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Sun, Hong

Publications and source records attributed to Sun, Hong.

At least 19 records

Ice Phase Classification Made Easy with Score-Based Denoising

Accurate identification of ice phases is essential for understanding various physicochemical phenomena. However, such classification for structures simulated with molecular dynamics is complicated by the complex symmetries of ice polymorphs and thermal fluctuations. For this purpose, both traditional order parameters and data-driven machine learning approaches have been employed, but they often rely on expert intuition, specific geometric information, or large training data sets. In this work, we present an unsupervised phase classification framework that combines a score-based denoiser model with a subsequent model-free classification method to accurately identify ice phases. Further, the denoiser model is trained on perturbed synthetic data of ideal reference structures, eliminating the need for large data sets and labeling efforts. The classification step utilizes the smooth overlap of atomic position (SOAP) descriptors as the atomic fingerprint, ensuring Euclidean symmetries and transferability to various structural systems. Our approach achieves a remarkable 100% accuracy in distinguishing ice phases of test trajectories using only seven ideal reference structures of ice phases as model inputs. This demonstrates the generalizability of the score-based denoiser model in facilitating phase identification for complex molecular systems. The proposed classification strategy can be broadly applied to investigate structural evolution and phase identification for a wide range of materials, offering new insights into the fundamental understanding of water and other complex systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-kernel Edge Attention Graph Autoencoder

MEAGraph (Multi-kernel Edge Attention Graph Autoencoder) is a graph-based autoencoder model designed for unsupervised data mining for datasets used in machine learning potentials. It provides accurate clustering for atomic environment identification, unsupervised and unlabeled data pruning for dataset construction.

Sun, Hong↗

Exploring structural transitions at grain boundaries in Nb using a generalized embedded atom interatomic potential

The advancement in experimental techniques, like the atom probe tomography and high resolution electron microscopy, is fueling interest in studying structural transformations of grain boundaries in metal and alloys to uncover correlations between mechanical properties and solute or impurity segregation to grain boundaries. Atomistic modeling is an important tool that can pinpoint the intricate dynamics of grain boundary phase transitions, but the lack of accurate interatomic potentials needed to simulate the complex dynamics of grain boundary structural transitions and identify different metastable phases has been the bottleneck. To this end, we use niobium as a model body centered cubic (BCC) metal and develop an interatomic potential to study grain boundary phase transitions. The potential for Nb is based on a generalization of the embedded atomic method potential and has sufficient flexibility to learn complex energy landscapes using a small set of training structures. We systematically test and validate the using data from ab initio density functional theory calculations and experiments. Using this potential, we calculate energies of multiple symmetric-tilt grain boundaries spanning a wide range of misorientation angles. Additionally, we explore different metastable structures of the Σ 27(552) [$1\overline{1}0$] grain boundary and use molecular dynamic simulations to study the coexistence of metastable phases and grain boundary transitions at finite temperature.

36 MATERIALS SCIENCE↗

Graph-EAM: An Interpretable and Efficient Graph Neural Network Potential Framework

The development of deep learning interatomic potentials has enabled efficient and accurate computations in quantum chemistry and materials science, circumventing computationally expensive ab initio calculations. However, the huge number of learnable parameters in deep learning models and their complex architectures hinder physical interpretability and affect the robustness of the derived potential. In this work, we propose graph-EAM, a lightweight graph neural network (GNN) inspired by the empirical embedded atom method to model the interatomic potential of single-element structures. Four material systems: platinum, niobium, silicon, and amorphous-carbon, for which quantum simulation data sets are publicly available, are examined to demonstrate that graph-EAM can achieve high energy and force prediction accuracy-comparable or better than existing state-of-the-art machine learning models-with much fewer parameters. It is also shown that the explicit inclusion of the angular information via three-body atomic density increases the prediction accuracy. In conclusion, the accuracy and efficiency of potentials obtained from graph-EAM can help accelerate the molecular dynamics simulation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Effect of different organic acid additives on the fermentation quality and bacterial community of paper mulberry (Broussonetia papyrifera) silage

To investigate the effects of different organic acid additives and their concentrations on the fermentation quality and bacterial community of paper mulberry silage, paper mulberry was left untreated (control) or was treated with ethylenediaminetetraacetic acid (EDTA), propionic acid (PA) or citric acid (CA), the amount of each additive was 2 g.kg −1 FM, 5 g.kg −1 FM and g.kg −1 FM. All groups were ensiled for 3, 7, 15, 30 and 60 days. Compared to the control, adding EDTA reduced protein breakdown, preserved more water-soluble carbohydrates of the silages (WSCs, 24.74 g.kg −1 DM), and high concentrations of EDTA inhibited the activity of undesirable microorganisms. Adding PA increased the abundance of Lactiplantibacillus and decreased the abundance of Enterococcus , and it caused a rapid decrease in the pH of the silage at an early stage (from 6.50 to 5.31) while altering the microbiota, and low concentrations of PA resulted in high LA (66.22 g.kg −1 DM) concentration and low PA (9.92 g.kg −1 DM) concentration at 60 days of ensiling. Different concentrations of additives altered the microbial community of paper mulberry to different degrees. High concentrations of PA and CA can increase the abundance of Lactiplantibacillus . High concentrations of CA resulted in a rapid decrease in silage pH at an early stage and higher WSC concentration. These results suggest that EDTA, PA and CA can be used as additives to improve the quality of paper mulberry silage.

Li, Mengxin↗

Angle-dependent magnetoresistance as a sensitive probe of the charge density wave in quasi-one-dimensional semimetal Ta 2 NiSe 7

The behavior of charge density waves (CDWs) in an external magnetic field is dictated by both orbital and Pauli (Zeeman) effects. A quasi-one-dimensional (Q1D) system features Q1D Fermi surfaces that allow these effects to be distinguished, which in turn can provide a sensitive probe to the underlying electronic states. Furthermore, we studied the field dependence of an incommensurate CDW in a transition-metal chalcogenide Ta 2 NiSe 7 with a Q1D chain structure. The angle-dependent magnetoresistance (MR) is found to be very sensitive to the relative orientation between the magnetic field and the chain direction. With an applied current fixed along the b axis (the chain direction), the angle-dependent MR shows a striking change of the symmetry below T CDW only for a rotating magnetic field in the ac plane. In contrast, the symmetry axis remains unchanged for other configurations (H in ab and bc planes). The orbital effect conforms to the lattice symmetry, while the Pauli effect in the form of μ B B/ℏv F can be responsible for such symmetry change, provided that the Fermi velocity v F is significantly anisotropic and the nesting vector changes in a magnetic field, which is corroborated by our first-principles calculations. Our results show that the angle-dependent MR is a sensitive transport probe of CDW and can be useful for the study of low-dimensional systems in general.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Bis‐isoindigos: New Electron‐Deficient Building Blocks for Constructing Conjugated Polymers with Extended Electron Delocalization

Abstract Incorporation of acceptor‐acceptor (A‐A) type moieties into donor‐acceptor (D‐A) type conjugated polymers becomes a new strategy to tune their electronic properties. In this work, we first demonstrate an efficient convergent route to prepare isoindigo‐based A‐A type building blocks ‐ bis‐isoindigos ‐ via the palladium‐catalyzed oxidative coupling. Bis‐isoindigo‐based polymers show high planarity and delocalized frontier molecular orbitals with lowered LUMO and intact HOMO energy levels, in comparison with their corresponding mono‐isoindigo counterparts. Moreover, fluorine substitution on donors only lowers HOMO levels of Bis‐IID polymers. This study asserts that the D‐A‐A strategy is effective in selectively tuning FMO energy levels of conjugated polymers, complementary to the D‐D‐A approach for the HOMO energy level tuning.

Luo, Xuyi↗

High ALDH activity defines ovarian cancer stem-like cells with enhanced invasiveness and EMT progress which are responsible for tumor invasion

Highlights: • Pluripotent, invasive and EMT-related genes are positively correlated. • The definition of ovarian ALDH{sup high} CSCLs is verified by their higher colony-formation, multipotent-genes expression and tumorigenicity. • Ovarian ALDH{sup high} CSCLs display advanced invasiveness, EMT progress and apoptosis-resistance. • ALDH{sup high} CSCLs take chief charge of EOC invasion, due to their elevated stemness and metastatic features. Epithelial ovarian cancer (EOC) is highly metastatic and current therapeutics are unsatisfactory. Cancer stem/stem-like cells (CSCs/CSCLs) represent a rare population of undifferentiated oncogenic cells responsible for tumor initiation and maintenance. We identified ovarian cancer ALDH{sup high} (aldehyde dehydrogenase) population could perform not only strengthened CSCLs properties embodied in colony-formation, CSCs-markers expression, and tumorigenesis in vivo, but also a greater invasive capacity with advanced EMT progress and anti-apoptosis compared with ALDH{sup low} cells. Furthermore, both the stemness and aggressive features, along with ALDH{sup high} percentages were in positive association with the invasiveness of cell lines for sorting, indicating the promotive role of ALDH{sup high} CSCLs in EOC neoplasia and metastasis, since the whole tumor was derived from the CSCLs with hyperactive self-renewal and aggression. Collectively, this study illustrates the interplay between ALDH{sup high} CSCLs and EOC invasion, and offers a novel application target for the EOC oncotherapy.

60 APPLIED LIFE SCIENCES↗

Synthesis and structural characterization of a Cu(I) complex with 4-(1H-imidazol-1-yl)phenyl)methanone ligands

A copper complex with V-shaped ligands, [(L{sup 1})Cu{sub 2}Cl{sub 2}]{sub n} (1), (L1 = 4-(1H-imidazol-1-yl)phenyl) methanone) has been synthesized and characterized by IR spectroscopy, elemental analyses and singlecrystal X-ray diffraction. The crystal of 1 is monoclinic, sp. gr. C2/{sub c} with the unit cell parameters a = 17.9496(13), b = 15.3440(13), c = 7.2983(7) Å, and β = 112.875(6)°, Z = 4, R{sub 1} = 0.0681, and wR{sub 2} = 0.1736 (I > 2 σ). The solid state structure of 1 consists of 2D metal aromatic chloride layers, which are propagating along the bc plane to form a 3D network through hydrogen bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SATB2 expression increased anchorage-independent growth and cell migration in human bronchial epithelial cells

The special AT-rich sequence-binding protein 2 (SATB2) is a protein that binds to the nuclear matrix attachment region of the cell and regulates gene expression by altering chromatin structure. In our previous study, we reported that SATB2 gene expression was induced in human bronchial epithelial BEAS-2B cells transformed by arsenic, chromium, nickel and vanadium. In this study, we show that ectopic expression of SATB2 in the normal human bronchial epithelial cell-line BEAS-2B increased anchorage-independent growth and cell migration, meanwhile, shRNA-mediated knockdown of SATB2 significantly decreased anchorage-independent growth in Ni transformed BEAS-2B cells. RNA sequencing analyses of SATB2 regulated genes revealed the enrichment of those involved in cytoskeleton, cell adhesion and cell-movement pathways. Our evidence supports the hypothesis that SATB2 plays an important role in BEAS-2B cell transformation. - Highlights: • We performed SATB2 overexpression in the BEAS-2B cell line. • We performed SATB2 knockdown in a Ni transformed BEAS-2B cell line. • SATB2 induced anchorage-independent growth and increased cell migration. • SATB2 knockdown significantly decreased anchorage-independent growth. • We identified alterations in gene involved in cytoskeleton, cell adhesion.

60 APPLIED LIFE SCIENCES↗

Gene expression and pathway analysis of human hepatocellular carcinoma cells treated with cadmium

Cadmium (Cd) is a toxic and carcinogenic metal naturally occurring in the Earth's crust. A common route of human exposure is via diet and cadmium accumulates in the liver. The effects of Cd exposure on gene expression in human hepatocellular carcinoma (HepG2) cells were examined in this study. HepG2 cells were acutely-treated with 0.1, 0.5, or 1.0 μM Cd for 24 h; or chronically-treated with 0.01, 0.05, or 0.1 μM Cd for three weeks and gene expression analysis was performed using Affymetrix GeneChip® Human Gene 1.0 ST Arrays. Acute and chronic exposures significantly altered the expression of 333 and 181 genes, respectively. The genes most upregulated by acute exposure included several metallothioneins. Downregulated genes included the monooxygenase CYP3A7, involved in drug and lipid metabolism. In contrast, CYP3A7 was upregulated by chronic Cd exposure, as was DNAJB9, an anti-apoptotic J protein. Genes downregulated following chronic exposure included the transcriptional regulator early growth response protein 1. Ingenuity Pathway Analysis revealed that the top networks altered by acute exposure were lipid metabolism, small molecule biosynthesis, cell morphology, organization, and development; while top networks altered by chronic exposure were organ morphology, cell cycle, cell signaling, and renal and urological diseases/cancer. Many of the dysregulated genes play important roles in cellular growth, proliferation, and apoptosis, and may be involved in carcinogenesis. In addition to gene expression changes, HepG2 cells treated with cadmium for 24 h indicated a reduction in global levels of histone methylation and acetylation that persisted 72 h post-treatment. - Highlights: • A common route of human exposure to the carcinogenic metal cadmium is via diet. • HepG2 cells were treated acutely or chronically with varying doses of cadmium. • Gene expression analysis was performed using Affymetrix Human Gene 1.0 Arrays. • Acute and chronic exposures altered the expression of 333 and 181 genes, respectively. • Acute cadmium exposure altered global levels of histone methylation and acetylation.

60 APPLIED LIFE SCIENCES↗

Tungsten-induced carcinogenesis in human bronchial epithelial cells

Metals such as arsenic, cadmium, beryllium, and nickel are known human carcinogens; however, other transition metals, such as tungsten (W), remain relatively uninvestigated with regard to their potential carcinogenic activity. Tungsten production for industrial and military applications has almost doubled over the past decade and continues to increase. Here, for the first time, we demonstrate tungsten's ability to induce carcinogenic related endpoints including cell transformation, increased migration, xenograft growth in nude mice, and the activation of multiple cancer-related pathways in transformed clones as determined by RNA sequencing. Human bronchial epithelial cell line (Beas-2B) exposed to tungsten developed carcinogenic properties. In a soft agar assay, tungsten-treated cells formed more colonies than controls and the tungsten-transformed clones formed tumors in nude mice. RNA-sequencing data revealed that the tungsten-transformed clones altered the expression of many cancer-associated genes when compared to control clones. Genes involved in lung cancer, leukemia, and general cancer genes were deregulated by tungsten. Taken together, our data show the carcinogenic potential of tungsten. Further tests are needed, including in vivo and human studies, in order to validate tungsten as a carcinogen to humans. - Highlights: • Tungsten (W) induces cell transformation and increases migration in vitro. • W increases xenograft growth in nude mice. • W altered the expression of cancer-related genes such as those involved in leukemia. • Some of the dysregulated leukemia genes include, CD74, CTGF, MST4, and HOXB5. • For the first time, data is presented that demonstrates tungsten's carcinogenic potential.

60 APPLIED LIFE SCIENCES↗

Superior magnetic and mechanical property of MnFe 3 N driven by electron correlation and lattice anharmonicity

Manganese-substitution-doped iron nitride MnFe 3 N holds great promise for applications in high-density magnetic recording and spintronic devices. However, existing theory contradicts experimental results on the structural and magnetic stability of MnFe 3 N, and the underlying mechanisms remain elusive. Here we demonstrate by first-principles calculations that the ferromagnetic state with enhanced magnetization in MnFe 3 N is driven by the electron correlation effect not previously considered. We further reveal a large nonlinear shear plasticity, which produces an unexpectedly high shear strength in MnFe 3 N despite its initial ductile nature near the equilibrium structure. Moreover, we identify strong lattice anharmonicity that plays a pivotal role in stabilizing MnFe 3 N under high pressures at room temperature. These remarkable properties stem from the intriguing bonding nature of the parent compound Fe 4 N. Lastly, our results explain experimental results and offer insights into the fundamental mechanisms for the superior magnetic and mechanical properties of MnFe 3 N.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗