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Nov 2023 • arXiv preprint arXiv:2311.00590

A Colour-Encoded Nanometric Ruler for Axial Super-Resolution Microscopies

Ilya Olevsko, Omer Shavit, Moshe Feldberg, Yossi Abulafia, Adi Salomon, Martin Oheim

Recent progress has boosted the resolving power of optical microscopies to spatial dimensions well below the diffraction limit. Yet, axial super-resolution and axial single-molecule localisation typically require more complicated implementations than their lateral counterparts. In the present work, we propose a simple solution for axial metrology by providing a multi-layered single-excitation, dual-emission test slide, in which axial distance is colour-encoded. Our test slide combines on a standard microscope coverslip substrate two flat, thin, uniform and brightly emitting fluorophore layers, separated by a nanometric transparent spacer layer having a refractive index close to a biological cell. The ensemble is sealed in an index-matched protective polymer. As a proof-of-principle, we estimate the light confinement resulting from evanescent-wave excitation in total internal reflection fluorescence (TIRF) microscopy. Our test sample permits, even for the non-expert user, a facile axial metrology at the sub-100-nm scale, a critical requirement for axial super-resolution, as well as near-surface imaging, spectroscopy and sensing.

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Nov 2023 • bioRxiv

Characterization of alternative splicing in high-risk Wilms’ tumors

Yaron Trink, Achia Urbach, Benjamin Dekel, Peter Hohenstein, Jacob Goldberger, Tomer Kalisky

The significant heterogeneity of Wilms’ tumors between different patients is thought to arise from genetic and epigenetic distortions that occur during various stages of fetal kidney development in a way that is poorly understood. To address this, we characterized the heterogeneity of alternative mRNA splicing in Wilms’ tumors using a publicly available RNAseq dataset of high-risk Wilms’ tumors and normal kidney samples. Through Pareto task inference and cell deconvolution, we found that the tumors and normal kidney samples are organized according to progressive stages of kidney development within a triangle-shaped region in latent space, whose vertices, or “archetypes,” resemble the cap mesenchyme, the nephrogenic stroma, and epithelial tubular structures of the fetal kidney. We identified a set of genes that are alternatively spliced between tumors located in different regions of latent space and found that many of these genes are associated with the Epithelial to Mesenchymal Transition (EMT) and muscle development. Using motif enrichment analysis, we identified putative splicing regulators, some of which are associated with kidney development. Our findings provide new insights into the etiology of Wilms’ tumors and suggest that specific splicing mechanisms in early stages of development may contribute to tumor development in different patients.

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Nov 2023 • Journal of the American Chemical Society

Near-Temperature-Independent Electron Transport Well beyond Expected Quantum Tunneling Range via Bacteriorhodopsin Multilayers

Sudipta Bera, Jerry A Fereiro, Shailendra K Saxena, Domenikos Chryssikos, Koushik Majhi, Tatyana Bendikov, Lior Sepunaru, David Ehre, Marc Tornow, Israel Pecht, Ayelet Vilan, Mordechai Sheves, David Cahen

A key conundrum of biomolecular electronics is efficient electron transport (ETp) through solid-state junctions up to 10 nm, often without temperature activation. Such behavior challenges known charge transport mechanisms, especially via nonconjugated molecules such as proteins. Single-step, coherent quantum-mechanical tunneling proposed for ETp across small protein, 2–3 nm wide junctions, but it is problematic for larger proteins. Here we exploit the ability of bacteriorhodopsin (bR), a well-studied, 4–5 nm long membrane protein, to assemble into well-defined single and multiple bilayers, from ∼9 to 60 nm thick, to investigate ETp limits as a function of junction width. To ensure sufficient signal/noise, we use large area (∼10–3 cm2) Au–protein–Si junctions. Photoemission spectra indicate a wide energy separation between electrode Fermi and the nearest protein-energy levels, as expected for a polymer of …

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Nov 2023 • Physical Review B

Periodically driven open quantum systems with vibronic interaction: Resonance effects and vibrationally mediated decoupling

Jakob Bätge, Yu Wang, Amikam Levy, Wenjie Dou, Michael Thoss

Periodic driving and Floquet engineering have emerged as invaluable tools for controlling and uncovering novel phenomena in quantum systems. In this study, we adopt these methods to manipulate nonequilibrium processes within electronic-vibronic open quantum systems. Through resonance mechanisms and by focusing on the limit-cycle dynamics and quantum thermodynamic properties, we illustrate the intricate interplay between the driving field and vibronic states and its overall influence on the electronic system. Specifically, we observe an effective decoupling of the electronic system from the periodic driving at specific frequencies, a phenomenon that is mediated by the vibrational mode interaction. Additionally, we engineer the driving field to obtain a partial removal of the Franck-Condon blockade. These insights hold promise for efficient charge current control. Our results are obtained from numerically …

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Nov 2023 • MDPI-Multidisciplinary Digital Publishing Institute, 2023

Acceleration of Biodiesel Production

Indra Neel Pulidindi, Aharon Gedanken

The development of renewable energy sources will help alleviate the twin problems of energy appetite and environmental pollution. Among such renewable sources, biofuels standout. Biodiesel is at the top of the list of biofuels that have the potential to substitute conventional fossil-based transportation fuels. The reprint comprises 11 chapters in total dealing with a variety of feedstock needed for the sustainable production of biodiesel, various catalysts that could be used for the accelerated production of biodiesel, and advances in reactor technology for the demand-based production of biodiesel. Indebtedness is due to various research groups, namely: Fahad Rehman and co-workers from Pakistan, Qatar, and the UK; Tao Lyu and co-workers from the UK, China, and Germany; Sandro L. Barbosa and co-workers from Brazil and the USA; Anita Salic and co-workers from Croatia; Fabrizio Roncaglia and co-workers …

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Nov 2023 • Ultrasonics Sonochemistry

Ultrasonic-assisted synthesis of lignin-capped Cu2O nanocomposite with antibiofilm properties

Moorthy Maruthapandi, Akanksha Gupta, Arumugam Saravanan, Gila Jacobi, Ehud Banin, John HT Luong, Aharon Gedanken

Under ultrasonication, cuprous oxide (Cu2O) microparticles (<5 µm) were fragmented into nanoparticles (NPs, ranging from 10 to 30 nm in diameter), and interacted strongly with alkali lignin (Mw= 10 kDa) to form a nanocomposite. The ultrasonic wave generates strong binding interaction between lignin and Cu2O. The L-Cu nanocomposite exhibited synergistic effects with enhanced antibiofilm activities against E. coli, multidrug-resistant (MDR) E. coli, S. aureus (SA), methicillin-resistant SA, and P. aeruginosa (PA). The lignin-Cu2O (L-Cu) nanocomposite also imparted notable eradication of such bacterial biofilms. Experimental evidence unraveled the destruction of bacterial cell walls by L-Cu, which interacted strongly with the bacterial membrane. After exposure to L-Cu, the bacterial cells lost the integrated structural morphology. The estimated MIC for biofilm inhibition for the five tested pathogens was 1 mg/mL L …

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Nov 2023 • Materials Today Energy

Evolution of ternary LixSnyOz artificial cathode-electrolyte interphase (ACEI) through ALD: a surface strengthened NCM811 with enhanced electrochemical performances for Li-ion …

Arka Saha, Ortal Shalev, Sandipan Maiti, Longlong Wang, Sri Harsha Akella, Bruria Schmerling, Sarah Targin, Maria Tkachev, Xiulin Fan, Malachi Noked

[(LiNi0.8Co0.1Mn0.1)O2], or NCM811, a member of the LixNi1−y−zCoyMnzO2 (NCM) family of cathode active materials (CAMs), is gaining recognition in the battery community as the CAM of choice for future high energy density lithium-ion batteries, given its high nickel content of c. 80%. Yet, its commercialization is impeded by its mechanochemical instability at a high state of charge (SOC), which results in severe capacity fading and active lithium loss during cycling. In this contribution, we report conformal nanometer-thick (c. 4–7 nm) lithiated tin-oxide ternary coatings (LixSnyOz) deposited on NCM811 cathode powder using the atomic layer deposition (ALD) technique. The first-of-its-kind ALD coating, where Li is being accompanied by a second metal ion (Sn); provides a combination of benefits: (i) it stabilizes the crystal structure, (ii) suppresses electrode polarization, (iii) lowers the voltage hysteresis, and (iv …

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Oct 2023 • ACS Applied Bio Materials

Bioimaging based on Poly (ethylenimine)-Coated Carbon Dots and Gold Nanoparticles for pH Sensing and Metal Enhanced Fluorescence

Shweta Pawar, Hamootal Duadi, Moran Friedman Gohas, Yoram Cohen, Dror Fixler

When exposed to specific light wavelengths, carbon dots (CDs), which tend to be fluorescent, can emit colorful light. It provides them with a lot of adaptability for different applications including bioimaging, optoelectronics, and even environmental sensing. Poly(ethylenimine) (PEI) coated carbon dots (PEI-CDs) with a long emission wavelength were synthesized via the hydrothermal method. The resultant CDs show strong fluorescence with quantum yield up to 20.2%. The PEI-CDs exist with distinct pH-sensitive features with pH values in the range of 2–14. The optical characteristics of CDs are pH-responsive due to the presence of different amine groups on PEI, which is a functional polycationic polymer. One of the most widely employed nanoparticles for improving the fluorescence plasmonic characteristics of a nanocomposite is gold. Gold nanoparticles were coupled with PEI-CDs in this assay by using the EDC …

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Oct 2023 • Nature Communications

CRISPR-Cas9 engineering of the RAG2 locus via complete coding sequence replacement for therapeutic applications

Daniel Allen, Orli Knop, Bryan Itkowitz, Nechama Kalter, Michael Rosenberg, Ortal Iancu, Katia Beider, Yu Nee Lee, Arnon Nagler, Raz Somech, Ayal Hendel

RAG2-SCID is a primary immunodeficiency caused by mutations in Recombination-activating gene 2 (RAG2), a gene intimately involved in the process of lymphocyte maturation and function. ex-vivo manipulation of a patient’s own hematopoietic stem and progenitor cells (HSPCs) using CRISPR-Cas9/rAAV6 gene editing could provide a therapeutic alternative to the only current treatment, allogeneic hematopoietic stem cell transplantation (HSCT). Here we show an innovative RAG2 correction strategy that replaces the entire endogenous coding sequence (CDS) for the purpose of preserving the critical endogenous spatiotemporal gene regulation and locus architecture. Expression of the corrective transgene leads to successful development into CD3+TCRαβ+ and CD3+TCRγδ+ T cells and promotes the establishment of highly diverse TRB and TRG repertoires in an in-vitro T-cell differentiation platform. Thus, our …

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Oct 2023 • Angewandte Chemie International Edition

Polymeric Carbon nitride with chirality inherited from supramolecular assemblies

Adi Azoulay, Sapir Shekef Aloni, Lidan Xing, Ayelet Tashakory, Yitzhak Mastai, Menny Shalom

The facile synthesis of chiral materials is of paramount importance for various applications. Supramolecular preorganization of monomers for thermal polymerization has been proven as an effective tool to synthesize carbon and carbon nitride‐based (CN) materials with ordered morphology and controlled properties. However, the transfer of an intrinsic chemical property, such as chirality from supramolecular assemblies to the final material after thermal condensation, was not shown. Here, we report the large‐scale synthesis of chiral CN materials capable of enantioselective recognition. To achieve this, we designed supramolecular assemblies with a chiral center that remains intact at elevated temperatures. The optimized chiral CN demonstrates an enantiomeric preference of ca. 14 %; CN electrodes were also prepared and show stereoselective interactions with enantiomeric probes in electrochemical …

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Oct 2023 • arXiv preprint arXiv:2210.02743

Tracking nanoscale perturbation in active disordered media

Renu Yadav, Patrick Sebbah, Maruthi M Brundavanam

The disorder induced feedback makes random lasers very susceptible to any changes in the scattering medium. The sensitivity of the lasing modes to perturbations in the disordered systems have been utilized to map the regions of perturbation. A tracking parameter, that takes into account the cumulative effect of changes in the spatial distribution of the lasing modes of the system has been defined to locate the region in which a scatterer is displaced by a few nanometers. We show numerically that the precision of the method increases with the number of modes. The proposed method opens up the possibility of application of random lasers as a tool for monitoring locations of nanoscale displacement which can be useful for single particle detection and monitoring.

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Oct 2023 • Nature Nanotechnology

High-energy all-solid-state lithium batteries enabled by Co-free LiNiO2 cathodes with robust outside-in structures

Longlong Wang, Ayan Mukherjee, Chang-Yang Kuo, Sankalpita Chakrabarty, Reut Yemini, Arrelaine A Dameron, Jaime W DuMont, Sri Harsha Akella, Arka Saha, Sarah Taragin, Hagit Aviv, Doron Naveh, Daniel Sharon, Ting-Shan Chan, Hong-Ji Lin, Jyh-Fu Lee, Chien-Te Chen, Boyang Liu, Xiangwen Gao, Suddhasatwa Basu, Zhiwei Hu, Doron Aurbach, Peter G Bruce, Malachi Noked

A critical current challenge in the development of all-solid-state lithium batteries (ASSLBs) is reducing the cost of fabrication without compromising the performance. Here we report a sulfide ASSLB based on a high-energy, Co-free LiNiO2 cathode with a robust outside-in structure. This promising cathode is enabled by the high-pressure O2 synthesis and subsequent atomic layer deposition of a unique ultrathin LixAlyZnzOδ protective layer comprising a LixAlyZnzOδ surface coating region and an Al and Zn near-surface doping region. This high-quality artificial interphase enhances the structural stability and interfacial dynamics of the cathode as it mitigates the contact loss and continuous side reactions at the cathode/solid electrolyte interface. As a result, our ASSLBs exhibit a high areal capacity (4.65 mAh cm−2), a high specific cathode capacity (203 mAh g−1), superior cycling stability (92% capacity retention …

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Oct 2023 • 2023 IEEE Nanotechnology Materials and Devices Conference (NMDC), 660-660, 2023

Unconventional Formation of a Zintl Compound in Nanowire Form

Man Suk Song, Lothar Houben, Nadav Rothem, Xi Wang, Beena Kalisky, Magdalena A Załuska-Kotur, Hyeonhu Bae, Binghai Yan, Ryszard Buczko, Perla Kacman, Haim Beidenkopf, Hadas Shtrikman

Nanowires consisting of Eu 3 In 2 As 4 were grown by MBE using an unconventional method. Eu 3 In 2 P 4 and Eu 3 InEu 3 were suggested to be an example of material with new magnetic Zintl phases already 20 years ago [1]. Recently, a vast selection of newly emerging compounds, in particular compounds based on InAs with the addition of strontium, barium or europium, such as Eu 3 In 2 As 4 have been included into the Zintl family of materials and widely studied [2]. Extensively conducted research showed a large variety of unique magnetic, electronic, and topological properties both in bulk and layers of Zintl materials. Here we present the formation of a Zintl phase obtained for the first time in nanowires. The properties of these nanowires, including their composition, crystal structure and magnetic order, were thoroughly characterized. The experimental study was supported by theoretical simulations related …

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Oct 2023

Roadmap on Label‐Free Super‐Resolution Imaging

Vasily N Astratov, Yair Ben Sahel, Yonina C Eldar, Luzhe Huang, Aydogan Ozcan, Nikolay Zheludev, Junxiang Zhao, Zachary Burns, Zhaowei Liu, Evgenii Narimanov, Neha Goswami, Gabriel Popescu, Emanuel Pfitzner, Philipp Kukura, Yi‐Teng Hsiao, Chia‐Lung Hsieh, Brian Abbey, Alberto Diaspro, Aymeric LeGratiet, Paolo Bianchini, Natan T Shaked, Bertrand Simon, Nicolas Verrier, Matthieu Debailleul, Olivier Haeberlé, Sheng Wang, Mengkun Liu, Yeran Bai, Ji‐Xin Cheng, Behjat S Kariman, Katsumasa Fujita, Moshe Sinvani, Zeev Zalevsky, Xiangping Li, Guan‐Jie Huang, Shi‐Wei Chu, Omer Tzang, Dror Hershkovitz, Ori Cheshnovsky, Mikko J Huttunen, Stefan G Stanciu, Vera N Smolyaninova, Igor I Smolyaninov, Ulf Leonhardt, Sahar Sahebdivan, Zengbo Wang, Boris Luk'yanchuk, Limin Wu, Alexey V Maslov, Boya Jin, Constantin R Simovski, Stephane Perrin, Paul Montgomery, Sylvain Lecler

Label‐free super‐resolution (LFSR) imaging relies on light‐scattering processes in nanoscale objects without a need for fluorescent (FL) staining required in super‐resolved FL microscopy. The objectives of this Roadmap are to present a comprehensive vision of the developments, the state‐of‐the‐art in this field, and to discuss the resolution boundaries and hurdles that need to be overcome to break the classical diffraction limit of the label‐free imaging. The scope of this Roadmap spans from the advanced interference detection techniques, where the diffraction‐limited lateral resolution is combined with unsurpassed axial and temporal resolution, to techniques with true lateral super‐resolution capability that are based on understanding resolution as an information science problem, on using novel structured illumination, near‐field scanning, and nonlinear optics approaches, and on designing superlenses based …

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Oct 2023 • 244th ECS Meeting (October 8-12, 2023)

A Scalable Approach to Synthesize Cobalt-Free LNMO Cathode Materials for High Energy Density Lithium Ion Batteries

Tao Hu, Yan Lin, Pekka Tynjälä, Shubo Wang, Gayathri Peta, Harishchandra Singh, Doron Aurbach, Ulla Lassi

Oct 2023 • Chemistry of Materials

Theoretical Insights into High-Entropy Ni-Rich Layered Oxide Cathodes for Low-Strain Li-Ion Batteries

Amreen Bano, Malachi Noked, Dan Thomas Major

Ni-rich, Co-free layered oxide cathode materials are promising candidates for next-generation Li-ion batteries due to their high energy density. However, these cathode materials suffer from rapid capacity fading during electrochemical cycling. To overcome this shortcoming, so-called high-entropy (HE) materials, which are obtained by incorporating multiple dopants, have been suggested. Recent experimental work has shown that HE Ni-rich cathode materials can offer excellent capacity retention on cycling, although a thorough rationale for this has yet to be provided. Here, we present classical and first-principles calculations to elucidate the salient features of HE layered oxides as cathode materials in Li-ion batteries. We suggest that a combination of five prime factors may be responsible for the enhanced performance of HE Ni-rich layered oxide cathode materials over other Ni-rich cathodes: (1) low crystal lattice …

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Oct 2023

How synchronized human networks escape local minima

Moti Fridman, Elad Shniderman, Yahav Avraham, Shir Shahal, Hamootal Duadi, Nir Davidson

Finding the global minimum in complex networks while avoiding local minima is challenging in many types of networks. We study the dynamics of complex human networks and observed that humans have different methods to avoid local minima than other networks. Humans can change the coupling strength between them or change their tempo. This leads to different dynamics than other networks and makes human networks more robust and better resilient against perturbations. We observed high-order vortex states, oscillation death, and amplitude death, due to the unique dynamics of the network. This research may have implications in politics, economics, pandemic control, decision-making, and predicting the dynamics of networks with artificial intelligence.

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Oct 2023 • bioRxiv

Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry

Eric Engelbrecht, Oscar L Rodriguez, Kaitlyn Shields, Steven Schulze, David Tieri, Uddalok Jana, Gur Yaari, William Lees, Melissa L Smith, Corey T Watson

Immunoglobulins (IGs), critical components of the human immune system, are composed of heavy and light protein chains encoded at three genomic loci. The IG Kappa (IGK) chain locus consists of two large, inverted segmental duplications. The complexity of IG loci has hindered effective use of standard high-throughput methods for characterizing genetic variation within these regions. To overcome these limitations, we leverage long-read sequencing to create haplotype-resolved IGK assemblies in an ancestrally diverse cohort (n=36), representing the first comprehensive description of IGK haplotype variation at population-scale. We identify extensive locus polymorphism, including novel single nucleotide variants (SNVs) and a common novel ~24.7 Kbp structural variant harboring a functional IGKV gene. Among 47 functional IGKV genes, we identify 141 alleles, 64 (45.4%) of which were not previously curated. We report inter-population differences in allele frequencies for 14 of the IGKV genes, including alleles unique to specific populations within this dataset. Finally, we identify haplotypes carrying signatures of gene conversion that associate with enrichment of SNVs in the IGK distal region. These data provide a critical resource of curated genomic reference information from diverse ancestries, laying a foundation for advancing our understanding of population-level genetic variation in the IGK locus.

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Oct 2023 • Sensors

Optical Multimode Fiber-Based Pipe Leakage Sensor Using Speckle Pattern Analysis

Jonathan Philosof, Yevgeny Beiderman, Sergey Agdarov, Yafim Beiderman, Zeev Zalevsky

Water is an invaluable resource quickly becoming scarce in many parts of the world. Therefore, the importance of efficiency in water supply and distribution has greatly increased. Some of the main tools for limiting losses in supply and distribution networks are leakage sensors that enable real-time monitoring. With fiber optics recently becoming a commodity, along with the sound advances in computing power and its miniaturization, multipurpose sensors relying on these technologies have gradually become common. In this study, we explore the development and testing of a multimode optic-fiber-based pipe monitoring and leakage detector based on statistical and machine learning analyses of speckle patterns captured from the fiber’s outlet by a defocused camera. The sensor was placed inside or over a PVC pipe with covered and exposed core configurations, while 2 to 8 mm diameter pipe leaks were simulated under varied water flow and pressure. We found an overall leak size determination accuracy of 75.8% for a 400 µm covered fiber and of 68.3% for a 400 µm exposed fiber and demonstrated that our sensor detected pipe bursts, outside interventions, and shocks. This result was consistent for the sensors fixed inside and outside the pipe with both covered and exposed fibers.

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Oct 2023 • Colloids and Interfaces

Recyclable Adsorbents for Potash Brine Desalination Based on Silicate Powder: Application, Regeneration and Utilization

Akmaral B Rakhym, Zarina Ye Baranchiyeva, Aruzhan K Kenessova, Bagashar B Zhaksybai, Diana N Dauzhanova, Yitzhak Mastai, Gulziya A Seilkhanova

Silicate mineral powders (SMP) from weathered granite soil from Kazakhstan are proposed for the desalination of potash brines containing sodium, potassium and chloride ions. Batch adsorption experiments using acid-treated silicate (AS) achieved a Na+/K+/Cl− recovery of ~13/28/6 mg/g. An isothermal study best fitted the Freundlich and Dubinin–Radushkevich models for Na+ and K+/Cl−. The kinetic data were best modeled by pseudo-second-order kinetics for Na+/K+ and pseudo-first-order for Cl−. Thermodynamic calculations showed spontaneity under natural conditions. For Na+/K+, physisorption is accompanied by ion exchange. To study the possibility of sorbent reuse, several cycles of K+/Na+ adsorption–desorption were carried out under optimal conditions. AS selectively adsorbed potassium ions, maintaining a high effectiveness during five cycles providing K-form silicate fertilizers. Leachates of spent AS contain high concentrations of K/Na/Ca/Mg and other microelements essential for plants. Thus, SMP resolve two issues: the desalination of brine and the provision of fertilizer.

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Oct 2023 • Nano Letters

Unveiling Local Optical Properties Using Nanoimaging Phase Mapping in High-Index Topological Insulator Bi2Se3 Resonant Nanostructures

Sukanta Nandi, Shany Z Cohen, Danveer Singh, Michal Poplinger, Pilkhaz Nanikashvili, Doron Naveh, Tomer Lewi

Topological insulators are materials characterized by an insulating bulk and high mobility topologically protected surface states, making them promising candidates for future optoelectronic and quantum devices. Although their electronic properties have been extensively studied, their mid-infrared (MIR) properties and prospective photonic capabilities have not been fully uncovered. Here, we use a combination of far-field and near-field nanoscale imaging and spectroscopy to study chemical vapor deposition-grown Bi2Se3 nanobeams (NBs). We extract the MIR optical constants of Bi2Se3, revealing refractive index values as high as n ∼ 6.4, and demonstrate that the NBs support Mie resonances across the MIR. Local near-field reflection phase mapping reveals domains of various phase shifts, providing information on the local optical properties of the NBs. We experimentally measure up to 2π phase-shift across the …

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