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Collective vortical motion and vorticity reversals of self-propelled particles on circularly patterned substrates

physical Review E 2023年第2期107卷 024606-024606页

作者： Haosheng Wen Yu Zhu Chenhui Peng P. B. Sunil Kumar Mohamed Laradji Department of Physics and Materials Science The University of Memphis Memphis Tennessee 38152 USA Biophysics Graduate Program The Ohio State University Columbus Ohio 43210 USA Department of Physics University of Science and Technology of China Hefei Anhui 230026 China Department of Physics Indian Institute of Technology Palakkad Palakkad 668557 Kerala India Department of Physics Indian Institute of Technology Madras Chennai 600036 Tamil Nadu India

The collective behavior of self-propelled particles (SPPs) under the combined effects of a circularly patterned substrate and circular confinement is investigated through coarse-grained molecular dynamics simulations of polarized and disjoint ring polymers. The study is performed over a wide range of values of the SPPs packing fraction ϕ¯, motility force FD, and area fraction of the patterned region. At low packing fractions, the SPPs are excluded from the system's center and exhibit a vortical motion that is dominated by the substrate at intermediate values of FD. This exclusion zone is due to the coupling between the driving force and torque induced by the substrate, which induces an outward spiral motion of the SPPs. For high values of FD, the SPPs exclusion from the center is dominated by the confining boundary. At high values of ϕ¯, the substrate pattern leads to reversals in the vorticity, which become quasiperiodic with increasing ϕ¯. We also found that the substrate pattern is able to separate SPPs based on their motilities.

关键词： Aggregation Collective behavior Flocking Self-assembly Active matter Theories of collective dynamics & active matter

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Evaluation of Thellungiella halophila ST7 for improving salt tolerance in cotton

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棉花学报 2022年第1期5卷 1-11页

作者： ALI Mohsin NAZISH Tahmina JAVAID Ayesha ZHU Yonghong LI Jing ZHANG Huangyang WU Jie XIANG Chengbin WU Shenjie ALFATIH Alamin Division of Molecular&Cell Biophysics School of Life SciencesHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovative Academy of Seed DesignChinese Academy of SciencesHefeiAnhuiChina Institute of Cotton Research Shanxi Agricultural UniversityYuncheng 044000China College of Life Sci-ences Shanxi Agricultural UniversityTaiyuan 030031China

Background: Gossypium hirsutum (upland cotton) is one of the principal fiber crops in the world. Cotton yield is highly affected by abiotic stresses, among which salt stress is considered as a major problem around the globe. Trans-genic approach is efficient to improve cotton salt tolerance but depending on the availability of salt tolerance genes. Results: In this study we evaluated salt tolerance candidate gene ST7 from Thellungiella halophila, encoding a homolog of Arabidopsis aluminum-induced protein, in cotton. Our results showed that ThST7 overexpression in cotton improved germination under NaCl stress as well as seedling growth. Our field trials also showed that ThST7 transgenic cotton lines produced higher yield under salt stress conditions. The improved salt tolerance of the transgenic cotton lines was partially contributed by enhanced antioxidation as shown by diaminobenzidine (DAB) and nitrotetrazolium blue chloride (NBT ) staining. Moreover, transcriptomic analysis of ThST7 overexpression lines showed a significant upregulation of the genes involved in ion homeostasis and antioxidation, consistent with the salt tolerance pheno-type of the transgenic cotton. Conclusions: Our results demonstrate that ThST7 has the ability to improve salt tolerance in cotton. The ThST7 trans-genic cotton may be used in cotton breeding for salt tolerance cultivars.

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Arabidopsis NLP7 improves nitrogen use efficiency and yield in cotton

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棉花学报 2022年第1期5卷 12-21页

作者： JAN Sami Ullah LIAQAT Ayesha ZHU Yonghong LI Jing ZHANG Huangyang ABDALLA Mohnad WU Jie XIANG Chengbin WU Shenjie ALFATIH Alamin School of Life Sciences Division of Molecular&Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovative Academy of Seed DesignChinese Academy of SciencesHefeiAnhui 230026China Institute of Cotton Research Shanxi Agricultural UniversityYuncheng 044000China College of Life Sciences Shanxi Agricultural UniversityTaiyuan 030031China

Background: Nitrogen (N) is a required macronutrient for cotton growth and productivity. Excessive N fertilizers are applied in agriculture for crop yield maximization, which also generates environmental pollution. Improving crop N use efficiency (NUE) is the most economical and desirable way of reducing fertilizer application and environmental pollution. NUE has been an important issue in cotton. So far there is no report on cotton NUE improvement via trans-genic approach. Nin-like proteins (NLP) are transcription factors regulating NUE. We previously demonstrated that AtNLP7 improved NUE and biomass when overexpressed in Arabidopsis. However, it is not known whether AtNLP7 can be used to improve NUE in crops. Results: To test the feasibility, we expressed AtNLP7 in cotton and evaluated NUE and yield of the transgenic cotton in the field. Transgenic cotton showed improved NUE and yield under both low and high N conditions. In addi- tion, plant biomass, amount of absorbed N, N contents, activities of N-assimilating enzymes, and the expression of N-related marker genes were significantly increased in transgenic cotton compared with the wild type control, sug-gesting that AtNLP7 enhances NUE in cotton. Conclusion: Together, our results demonstrate that AtNLP7 is a promising candidate to improve NUE and yield in cotton.

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Thellungiella halophila ST5 improves salt tolerance in cotton

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棉花学报 2022年第1期5卷 22-33页

作者： NAZISH Tahmina JAVAID Ayesha ALI Mohsin ZHU Yonghong LI Jing ZHANG Huangyang WU Jie XIANG Chengbin WU Shenjie ALFATIH Alamin School of Life Sciences Division of Molecular and Cell BiophysicsHefei National Science Center for Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaThe Innovative Academy of Seed DesignChinese Academy of SciencesHefei 230026AnhuiChina Institute of Cotton Research Shanxi Agricultural UniversityYuncheng 044000ShanxiChina College of Life Sciences Shanxi Agricultural UniversityTaiyuan 030031ShanxiChina

Background: Salinity is a major abiotic stress to global agriculture which hampers crop growth and development, and eventually reduces yield. Transgenic technology is an effective and efficient approach to improve crop salt toler-ance but depending on the availability of effective genes. We previously isolated Salt Tolerance5 (ThST5) from the halophyte Thellungiella halophila, an ortholog of Arabidopsis SPT4-2 which encodes a transcription elongation factor. However, SPT4-2-confered salt tolerance has not been evaluated in crops yet. Here we report the evaluation of ThST5-conferred salt tolerance in cotton (Gossypium hirsutum L.). Results: The ThST5 overexpression transgenic cotton plants displayed enhanced tolerance to salt stress during seed germination and seedling stage compared with wild type. Particularly, the transgenic plants showed improved salin-ity tolerance as well as yield under saline field conditions. Comparative transcriptomic analysis showed that ThST5 improved salt tolerance of transgenic cotton mainly by maintaining ion homeostasis. In addition, ThST5 also orches-trated the expression of genes encoding antioxidants and salt-responsive transcription factors. Conclusion: Our results demonstrate that ThST5 is a promising candidate to improve salt tolerance in cotton.

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Advancing electrochemical impedance analysis through innovations in the distribution of relaxation times method

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Joule 2024年第7期8卷 1958-1981页

作者： Maradesa, Adeleke Py, Baptiste Huang, Jake Lu, Yang Iurilli, Pietro Mrozinski, Aleksander Law, Ho Mei Wang, Yuhao Wang, Zilong Li, Jingwei Xu, Shengjun Meyer, Quentin Liu, Jiapeng Brivio, Claudio Gavrilyuk, Alexander Kobayashi, Kiyoshi Bertei, Antonio Williams, Nicholas J. Zhao, Chuan Danzer, Michael Zic, Mark Wu, Phillip Yrjänä, Ville Pereverzyev, Sergei Chen, Yuhui Weber, André Kalinin, Sergei V. Schmidt, Jan Philipp Tsur, Yoed Boukamp, Bernard A. Zhang, Qiang Gaberšček, Miran O'Hayre, Ryan Ciucci, Francesco Department of Mechanical and Aerospace Engineering The Hong Kong University of Science and Technology Hong Kong Metallurgical and Materials Engineering Colorado School of Mines Golden80401 United States Beijing Key Laboratory of Green Chemical Reaction Engineering and Technology Department of Chemical Engineering Tsinghua University Beijing China Green Energy Storage Trento38123 Italy Department of Manufacturing and Production Engineering Faculty of Mechanical Engineering and Ship Technology Institute of Machine and Materials Technology Gdańsk University of Technology Gdańsk Poland Electrode Design for Electrochemical Energy Systems University of Bayreuth Bayreuth Germany School of Chemistry University of New South Wales Sydney Australia School of Advanced Energy Sun Yat-Sen University Shenzhen China Sustainable Energy Center CSEM Neuchâtel2002 Switzerland Interdisciplinary Faculty of Science and Engineering Shimane University Matsue Japan Centre for Electronic and Optical Materials National Institute for Materials Science Tsukuba Japan Department of Civil and Industrial Engineering University of Pisa Pisa Italy Department of Materials Imperial College London Exhibition Road LondonSW7 2AZ United Kingdom Department of Chemical Engineering Massachusetts Institute of Technology Cambridge02139 United States Electrical Energy Systems University of Bayreuth Bayreuth Germany Ruder Boskovic Institute Zagreb Croatia Department of Materials and Minerals Resources Engineering National Taipei University Taipei Taiwan Finland Johann Radon Institute for Computational and Applied Mathematics Linz Austria School of Science and Engineering Nanjing Tech. University Nanjing China Karlsruhe Germany Department of Materials Science and Engineering University of Tennessee KnoxvilleTN37996 United States Physical Science Division Pacific Northwest National Laboratory RichlandWA99354 United States Systems Engineering for Electrical Energy Storage University of B

Electrochemical impedance spectroscopy (EIS) is widely used in electrochemistry, energy sciences, biology, and beyond. Analyzing EIS data is crucial, but it often poses challenges because of the numerous possible equivalent circuit models, the need for accurate analytical models, the difficulties of nonlinear regression, and the necessity of managing large datasets within a unified framework. To overcome these challenges, non-parametric models, such as the distribution of relaxation times (DRT, also known as the distribution function of relaxation times, DFRT), have emerged as promising tools for EIS analysis. For example, the DRT can be used to generate equivalent circuit models, initialize regression parameters, provide a time-domain representation of EIS spectra, and identify electrochemical processes. However, mastering the DRT method poses challenges as it requires mathematical and programming proficiency, which may extend beyond experimentalists’ usual expertise. Post-inversion analysis of DRT data can be difficult, especially in accurately identifying electrochemical processes, leading to results that may not always meet expectations. This article examines non-parametric EIS analysis methods, outlining their strengths and limitations from theoretical, computational, and end-user perspectives, and provides guidelines for their future development. Moreover, insights from survey data emphasize the need to develop a large impedance database, akin to an impedance genome. In turn, software development should target one-click, fully automated DRT analysis for multidimensional EIS spectra interpretation, software validation, and reliability. Particularly, creating a collaborative ecosystem hinged on free software could promote innovation and catalyze the adoption of the DRT method throughout all fields that use impedance data. © 2024 Elsevier Inc.

关键词： Electrochemical impedance spectroscopy

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Influence of long range forces on the transition states and dynamics of NaCl ion-pair dissociation in water

arXiv

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arXiv 2021年

作者： Wang, Dedi Zhao, Renjie Weeks, John D. Tiwary, Pratyush Biophysics Program Institute for Physical Science and Technology University of Maryland College Park20742 United States Chemical Physics Program Institute for Physical Science and Technology University of Maryland College Park20742 United States Department of Chemistry and Biochemistry Institute for Physical Science and Technology University of Maryland College Park20742 United States

We study NaCl ion-pair dissociation in a dilute aqueous solution using computer simulations both for the full system with long range Coulomb interactions and for a well chosen reference system with short range intermolecular interactions. Analyzing results using concepts from Local Molecular Field (LMF) theory and the recently proposed AI-based analysis tool "State predictive information bottleneck" (SPIB) we show that the system with short range interactions can accurately reproduce the transition rate for the dissociation process, the dynamics for moving between the underlying metastable states, and the transition state ensemble. Contributions from long range interactions can be largely neglected for these processes because long range forces from the direct interionic Coulomb interactions are almost completely canceled (> 90%) by those from solvent interactions over the length scale where the transition takes place. Thus for this important monovalent ion-pair system, short range forces alone are able to capture detailed consequences of the collective solvent motion, allowing the use of physically suggestive and computationally efficient short range models for the disassociation event. We believe that the framework here should be applicable to disentangling mechanisms for more complex processes such as multivalent ion disassociation, where previous work has suggested that long range contributions may be more important. © 2021, CC BY.

关键词： Dissociation

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Electrical potential sensing with fluorine-doped tin oxide-coated lossy-mode resonance probe 27

Electrical potential sensing with fluorine-doped tin oxide-c...

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27th International Conference on Optical Fiber Sensors, OFS 2022

作者： Śmietana, Mateusz Janczuk-Richter, Marta Sezemsky, Petr Stranak, Vitezslav Koba, Marcin Niedziólka-Jönsson, Joanna Institute of Microelectronics and Optoelectronics Warsaw University of Technology Koszykowa 75 Warsaw Poland Institute of Physical Chemistry Polish Academy of Sciences Kasprzaka 44/52 Warsaw01-224 Poland Faculty of Science Institute of Physics and Biophysics University of South Bohemia Branisovska 1760 Ceske Budejovice370 05 Czech Republic National Institute of Telecommunications Szachowa 1 Warsaw04-894 Poland

Optical fiber probe based on fluorine-doped tin oxide thin film has been applied for electric potential measurements in electrochemical configuration. The sensitivity reaches up to 35 nm/V in potential range -0.6 V to... 详细信息

ISBN: (纸本)9781957171142

关键词： Electric potential

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Arabidopsis NLP7 improves nitrogen use efficiency and yield in cotton

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Journal of Cotton Research 2022年第1期5卷 12-21页

Background: Nitrogen(N) is a required macronutrient for cotton growth and productivity. Excessive N fertilizers are applied in agriculture for crop yield maximization, which also generates environmental pollution. Improving crop N use efficiency(NUE) is the most economical and desirable way of reducing fertilizer application and environmental pollution. NUE has been an important issue in cotton. So far there is no report on cotton NUE improvement via transgenic approach. Nin-like proteins(NLP) are transcription factors regulating NUE. We previously demonstrated that At NLP7 improved NUE and biomass when overexpressed in Arabidopsis. However, it is not known whether At NLP7 can be used to improve NUE in ***: To test the feasibility, we expressed At NLP7 in cotton and evaluated NUE and yield of the transgenic cotton in the field. Transgenic cotton showed improved NUE and yield under both low and high N conditions. In addition, plant biomass, amount of absorbed N, N contents, activities of N-assimilating enzymes, and the expression of N-related marker genes were significantly increased in transgenic cotton compared with the wild type control, suggesting that At NLP7 enhances NUE in ***: Together, our results demonstrate that At NLP7 is a promising candidate to improve NUE and yield in cotton.

关键词： Nitrogen Nitrogen metabolism Nitrogen use efficiency(NUE) Nin-like protein(NLP) AtNLP7 Cotton(Gossypium hirsutum)

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Thellungiella halophila ST5 improves salt tolerance in cotton

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Journal of Cotton Research 2022年第1期5卷 22-33页

Background: Salinity is a major abiotic stress to global agriculture which hampers crop growth and development, and eventually reduces yield. Transgenic technology is an e ective and e cient approach to improve crop salt tolerance but depending on the availability of e ective genes. We previously isolated Salt Tolerance5(ThST5) from the halophyte Thellungiella halophila, an ortholog of Arabidopsis SPT4-2 which encodes a transcription elongation factor. However, SPT4-2-confered salt tolerance has not been evaluated in crops yet. Here we report the evaluation of Th ST5-conferred salt tolerance in cotton(Gossypium hirsutum L.).Results: The ThST5 overexpression transgenic cotton plants displayed enhanced tolerance to salt stress during seed germination and seedling stage compared with wild type. Particularly, the transgenic plants showed improved salinity tolerance as well as yield under saline field conditions. Comparative transcriptomic analysis showed that ThST5 improved salt tolerance of transgenic cotton mainly by maintaining ion homeostasis. In addition, ThST5 also orchestrated the expression of genes encoding antioxidants and salt-responsive transcription ***: Our results demonstrate that ThST5 is a promising candidate to improve salt tolerance in cotton.

关键词： Salinity Thellungiella halophila Salt Tolerance5(ThST5) Salt tolerance Cotton(Gossypium hirsutum L.) Ion homeostasis

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Evaluation of Thellungiella halophila ST7 for improving salt tolerance in cotton

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Journal of Cotton Research 2022年第1期5卷 1-11页

Background: Gossypium hirsutum(upland cotton) is one of the principal fiber crops in the world. Cotton yield is highly affected by abiotic stresses, among which salt stress is considered as a major problem around the globe. Transgenic approach is efficient to improve cotton salt tolerance but depending on the availability of salt tolerance ***: In this study we evaluated salt tolerance candidate gene ST7 from Thellungiella halophila, encoding a homolog of Arabidopsis aluminum-induced protein, in cotton. Our results showed that ThST7 overexpression in cotton improved germination under NaCl stress as well as seedling growth. Our field trials also showed that ThST7 transgenic cotton lines produced higher yield under salt stress conditions. The improved salt tolerance of the transgenic cotton lines was partially contributed by enhanced antioxidation as shown by diaminobenzidine(DAB) and nitrotetrazolium blue chloride(NBT) staining. Moreover, transcriptomic analysis of ThST7 overexpression lines showed a significant upregulation of the genes involved in ion homeostasis and antioxidation, consistent with the salt tolerance phenotype of the transgenic ***: Our results demonstrate that ThST7 has the ability to improve salt tolerance in cotton. The ThST7 transgenic cotton may be used in cotton breeding for salt tolerance cultivars.

关键词： Gossypium hirsutum Aluminum-induced protein Salinity Thellungiella halophila ST7 Salt tolerance

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