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    Advanced Theory And Simulations

    Advanced Theory And Simulations

    JournalISSN 2513-0390eISSN 2513-0390中科院 工程技术 3区

    年发文量

    研究主题

    论文(2232)

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    1Computational Prioritization of Gc1qr Binding Candidates at the C1q Interaction Surface
    Ibrahim Maher,Ibrahim Khater,Mona H. Ibraheim

    ABSTRACT Cancer cells evade complement‐mediated immune clearance by secreting the receptor gC1qR, which binds C1q and inhibits classical pathway activation. Disrupting the C1q‐gC1qR interaction offers a novel immunotherapeutic strategy to restore antitumor immunity. Here, we conducted an in silico study to characterize the C1q‐gC1qR interface and identify small‐molecule candidates. Protein‐protein docking and MM/GBSA calculations revealed hydrogen bonds and identified Lys173 and Lys200 on C1q as critical hotspot residues, with a binding free energy of −107.79 kcal/mol. Pharmacophore models were generated using ZINCPharmer, screening 3465 ligands from the ZINC database. A 2D‐QSAR model was established using PaDEL descriptors and multiple linear regression on a dataset of 123 ligands, divided into a training set ( n = 86, R 2 = 0.886) and a test set ( n = 37, R 2 = 0.837) for prediction. Re‐docking with AutoDock Vina prioritized two compounds, ZINC95486185 and ZINC95486376, exhibiting binding affinities of −8.98 ± 0.4 kcal/mol and −8.90 ± 0.06 kcal/mol, respectively. PLIP analysis demonstrated hydrophobic interactions with gC1qR residues Ala81, Phe82, Phe85, and Asp88. ADMET profiling indicated pharmacokinetics, non‐mutagenicity, and low solubility, suggesting parenteral administration. 100‐ns molecular dynamics simulations demonstrated the structural stability of ZINC95486376, highlighting it as a promising candidate for restoring complement‐dependent antitumor immunity.

    2026
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    2Performance Optimization of a Kretschmann‐Configured Multilayer MgO/Ag/HfO 2 /2D‐WS 2 SPR Biosensor for Refractive Index‐Based Cancer Cell Detection: A TMM and FEM Approach
    Deepak Garg,Ajeet Kumar,Saurabh Mani Tripathi

    ABSTRACT Cancer remains a major global health burden, causing millions of deaths each year. Therefore, the development of rapid and efficient diagnostic methods is necessary to facilitate effective management and control. In this study, a computational study of a highly sensitive Kretschmann‐configured surface plasmon resonance (SPR) based biosensor is presented for detection of cancerous cells. The proposed biosensor is made up of a multilayer structure comprising a BK7 prism, magnesium oxide (MgO) as an adhesive layer, silver (Ag) as the plasmonic material, hafnium dioxide (HfO 2 ) as the dielectric layer, and a two‐dimensional (2D) material, tungsten disulfide (WS 2 ), to enhance optical performance. Performance metrics were analyzed for sensitivity using the transfer matrix method (TMM) in MATLAB (R2018b), with results validated by the finite element method (FEM) in COMSOL Multiphysics. Optimization of the thicknesses of different layers yielded maximum sensitivity values of 364.28, 320.83, and 245 deg/RIU for the Jurkat, HeLa, and Basal cells, respectively. Furthermore, the proposed biosensor performs well across a wide refractive index range of 1.30–1.39, achieving a linear coefficient of determination (R 2 ) value of 0.9679. The proposed biosensor can serve as a promising candidate for efficient cancer cell detection, as well as for various sensing applications.

    2026
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    3Millimeter‐Wave Orbital Angular Momentum Mode Conversion Based on Multilayer Quasi‐Optical Diffractive Neural Network
    Jiaqi Cai,Jiexin Lai,Yuda Wu, Shufang Li

    ABSTRACT Orbital angular momentum (OAM) modes provide additional degrees of freedom for high‐capacity communication, advanced radar, and quantum information processing in millimeter‐wave and terahertz bands. This work investigates a multilayer quasi‐optical phase diffraction network operating at 150 GHz, in which each layer is represented by a 3D‐printable dielectric‐column array. The phase profiles are optimized with a differentiable angular‐spectrum model and Adam, and the resulting 3D dielectric structures are evaluated by CST full‐wave electromagnetic simulation. The inter‐layer spacing and higher‐order channel weights are examined separately. The fixed structure is also evaluated over frequency, and a second optimized design is used to test nonuniform OAM mappings. All CST results use the same definitions of Mode Purity and target‐normalized XT. The resulting passive three‐layer structure uses fabrication‐compatible dielectric columns and supports the four designed OAM conversion channels.

    2026
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    4An Effective Computational Framework Based on Re‐Defined Uniform Hyperbolic Polynomial B‐Spline for Solving Time‐Fractional Reaction Diffusion Equation
    Emre Kırlı

    ABSTRACT In this study, a robust computational scheme is designed to solve time‐fractional reaction‐diffusion equation involving the Caputo–Fabrizio derivative. The time‐fractional reaction–diffusion equation provides an effective mathematical framework for modeling the temporal evolution of physical processes while incorporating memory effects arising from their past states. The Caputo–Fabrizio fractional derivative in conjunction with the ‐weighted scheme is employed for temporal integration of the considered problem. The redefined uniform hyperbolic polynomial B‐spline, which improves flexibility and accuracy across the computational domain, is designed to discretize the spatial variables. The stability and convergence analyzes of the developed technique are performed to justify the developed technique's the reliability. The developed scheme is applied to three benchmark problems to assess its feasibility and efficiency. The findings obtained through the numerical experiments reveal that the developed scheme provides significantly more accurate results compared to the polynomial B‐spline method, highlighting its robustness and computational efficiency.

    2026
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    5Pressure‐Induced Electronic and Dynamical Instability IncubicAgMgX 3 (X = F, Cl, Br) Halide Perovskites at High Pressure: A First‐Principles Study
    Yu. N. Zhuravlev, Z.Y. Khattari

    ABSTRACT A systematic study of the structural, electronic, elastic, and vibrational properties of cubic halide perovskites AgMgX 3 (X = F, Cl, Br) under hydrostatic pressure (0–50 GPa) was performed using Density functional theory (DFT) with two codes: the all‐electron Gaussian‐basis‐set code CRYSTAL for the electronic and spectroscopic properties, and the plane‐wave pseudopotential code CASTEP for the vibrational and thermodynamic properties. Lattice constants increase from F to Br, while bulk moduli decrease from 92.31 to 34.26 GPa. The bandgap of AgMgF 3 increases with pressure, whereas it decreases for AgMgCl 3 and AgMgBr 3 . This opposite behavior arises from different valence‐band characters: Ag d‐states in AgMgF 3 vs. halogen p‐states in the chloride and bromide. Full Brillouin‐zone phonon dispersions reveal that the cubic phase of all three compounds is dynamically unstable, with an R‐point soft mode corresponding to out‐of‐phase rotations of the MgX 6 octahedra. For AgMgF 3 , the rhombohedral phase is lower in enthalpy than the cubic phase by 54–118 meV per formula unit, confirming it as the ground state. For AgMgCl 3 and AgMgBr 3 , the relaxation does not converge to a well‐defined minimum, so their ground states remain undetermined. AgMgF 3 is promising for deep UV photodetectors, provided its rhombohedral polymorph is stabilized.

    2026
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    高被引作者

    作者引用发文
    Paul Erhart7984
    Erik Fransson7984
    Fredrik Eriksson4682
    Tiejun Cui3557
    Markus Suta2841
    A. (Andries) Meijerink2841
    Piotr B. Rozyczko2551
    Thomas H. Rod2551
    J. Magnus Rahm2551
    Mattias Ångqvist2551

    高产作者

    作者引用发文
    Mostaghaci Babak015
    Ortwin Renn014
    Yong-Wei Zhang014
    Yifei Mo014
    Javier Llorca014
    Sean Smith013
    Duoduo Liang013
    Emily Carter013
    James Cook013
    Xin-Cheng Xie013

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