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Stereoselective recognition of morphine enantiomers by μ-opioid receptor

National Science Review 2024年第3期11卷 183-191页

作者： Yibo Wang Van A.Ngo Xiaohui Wang Laboratory of Chemical Biology Changchun Institute of Applied ChemistryChinese Academy of Sciences Advanced Computing for Life Sciences and Engineering Group Science Engagement Section National Center for Computational Sciences Oak Ridge National Lab School of Applied Chemistry and Engineering University of Science and Technology of China Beijing National Laboratory for Molecular Sciences

Stereospecific recognition of chiral molecules plays a crucial role in biological systems. The μ-opioid receptor（MOR） exhibits binding affinity towards（-）-morphine, a well-established gold standard in pain management, while it shows minimal binding affinity for the（+）-morphine enantiomer, resulting in a lack of analgesic activity. Understanding how MOR stereoselectively recognizes morphine enantiomers has remained a puzzle in neuroscience and pharmacology for over half-a-century due to the lack of direct observation techniques. To unravel this mystery, we constructed the binding and unbinding processes of morphine enantiomers with MOR via molecular dynamics simulations to investigate the thermodynamics and kinetics governing MOR's stereoselective recognition of morphine enantiomers. Our findings reveal that the binding of（-）-morphine stabilizes MOR in its activated state, exhibiting a deep energy well and a prolonged residence time. In contrast,（+）-morphine fails to sustain the activation state of ***, the results suggest that specific residues, namely D1142.50and D1473.32, are deprotonated in the active state of MOR bound to（-）-morphine. This work highlights that the selectivity in molecular recognition goes beyond binding affinities, extending into the realm of residence time.

关键词： stereoselective recognition thermodynamics and kinetics residence time morphine enantiomers μ-opioid receptor

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A TRUST-REGION METHOD FOR SOLVING TRUNCATED COMPLEX SINGULAR VALUE DECOMPOSITION

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Journal of Computational Mathematics 2024年第4期42卷 999-1031页

作者： Jiaofen Li Lingchang Kong Xuefeng Duan Xuelin Zhou Qilun Luo School of Mathematics and Computing Science Guangxi Colleges and Universities Key Laboratory of Data Analysis and ComputationGuangxi Key Laboratory of Automatic Detecting Technology and InstrumentsGuilin University of Electronic TechnologyCenter for Applied Mathematics of Guangxi(GUET)Guilin 541004China School of Mathematical Sciences South China Normal UniversityGuangzhou 510000China School of Mathematics and Computing Science Guilin University of Electronic TechnologyGuilin 541004China School of Mathematics and Computing Science Guangxi Colleges and Universities Key Laboratory of Data Analysis and ComputationGuilin University of Electronic TechnologyCenter for Applied Mathematics of Guangxi(GUET)Guilin 541004China School of Mathematics and Statistics Yunan UniversityKunming 650000China

The truncated singular value decomposition has been widely used in many areas of science including engineering,and statistics,*** this paper,the original truncated complex singular value decomposition problem is formulated as a Riemannian optimiza-tion problem on a product of two complex Stiefel manifolds,a practical algorithm based on the generic Riemannian trust-region method of Absil et *** presented to solve the underlying problem,which enjoys the global convergence and local superlinear conver-gence *** experiments are provided to illustrate the efficiency of the proposed *** with some classical Riemannian gradient-type methods,the existing Riemannian version of limited-memory BFGS algorithms in the MATLAB toolbox Manopt and the Riemannian manifold optimization library ROPTLIB,and some latest infeasible methods for solving manifold optimization problems,are also provided to show the merits of the proposed approach.

关键词： Truncated singular value decomposition Riemannian optimization Trust-region method

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Strengthening-softening transition and maximum strength in Schwarz nanocrystals

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Nano Materials Science 2024年第3期6卷 320-328页

作者： Hanzheng Xing Jiaxi Jiang Yujia Wang Yongpan Zeng Xiaoyan Li Center for Advanced Mechanics and Materials Applied Mechanics LaboratoryDepartment of Engineering MechanicsTsinghua UniversityBeijing100084China Institute of High Performance Computing(IHPC) Agency for ScienceTechnology and Research(A*STAR)Singapore138632Singapore

Recently,a Schwarz crystal structure with curved grain boundaries(GBs)constrained by twin-boundary(TB)networks was discovered in nanocrystalline Cu through experiments and atomistic *** Cu with nanosized Schwarz crystals exhibited high strength and excellent thermal ***,the grainsize effect and associated deformation mechanisms of Schwarz nanocrystals remain ***,we performed large-scale atomistic simulations to investigate the deformation behaviors and grain-size effect of nanocrystalline Cu with Schwarz *** simulations showed that similar to regular nanocrystals,Schwarz nanocrystals exhibit a strengthening-softening transition with decreasing grain *** critical grain size in Schwarz nanocrystals is smaller than that in regular nanocrystals,leading to a maximum strength higher than that of regular *** simulations revealed that the softening in Schwarz nanocrystals mainly originates from TB migration(or detwinning)and annihilation of GBs,rather than GB-mediated processes(including GB migration,sliding and diffusion)dominating the softening in regular *** analyses of simulation data further showed that compared with those in regular nanocrystals,the GB-mediated processes in Schwarz nanocrystals are suppressed,which is related to the low volume fraction of amorphous-like GBs and constraints of TB *** smaller critical grain size arises from the suppression of GB-mediated processes.

关键词： Schwarz nanocrystal Curved grain boundary Atomistic simulation Grain size effect Maximum strength

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On a class of nonlinear elliptic problems with double phase effects and laplacian-type operators in Musielak-Orlicz-Sobolev spaces

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Annali dell'Universita di Ferrara 2025年第2期71卷 1-20页

作者： Moujani, Hasna El Mfadel, Ali Kassidi, Abderrazak El Omari, M.’hamed Laboratory of Applied Mathematics and Scientific Computing Sultan Moulay Slimane University Beni Mellal Morocco Higher School of Technology Sultan Moulay Slimane University Khenifra Morocco

This paper addresses the existence of weak solutions for a class of nonlinear Dirichlet boundary value problems governed by a double phase operator. The main results are established under precise assumptions on the nonlinearity of the second term. The analysis is carried out within the advanced framework of Musielak-Orlicz-Sobolev spaces, which accommodate the variable growth conditions induced by the double phase structure. To handle challenges related to weak convergence, we employ the Young measures technique. Additionally, approximate solutions are systematically constructed through the Galerkin method, ensuring a rigorous and structured approach to the problem. © The Author(s) under exclusive license to Università degli Studi di Ferrara 2025.

关键词： (α,β)-Laplacian-like operator Fractional double phase problem Galerkin method Weak solution Young measure

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Passive on-chip isolators based on the thin-film lithium niobate platform

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Chinese Physics B 2025年第3期34卷 408-413页

作者： Jiacheng Liu Gongyu Xia Qilin Hong Pingyu Zhu Kai-Kai Zhang Keyu Xia Ping Xu Shiqiao Qin Zhihong Zhu College of Advanced Interdisciplinary Studies&Hunan Provincial Key Laboratory of Novel Nano Optoelectronic Information Materials and Devices National University of Defense TechnologyChangsha 410073China Institute for Quantum Information and State Key Laboratory of High-Performance Computing College of Computer Science and TechnologyNational University of Defense TechnologyChangsha 410073China College of Engineering and Applied Sciences National Laboratory of Solid State Microstructuresand Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210023China

Optical isolators,the photonic analogs of electronic diodes,are essential for ensuring the unidirectional flow of light in optical systems,thereby mitigating the destabilizing effects of back ***-film lithium niobate(TFLN),hailed as“the silicon of photonics,”has emerged as a pivotal material in the realm of chip-scale nonlinear optics,propelling the demand for compact optical *** report a breakthrough in the development of a fully passive,integrated optical isolator on the TFLN platform,leveraging the Kerr effect to achieve an impressive 10.3 dB of isolation with a minimal insertion loss of 1.87 *** theoretical simulations have demonstrated that our design,when applied to a microring resonator with a Q factor of 5×10^(6),can achieve 20 dB of isolation with an input power of merely 8 *** advancement underscores the immense potential of lithium niobate-based Kerr-effect isolators in propelling the integration and application of high-performance on-chip lasers,heralding a new era in integrated photonics.

关键词： thin-film lithium niobate Kerr effect optical isolator

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MONOTONICITY CORRECTIONS FOR NINE-POINT SCHEME OF DIFFUSION EQUATIONS

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Journal of Computational Mathematics 2024年第5期42卷 1305-1327页

作者： Wang Kong Zhenying Hong Guangwei Yuan Zhiqiang Sheng School of Mathematics Nanjing University of Aeronautics and AstronauticsNanjing 211106China Key Laboratory of Mathematical Modelling and High Performance Computing of Air Vehicles(NUAA) MIITNanjing 211106China Laboratory of Computational Physics Institute of Applied Physics and Computational MathematicsBeijing 100088China HEDPS Center for Applied Physics and TechnologyPeking UniversityBeijing 100871China

In this paper,we present a nonlinear correction technique to modify the nine-point scheme proposed in[SIAM ***.,30:3(2008),1341-1361]such that the resulted scheme preserves the *** first express the flux by the cell-centered unknowns and edge unknowns based on the stencil of the nine-point ***,we use a nonlinear combination technique to get a monotone *** order to obtain a cell-centered finite volume scheme,we need to use the cell-centered unknowns to locally approximate the auxiliary *** present a new method to approximate the auxiliary unknowns by using the idea of an improved multi-points flux *** numerical results show that the new proposed scheme is robust,can handle some distorted grids that some existing finite volume schemes could not handle,and has higher numerical accuracy than some existing positivity-preserving finite volume schemes.

关键词： Monotonicity corrections Diffusion equation Improved MPFA Distorted meshes

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Numerical Analysis of Generalized Fractional Form of Newton’s Cooling Law Under a Variable Environment Temperature

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International Journal of applied and Computational Mathematics 2024年第2期10卷 1-24页

作者： Hatime, Naoufel Melliani, Said El Mfadel, Ali Elomari, M’hamed Laboratory of Applied Mathematics and Scientific Computing Sultan Moulay Slimane University Beni Mellal Morocco Superior School of Technology Sultan Moulay Slimane University Khenifra Morocco

In this article, we study two proposed fractional models. Initially, we introduce a new generalized Marshall–Hoare model using the Mittag-Leffler type function to simulate the cooling of the internal solid organs during the time immediately after death. Furthermore, we provide an explicit solution for this new model. Secondly, by using Ψ-Caputo derivative of order α∈(0,1), we study Newton’s law of cooling under a general variable ambient temperature with two heat transfer coefficients. By transforming the main problem to a general delayed Volterra integral equation of the second kind and in light of the Banach fixed point theorem, we establish the existence and uniqueness results under a condition on both heat transfer coefficients. Additionally, via the delayed Henry–Gronwall integral inequality, we derive a criterion for finite-time stability. Moreover, we give a first-order numerical scheme to approximate our proposed model by approximating the integral form of the given solution. Finally, to show the efficacy and precision of our model, we look into a pharmacokinetics clinical trial. Our delayed fractional model anticipates values of drug concentration in plasma as close as possible to the ones observed in experimental data. © The Author(s), under exclusive licence to Springer Nature India Private Limited 2024.

关键词： 26A33 34A08 34A45 34K37 90C32 Delay Marshall–Hoare model Modelling nature Newton’s law of cooling Ψ-Caputo fractional derivative

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ONNXPruner: ONNX-Based General Model Pruning Adapter

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IEEE Transactions on Pattern Analysis and Machine Intelligence 2025年第7期47卷 5806-5817页

作者： Ren, Dongdong Li, Wenbin Ding, Tianyu Wang, Lei Fan, Qi Huo, Jing Pan, Hongbing Gao, Yang Nanjing University School of Electronic Science and Engineering China Nanjing University State Key Laboratory for Novel Software Technology School of Intelligence Science and Technology China Microsoft Corporation Applied Sciences Group RedmondWA98052 United States University of Wollongong School of Computing and Information Technology NSW2522 Australia

Recent advancements in model pruning have focused on developing new algorithms and improving upon benchmarks. However, the practical application of these algorithms across various models and platforms remains a significant challenge. To address this challenge, we propose ONNXPruner, a versatile pruning adapter designed for the ONNX format models. ONNXPruner streamlines the adaptation process across diverse deep learning frameworks and hardware platforms. A novel aspect of ONNXPruner is its use of node association trees, which automatically adapt to various model architectures. These trees clarify the structural relationships between nodes, guiding the pruning process, particularly highlighting the impact on interconnected nodes. Furthermore, we introduce a tree-level evaluation method. By leveraging node association trees, this method allows for a comprehensive analysis beyond traditional single-node evaluations, enhancing pruning performance without the need for extra operations. Experiments across multiple models and datasets confirm ONNXPruner's strong adaptability and increased efficacy. Our work aims to advance the practical application of model pruning. © 1979-2012 IEEE.

关键词： Adaptation Models Training Filters Deep Learning Computational Modeling Software Interoperability Load Modeling Software Algorithms Electronic Mail General Model Pruning ONNX Tree Level Evaluation Deep Neural Network Model Pruning Deep Learning Model Architecture Deep Learning Framework Hardware Platform Superior Performance Deep Neural Network Feature Maps Py Torch Image Net Training Images Sparse Matrix Root Node Type Of Operation Single Node Deep Neural Network Model Validation Images Extra Components Importance Of Filtering Pruning Method Squeeze Net

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A low Mach number asymptotic analysis of dissipation-reducing methods for curing shock instability

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applied Mathematics and Mechanics(English Edition) 2025年第4期46卷 723-744页

作者： Hongping GUO Xun WANG Zhijun SHEN National Key Laboratory of Computational Physics Institute of Applied Physics and Computational MathematicsBeijing100088China Faculty of Mathematics Baotou Teachers’CollegeBaotouInner Mongolia Autonomous Region014030China School of Mathematical Sciences Peking UniversityBeijing100871China PKU-Changsha Institute for Computing and Digital Economy Changsha410205China Center for Applied Physics and Technology Peking UniversityBeijing100871China

We are intrigued by the issues of shock instability,with a particular emphasis on numerical schemes that address the carbuncle phenomenon by reducing dissipation rather than increasing *** a specific class of planar flow fields where the transverse direction exhibits vanishing but non-zero velocity components,such as a disturbed onedimensional(1D)steady shock wave,we conduct a formal asymptotic analysis for the Euler system and associated numerical *** analysis aims to illustrate the discrepancies among various low-dissipative numerical ***,a numerical stability analysis of steady shock is undertaken to identify the key factors underlying shock-stable *** verify the stability mechanism,a consistent,low-dissipation,and shock-stable HLLC-type Riemann solver is presented.

关键词： Riemann solver numerical shock instability low Mach number HLLC

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EXISTENCE AND STABILITY OF SOLUTIONS FOR NONLINEAR FRACTIONAL DIFFERENTIAL EQUATIONS INVOLVING THE GRÖNWALL-FREDHOLM-TYPE INEQUALITY

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Journal of Mathematical Sciences (United States) 2025年第2期289卷 323-342页

作者： Hatime, Naoufel El Mfadel, Ali Elomari, M.’hamed Melliani, Said Laboratory of Applied Mathematics and Scientific Computing Sultan Moulay Slimane University PO Box 532 Beni Mellal 23000 Morocco Superior School of Technology Sultan Moulay Slimane University Khenifra Morocco

In this work, we have explored a fractional Newton’s Second Law of motion involving the ψ-Caputo operator of order α∈(1,2]. We proved the existence and uniqueness of solutions for different classes of force functions f acting on a specific object in mention. We have used some well-known fixed point theorems and fractional calculus methods. We have proved Ulam-Hyers stability, generalized Ulam-Hyers stability, Ulam-Hyers-Rassias stability, and generalized Ulam-Hyers-Rassias stability for the main problem. Mainly, this manuscript can be divided into four major parts. In the first part, we derive the necessary conditions to assure the existence and the uniqueness of a solution. In the second part, we develop some new Grönwall-Fredholm inequalities type, and in the third part, we prove that our problem is stable with respect to all Ulam’s stability types, and we have found a simpler condition under which the UHR and HUHR stability types persist, making our findings more accessible and applicable in a large class of fractional problems. Finally, we give two examples to establish our theoretical results. © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2024.

关键词： Fixed point theorem Fractional differential equations Grönwall type inequality Ulam-Hyers stability ψ-Caputo

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