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The ecotoxicological effects of thiamethoxam on photosynthesis and nitrogen fixation in cyanobacteria: From inhibition to recovery

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Journal of Environmental sciences 2025年

作者： Jiale Zhang Shiye Zhu Xiyan Xu Youzheng Chai Jihai Shao Gen Lu Jianhua Zeng Ma Bai Anwei Chen College of Environment and Ecology Hunan Agricultural University Changsha 410128 China School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China Center for Water and Ecology State Key Joint Laboratory of Environment Simulation and Pollution Control School of Environment Tsinghua University Beijing 100084 China Institute of Resource Biology and Biotechnology Department of Biotechnology College of Life Science and Technology Huazhong University of Science and Technology Wuhan 430074 China School of Food Engineering Anhui Science and Technology University Fengyang AnHui 233100 China College of Chemistry & Pharmacy Northwest A&F University Yangling Shaanxi 712100 China

Thiamethoxam (THX) is a highly efficacious, broad-spectrum neonicotinoid insecticide that is prevalently detected in contemporary environmental settings. Although considerable research has been conducted on the adverse effects of THX on non-target organisms, there is a paucity of knowledge regarding its impact on nitrogen (N)-fixing cyanobacteria, which play a crucial role in the N-cycle. This study examined the impact of the neonicotinoid pesticide THX on N-fixing cyanobacteria Nostoc sp. PCC7120. It combined biochemical and molecular data to clarify the toxicity and recovery mechanism of Nostoc sp. PCC7120 exposed to THX. The results show that at low THX concentrations, cyanobacteria exhibited hormetic responses and then enter recovery phases, whereas at high concentrations, they showed toxicity phases before entering recovery phases. The main changes were in cell growth, antioxidant system, photosynthetic performance and N-fixation. The starch granules and vacuoles of Nostoc sp. PCC7120 became larger after THX treatment, indicating a shift in resources from growth to storage. Additionally, molecular stimulations indicated that THX could bind to molybdenum-iron cofactor sites of nitrogenase to destroy N-fixation, and also bind to Q A and Q B sites of photosynthetic proteins (D1 and D2) to affect photosynthesis. These findings provide a valuable reference for the ecological risks of THX and biogeochemical N-cycle.

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A multigrid-reduction-in-time solver with a new two-level convergence for unsteady fractional Laplacian problems

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arXiv 2019年

作者： Yue, Xiaoqiang Pan, Kejia Zhou, Jie Weng, Zhifeng Shu, Shi Tang, Juan Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational Science Xiangtan University Xiangtan411105 China School of Mathematics and Statistics HNP-LAMA Central South University Changsha410083 China School of Mathematical Sciences Fujian Province University Key Laboratory of Computation Science Huaqiao University Quanzhou362021 China

The multigrid-reduction-in-time (MGRIT) technique has proven to be successful in achieving higher run-time speedup by exploiting parallelism in time. The goal of this article is to develop and analyze a MGRIT algorithm, using FCF-relaxation with time-dependent time-grid propagators, to seek the finite element approximations of unsteady fractional Laplacian problems. The multigrid with line smoother proposed in [L. Chen, R. H. Nochetto, et al., Math. Comp. 85 (2016) 2583–2607] is chosen to be the spatial solver. Motivated by [B. S. Southworth, SIAM J. Matrix Anal. Appl. 40 (2019) 564–608], we provide a new temporal eigenvalue approximation property and then deduce a generalized two-level convergence theory which removes the previous unitary diagonalization assumption on the fine and coarse time-grid propagators required in [X. Q. Yue, S. Shu, et al., Comput. Math. Appl. 78 (2019) 3471–3484]. Numerical computations are included to confirm the theoretical predictions and demonstrate the sharpness of the derived convergence upper bound. Copyright © 2019, The Authors. All rights reserved.

关键词： Finite element method

Adaptive-multilevel BDDC algorithm for three-dimensional plane wave Helmholtz systems

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arXiv 2019年

作者： Peng, Jie Shu, Shi Wang, Junxian Zhong, Liuqiang School of Mathematical Sciences South China Normal University Guangzhou510631 China School of Mathematics and Computational Science Xiangtan University Xiangtan411105 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan411105 China

In this paper we are concerned with the weighted plane wave least-squares (PWLS) method for three-dimensional Helmholtz equations, and develop the multi-level adaptive BDDC algorithms for solving the resulting discrete system. In order to form the adaptive coarse components, the local generalized eigenvalue problems for each common face and each common edge are carefully designed. The condition number of the two-level adaptive BDDC preconditioned system is proved to be bounded above by a user-defined tolerance and a constant that is only dependent on the maximum number of faces and edges per subdomain and the number of subdomains sharing a common edge. The effectiveness of these algorithms is illustrated on benchmark problem. The numerical results show the robustness of our two-level adaptive BDDC algorithms with respect to the wave number, the number of subdomains and the mesh size, and appear that our multi-level adaptive BDDC algorithm can reduce the number of dofs at the coarse problem and can be used to solving large wave number problems efficiently. Copyright © 2019, The Authors. All rights reserved.

关键词： Elastic waves

SATURATION AND RELIABLE HIERARCHICAL A POSTERIORI MORLEY FINITE ELEMENT ERROR CONTROL

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Journal of computational Mathematics 2018年第6期36卷 833-844页

作者： Carsten Carstensen Dietmar Gallistl Yunqing Huang Humboldt-Universitat zu Berlin Institut fiir Mathematik Unter den Linden 6 10099 Berlin Germany Department of Applied Mathematics University of Twente P.O. Box 217 7500 AE Enschede Institute for Computational and Applied Mathematics and Hunan Key Laboratory for Computation & Simulation in Science & Engineering Xiangtan University Xiangtan 411105 China

This paper proves the saturation assumption for the nonconforming Morley finite ele- ment discretization of the biharmonic equation. This asserts that the error of the Morley approximation under uniform refinement is strictly reduced by a contraction factor smaller than one up to explicit higher-order data approximation terms. The refinement has at least to bisect any edge such as red refinement or 3-bisections on any triangle. This justifies a hierarchical error estimator for the Morley finite element method, which simply compares the discrete solutions of one mesh and its red-refinement. The related adaptive mesh-refining strategy performs optimally in numerical experiments. A remark for Crouzeix-Raviart nonconforming finite element error control is included.

关键词： Saturation Hierarchical error estimation Finite element Nonconforming Biharmonie Morley Kirchhoff plate Crouzeix-Raviart

DeePMD-kit v2: A software package for Deep Potential models

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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

Fully Discrete Galerkin Finite Element Method for the Cubic Nonlinear Schr(o)dinger Equation

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高等学校计算数学学报（英文版） 2017年第3期10卷 671-688页

作者： Jianyun Wang Yunqing Huang School of Science Hunan University of Technology Zhuzhou 412007 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational Science Xiangtan University Xiangtan 411105 China

This paper is concemed with numerical method for a two-dimensional timedependent cubic nonlinear Schr(o)dinger *** approximations are obtained by the Galerkin finite element method in space in conjunction with the backward Euler method and the Crank-Nicolson method in time,*** prove optimal L2 error estimates for two fully discrete schemes by using elliptic projection ***,a numerical example is provided to verify our theoretical results.

关键词： Finite element method nonlinear Schr(o)dinger equations backward Euler scheme Crank-Nicolson scheme

A finite element method of the self-consistent field theory on general curved surfaces

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arXiv 2018年

作者： Wei, Huayi Xu, Ming Si, Wei Jiang, Kai School of Mathematics and Computational Science Xiangtan University Xiangtan Hunan411105 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering

Block copolymers provide a wonderful platform in studying the soft condensed matter systems. Many fascinating ordered structures have been discovered in bulk and confined systems. Among various theories, the self-consistent field theory (SCFT) has been proven to be a powerful tool for studying the equilibrium ordered structures. Many numerical methods have been developed to solve the SCFT model. However, most of these focus on the bulk systems, and little work on the confined systems, especially on general curved surfaces. In this work, we developed a linear surface finite element method, which has a rigorous mathematical theory to guarantee numerical precsion, to study the self-assembled phases of block copolymers on general curved surfaces based on the SCFT. Furthermore, to capture the consistent surface for a given self-assembled pattern, an adaptive approach to optimize the size of the general curved surface has been proposed. To demonstrate the power of this approach, we investigate the self-assembled patterns of diblock copolymers on several distinct curved surfaces, including five closed surfaces and an unclosed surface. Numerical results illustrate the efficiency of the proposed method. The obtained ordered structures are consistent with the previous results on standard surfaces, such as sphere and torus. Certainly, the proposed numerical framework has the capability of studying the phase behaviors on general surfaces precisely. Copyright © 2018, The Authors. All rights reserved.

关键词： Mean field theory

High-order energy stable schemes of incommensurate phase-field crystal model

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arXiv 2018年

作者： Jiang, Kai Si, Wei School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan411105 China

This article focuses on the development of high-order energy stable schemes for the multi-length-scale incommensurate phase-field crystal model which is able to study the phase behavior of aperiodic structures. These high-order schemes based on the scalar auxiliary variable (SAV) and spectral deferred correction (SDC) approaches are suitable for the L2 gradient flow equation, i.e., the Allen-Cahn dynamic equation. Concretely, we propose a second-order Crank-Nicolson (CN) scheme of the SAV system, prove the energy dissipation law, and give the error estimate in the almost periodic function sense. Moreover, we use the SDC method to improve the computational accuracy of the SAV/CN scheme. Numerical results demonstrate the advantages of high-order numerical methods in numerical computations and show the influence of length-scales on the formation of ordered structures. Copyright © 2018, The Authors. All rights reserved.

关键词： Numerical methods

Recovery based finite element method for biharmonic equation in two dimensional

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arXiv 2018年

作者： Huang, Yunqing Wei, Huayi Yang, Wei Yi, Nianyu Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational Science Xiangtan University Xiangtan411105 China

We design and numerically validate a recovery based linear finite element method for solving the biharmonic equation. The main idea is to replace the gradient operator ∇ on linear finite element space by G(∇) in the weak formulation of the biharmonic equation, where G is the recovery operator which recovers the piecewise constant function into the linear finite element space. By operator G, Laplace operator ∆ is replaced by ∇ · G(∇). Furthermore the boundary condition on normal derivative ∇u · n is treated by the boundary penalty method. The explicit matrix expression of the proposed method is also introduced. Numerical examples on uniform and adaptive meshes are presented to illustrate the correctness and effectiveness of the proposed *** Codes 65N30 Copyright © 2018, The Authors. All rights reserved.

关键词： Finite element method