, and systems such as molecules and amorphous materials.

cond-mat.mtrl-sci↗

arXiv2022

A cloud platform for automating and sharing analysis of raw simulation data from high throughput polymer molecular dynamics simulations

Open material databases storing hundreds of thousands of material structures and their corresponding properties have become the cornerstone of modern computational materials science. Yet, the raw outputs of the simulations, such as the trajectories from molecular dynamics simulations and charge densities from density functional theory calculations, are generally not shared due to their huge size. In this work, we describe a cloud-based platform to facilitate the sharing of raw data and enable the fast post-processing in the cloud to extract new properties defined by the user. As an initial demonstration, our database currently includes 6286 molecular dynamics trajectories for amorphous polymer electrolytes and 5.7 terabytes of data. We create a public analysis library at https://github.com/TRI-AMDD/htp_md to extract multiple properties from the raw data, using both expert designed functions and machine learning models. The analysis is run automatically with computation in the cloud, and results then populate a database that can be accessed publicly. Our platform encourages users to contribute both new trajectory data and analysis functions via public interfaces. Newly analyzed properties will be incorporated into the database. Finally, we create a front-end user interface at https://www.htpmd.matr.io for browsing and visualization of our data. We envision the platform to be a new way of sharing raw data and new insights for the computational materials science community.

cond-mat.mtrl-sci↗

arXiv2022

Calibrating DFT formation enthalpy calculations by multi-fidelity machine learning

Machine learning materials properties measured by experiments is valuable yet difficult due to the limited amount of experimental data. In this work, we use a multi-fidelity random forest model to learn the experimental formation enthalpy of materials with prediction accuracy higher than the empirically corrected PBE functional (PBEfe) and meta-GGA functional (SCAN), and it outperforms the hotly studied deep neural-network based representation learning and transfer learning. We then use the model to calibrate the DFT formation enthalpy in the Materials Project database, and discover materials with underestimated stability. The multi-fidelity model is also used as a data-mining approach to find how DFT deviates from experiments by the explaining the model output.

cond-mat.mtrl-sci↗

arXiv2020

Screening and understanding Li adsorption on 2-dimensional metallic materials by learning physics

Two-dimensional (2D) materials have received considerable attention as possible electrodes in Li-ion batteries (LIBs), although a deeper understanding of the Li adsorption behavior as well as broad screening of the materials space is still needed. In this work, we build a high-throughput screening scheme that incorporates a learned interaction. First, density functional theory and graph convolution networks are utilized to calculate minimum Li adsorption energies for a small set of 2D metallic materials. The data is then used to find a dependence of the minimum Li adsorption energies on the sum of ionization potential, work function of the 2D metal, and coupling energy between Li+ and substrate. Our results show that variances of elemental properties and density are the most correlated features with coupling. To illustrate the applicability of this approach, the model is employed to show that some fluorides and chromium oxides are potential high-voltage materials with adsorption energies < -7 eV, and the found physics is used as the design principle to enhance the Li adsorption ability of graphene. This physics-driven approach shows higher accuracy and transferability compared with purely data-driven models.

cond-mat.mtrl-sci↗

arXiv2020

Charting Lattice Thermal Conductivity of Inorganic Crystals

Thermal conductivity is a fundamental material property but challenging to predict, with less than 5% out of about $10^5$ synthesized inorganic materials being documented. In this work, we extract the structural chemistry that governs lattice thermal conductivity, by combining graph neural networks and random forest approaches. We show that both mean and variation of unit-cell configurational properties, such as atomic volume and bond length, are the most important features, followed by mass and elemental electronegativity. We chart the structural chemistry of lattice thermal conductivity into extended van-Arkel triangles, and predict the thermal conductivity of all known inorganic materials in the Inorganic Crystal Structure Database. For the latter, we develop a transfer learning framework extendable for other applications.

cond-mat.mtrl-sci↗

arXiv2019

Predicting charge density distribution of materials using a local-environment-based graph convolutional network

Electron charge density distribution of materials is one of the key quantities in computational materials science as theoretically it determines the ground state energy and practically it is used in many materials analyses. However, the scaling of density functional theory calculations with number of atoms limits the usage of charge-density-based calculations and analyses. Here we introduce a machine learning scheme with local-environment-based graphs and graph convolutional neural networks to predict charge density on grid-points from crystal structure. We show the accuracy of this scheme through a comparison of predicted charge densities as well as properties derived from the charge density, and the scaling is O(N). More importantly, the transferability is shown to be high with respect to different compositions and structures, which results from the explicit encoding of geometry.

physics.comp-ph↗

arXiv2017

Atomistic simulation of the Coupled adsorption and unfolding of protein GB1 on the polystyrenes nanoparticle surface

Protein adsorption/desorption upon nanoparticle surfaces is an important process to understand for developing new nanotechnology involving biomaterials, while atomistic picture of the process and its coupling with protein conformational change is lacking. Here we report our study on the adsorption of protein GB1 upon a polystyrene nanoparticle surface using atomistic molecular dynamic simulations. Enabled by metadynamics, we explored the relevant phase space and identified three protein states; each protein state involved both the adsorbed and desorbed states. We also studied the change of secondary and tertiary structures of GB1 during adsorption, and the dominant interactions between protein and surface in different adsorbing stages. From the simulation results we obtained a scenario that is more rational and complete than the conventional one. We believe the new scenario is more appropriate as a theoretical model in understanding and explaining experimental signals. Introduction

physics.bio-ph↗