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Jan 2023 • Proc. of SPIE Vol

Frontiers in Biological Detection: From Nanosensors to Systems XV

Amos Danielli, Benjamin L Miller, Sharon M Weiss

PROCEEDINGS OF SPIE Page 1 PROCEEDINGS OF SPIE SPIEDigitalLibrary.org/conference-proceedings-of-spie Front Matter: Volume 12397 , "Front Matter: Volume 12397," Proc. SPIE 12397, Frontiers in Biological Detection: From Nanosensors to Systems XV, 1239701 (2 May 2023); doi: 10.1117/12.2679008 Event: SPIE BiOS, 2023, San Francisco, California, United States Downloaded From: https://www.spiedigitallibrary.org/conference-proceedings-of-spie on 04 May 2023 Terms of Use: https://www.spiedigitallibrary.org/terms-of-use Page 2 PROGRESS IN BIOMEDICAL OPTICS AND IMAGING Vol. 24 No. 46 Volume 12397 Proceedings of SPIE, 1605-7422, V. 12397 SPIE is an international society advancing an interdisciplinary approach to the science and application of light. Frontiers in Biological Detection: From Nanosensors to Systems XV Amos Danielli Benjamin L. Miller Sharon M. Weiss Editors 29 …

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Jan 2023 • Power Ultrasonics, 431-454, 2023

Power ultrasound for the production of nanomaterials

A Gedanken, I Perelshtein, N Perkas

Sonochemistry in now well recognized as a technique for the fabrication of nanomaterials. This is reflected in the many review articles on sonochemistry and nanoparticles that have been published over the last few years. It is so happened that Suslick, one of the forefathers of this field, has lately written a very comprehensive review on this topic (Bang, 2010). In his review, Suslick has summarized the work published on sonochemistry and nanomaterials until 2010. The current review will try to scan the work done in this area until the end of 2012. The current review will concentrate first on explaining why nano? Namely, when, why, and what kind of nanomaterials are produced upon the collapse of the acoustic bubble?

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Jan 2023 • Materials Reports: Energy, 100178, 2023

Recent progress in C–N coupling for electrochemical CO2 reduction with inorganic nitrogenous species in aqueous solution

Shuxia Liu, Tanyuan Wang, Lior Elbaz, Qing Li

The electrocatalytic CO2 reduction in aqueous solution mainly involves bond cleavage and formation between C, H and O, and it is highly desirable to expand the bond formation reaction of C with other atoms to obtain novel and valuable chemicals. The electrochemical synthesis of N-containing organic chemicals in electrocatalytic CO2 reduction via introducing N sources is an effective strategy to expand the product scope, since chemicals containing C–N bonds (e.g. amides and amines) are important reactants/products for medicine, agriculture and industry. This article focuses on the research progress of C–N coupling from CO2 and inorganic nitrogenous species in aqueous solution. Firstly, the reaction pathways related to the reaction intermediates for urea, formamide, acetamide, methylamine and ethylamine are highlighted. Then, the electrocatalytic performance of different catalysts for these several N …

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Jan 2023 • Analysis & Sensing 3 (1), e202200053, 2023

Measurement of protein dynamics from site directed Cu (II) labeling

Kevin Singewald, Hannah Hunter, Timothy F Cunningham, Sharon Ruthstein, Sunil Saxena

This review describes the use of Electron Paramagnetic Resonance (EPR) to measure residue specific dynamics in proteins with a specific focus on Cu(II)‐based spin labels. First, we outline approaches used to measure protein motion by nitroxide‐based spin labels. Here, we describe conceptual details and outline challenges that limit the use of nitroxide spin labels to solvent‐exposed α‐helical sites. The bulk of this review showcases the use of newly developed Cu(II)‐based protein labels. In this approach, the strategic mutation of native residues on a protein to generate two neighboring Histidine residues (i.e., the dHis motif) is exploited to enable a rigid site‐selective binding of a Cu(II) complex. The chelation of the Cu(II) complex to dHis directly anchors the Cu(II) spin label to the protein backbone. The improvement in rigidity expands both the spin‐labeling toolkit as well as the resolution of many EPR …

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Jan 2023 • Optics Express

Thermo-elastic gigahertz-frequency oscillator through surface acoustic wave-silicon photonics

Maayan Priel, Saawan Kumar Bag, Matan Slook, Leroy Dokhanian, Inbar Shafir, Mirit Hen, Moshe Katzman, Etai Grunwald, Dvir Munk, Moshe Feldberg, Tali Sharabani, Naor Inbar, Gil Bashan, Avi Zadok

Opto-electronic oscillators are sources of microwave-frequency tones that may reach very low noise levels. Much effort is being dedicated to the realization of oscillators based on photonic integrated devices. In this work, we propose and demonstrate a thermo-elastic opto-electronic oscillator at 2.213 GHz frequency based on a standard silicon-photonic integrated circuit. A microwave-frequency electrical signal modulates an optical pump wave carrier. The modulated waveform launches surface acoustic waves in a silicon-on-insulator substrate, through absorption in a metallic grating and thermo-elastic actuation. The waveform is reconverted to the optical domain through photoelastic modulation of an optical probe wave carrier in a standard racetrack resonator waveguide. Both the thermo-elastic actuation and the photoelastic modulation are radio-frequency selective. The output probe wave is detected, and the receiver voltage is amplified and fed back to modulate the optical pump input. Sufficient gain drives the loop into oscillations. The oscillator does not involve piezoelectricity and can be realized on any substrate. Long acoustic delays may be implemented in compact devices. The frequency of operation is scalable to tens of GHz. The principle may be useful in integrated microwave-photonic signal processing and in the elastic analysis of surfaces and thin layers.

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Jan 2023 • arXiv preprint arXiv:2301.01581

Universal to Non-Universal Transition of the statistics of Rare Events During the Spread of Random Walks

RK Singh, Stanislav Burov

Particle hopping is a common feature in heterogeneous media. We explore such motion by using the widely applicable formalism of the continuous time random walk and focus on the statistics of rare events. Numerous experiments have shown that the decay of the positional probability density function P (X, t), describing the statistics of rare events, exhibits universal exponential decay. We show that such universality ceases to exist once the threshold of exponential distribution of particle hops is crossed. While the mean hop is not diverging and can attain a finite value; the transition itself is critical. The exponential universality of rare events arises due to the contribution of all the different states occupied during the process. Once the reported threshold is crossed, a single large event determines the statistics. In this realm, the big jump principle replaces the large deviation principle, and the spatial part of the decay is unaffected by the temporal properties of rare events.

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Jan 2023 • Polymer-Based Nanoscale Materials for Surface Coatings, 479-500, 2023

Superhydrophobic nanoscale materials for surface coatings

Sayan Ganguly, Shlomo Margel

Superhydrophobic surface preparation is developed by inspiration from nature. As it is a natural fact that lotus leaves are water repellant, thus researchers tried their best to develop superhydrophobic coatings by using several materials. The materials are categorized by inorganic, organic, and their synergistic hybrids. Polymeric coatings are more usable by scientists because of its tunable chemical features and their internal morphologies. This chapter will discuss in brief the coating materials and how polymer systems influenced the superhydrophobicity.

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Jan 2023 • Proc. of SPIE Vol

Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XX

Dror Fixler, Ewa M Goldys, Sebastian Wachsmann-Hogiu

PROCEEDINGS OF SPIE Page 1 PROCEEDINGS OF SPIE SPIEDigitalLibrary.org/conference-proceedings-of-spie Front Matter: Volume 12394 , "Front Matter: Volume 12394," Proc. SPIE 12394, Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XX, 1239401 (2 May 2023); doi: 10.1117/12.2678752 Event: SPIE BiOS, 2023, San Francisco, California, United States Downloaded From: https://www.spiedigitallibrary.org/conference-proceedings-of-spie on 03 May 2023 Terms of Use: https://www.spiedigitallibrary.org/terms-of-use Page 2 PROGRESS IN BIOMEDICAL OPTICS AND IMAGING Vol. 24 No. 43 Volume 12394 Proceedings of SPIE, 1605-7422, V. 12394 SPIE is an international society advancing an interdisciplinary approach to the science and application of light. Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XX Dror Fixler Ewa M. Goldys Sebastian Wachsmann-…

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Jan 2023 • Biochemistry

Conformations and Local Dynamics of the CopY Metal Sensor Revealed by EPR Spectroscopy

Melanie Hirsch, Lukas Hofmann, Yulia Shenberger, Lada Gevorkyan-Airapetov, Sharon Ruthstein

Metal transcription factors regulate metal concentrations in eukaryotic and prokaryotic cells. Copper is a metal ion that is being tightly regulated, owing to its dual nature. Whereas copper is an essential nutrient for bacteria, it is also toxic at high concentrations. CopY is a metal-sensitive transcription factor belonging to the copper-responsive repressor family found in Gram-positive bacteria. CopY represses transcription in the presence of Zn(II) ions and initiates transcription in the presence of Cu(I) ions. The complete crystal structure of CopY has not been reported yet, therefore most of the structural information on this protein is based on its similarity to the well-studied MecI protein. In this study, electron paramagnetic resonance (EPR) spectroscopy was used to characterize structural and local dynamical changes in Streptococcus pneumoniae CopY as a function of Zn(II), Cu(I), and DNA binding. We detected different …

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Jan 2023 • Materials Today Energy

Aqueous proton batteries based on acetic acid solutions: mechanistic insights

Bar Gavriel, Gil Bergman, Meital Turgeman, Amey Nimkar, Yuval Elias, Mikhael D Levi, Daniel Sharon, Netanel Shpigel, Doron Aurbach

Large grid energy storage devices are critical for the success of the clean and sustainable energy revolution. As Li-ion batteries are earmarked for electric vehicles and portable devices such as laptops and cellphones, other electrochemical systems should be developed that enable cost-effective, safe, and durable large-scale energy storage. Due to the low cost and non-flammability of aqueous electrolyte solutions, much effort is being put into the development of ‘beyond-Li’ batteries and super capacitors that can work in these environments. Here, we propose new proton batteries comprising an acetic acid electrolyte solution, NiII [FeIII(CN)6]2/3·4H2O Prussian blue analog cathodes, and Ti3C2Tx MXene anodes. Both electrodes were investigated independently to discover ideal settings for the electrochemical performance and stability. Significant attention was given to the cathodes' protons storage mechanism. In …

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Jan 2023 • Plos one

Study of entanglement via a multi-agent dynamical quantum game

Amit Te’eni, Bar Y Peled, Eliahu Cohen, Avishy Carmi

At both conceptual and applied levels, quantum physics provides new opportunities as well as fundamental limitations. We hypothetically ask whether quantum games inspired by population dynamics can benefit from unique features of quantum mechanics such as entanglement and nonlocality. For doing so, we extend quantum game theory and demonstrate that in certain models inspired by ecological systems where several predators feed on the same prey, the strength of quantum entanglement between the various species has a profound effect on the asymptotic behavior of the system. For example, if there are sufficiently many predator species who are all equally correlated with their prey, they are all driven to extinction. Our results are derived in two ways: by analyzing the asymptotic dynamics of the system, and also by modeling the system as a quantum correlation network. The latter approach enables us to apply various tools from classical network theory in the above quantum scenarios. Several generalizations and applications are discussed.

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Jan 2023 • Analysis & Sensing

Cover Feature: Measurement of Protein Dynamics from Site Directed Cu (II) Labeling (Anal. Sens. 1/2023)

Kevin Singewald, Hannah Hunter, Timothy F Cunningham, Sharon Ruthstein, Sunil Saxena

The cover feature image illustrates two sites of a protein with different site specific reorientational dynamics (purple). Such differences can be measured by newly developed site-directed Cu (II) labeling methodology. The resultant EPR lineshape at physiological temperatures is sensitive to the timescale of backbone motion. Importantly, this methodology enables site-specific detection on both α-helices and β-sheets via EPR. Thus, the role of protein dynamics to protein function can be elucidated. More information can be found in the Review by Sunil Saxena and co-workers.

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Jan 2023 • The Journal of Physical Chemistry Letters

It Is a Trap!: The Effect of Self-Healing of Surface Defects on the Excited States of CdSe Nanocrystals

Alexandra R McIsaac, Tamar Goldzak, Troy Van Voorhis

Colloidal semiconductor nanocrystals have attracted much interest due to their unique optical properties, with applications ranging from displays to biomedical imaging. Nanocrystal optical properties depend on the structure of the surface, where defects can lead to traps. CdSe nanocrystals undergo surface reorganization, or self-healing, to eliminate defects, removing midgap traps from the band structure. However, the effect of this process on the optical spectrum is not well studied. Here, we show that self-healing not only eliminates midgap traps from the band structure but also brightens the spectrum and causes the excitonic states to emerge as the dominant features, in agreement with experimental annealing studies. We find that self-healing can lead to new traps like bonded Se–Se or Cd–Cd dimers, and their behavior is different from that of undercoordinated atom traps. These results suggest that eliminating …

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Jan 2023 • ACS Sustainable Chemistry & Engineering

Rechargeable Seawater Batteries Based on Polyimide Anodes

Amey Nimkar, Bar Gavriel, Gil Bergman, Meital Turgeman, Tianju Fan, Netanel Shpigel, Doron Aurbach

Being nearly unlimited natural resource containing mostly Na cations, the use of seawater as an electrolyte solution (aka seawater batteries) for electrochemical energy storage has received growing attention. To date, the vast majority of studies have focused on the use of seawater in Na-metal batteries protected by ion-conductive membranes hermetic to water. These systems, however, are complex and expensive, and suffer from a short cycling life. Here, we present alternative seawater batteries that utilize polyimide anodes. With its high capacity of more than 140 mAh/g, impressive rate capability, and excellent long-term stability (98% capacity retention after more than 9000 cycles), the prepared polyimide electrodes demonstrated to be promising candidate anodes for seawater electrochemical energy storage devices. Looking for a suitable cathode, we explored the use of nickel hexacyanoferrate (Ni-HCF) and …

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Jan 2023 • Polymeric Nanocomposite Materials for Sensor Applications, 323-342, 2023

Polymer composites for biosensors

Poushali Das, Akanksha Gupta, Moorthy Maruthapandi, Arumugam Saravanan, Seshasai Srinivasan, Amin Reza Rajabzadeh, Aharon Gedanken

Biosensors are analytical devices with a wide range of uses in various fields such as food, military, environmental monitoring, and clinical diagnostics. Similarly, polymers and their composites have sparked a lot of interest in biosensing because of their properties, including compatibility with biological molecules, efficient electron transfer during biochemical reactions, bioreagent loading, and biomolecule immobilization. Different nanoparticles such as carbon nanotubes, graphenes, gold nanoparticles, etc., have been efficiently integrated into the polymer matrix to improve performance features such as rapid response, high selectivity, improved sensitivity, long-term stability, and lower detection limit. Polymers in combination with nanomaterials provide a three-dimensional matrix that preserves biomolecule activity and provides an excellent platform for immobilization due to their good durability, porosity, selectivity …

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Jan 2023 • bioRxiv

Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins

Ganesh Agam, Christian Gebhardt, Milana Popara, Rebecca Maechtel, Julian Folz, Ben Ambrose, Neharika Chamachi, Sang Yoon Chung, Timothy D Craggs, Marijn de Boer, Dina Grohmann, Taekjip Ha, Andreas Hartmann, Jelle Hendrix, Verena Hirschfeld, Christian G Huebner, Thorsten Hugel, Dominik Kammerer, Hyun Seo Kang, Achillefs Kapanidis, Georg Krainer, Kevin Kramm, Edward Lemke, Eitan Lerner, Emmanuel Margeat, Kirsten Martens, Jens Michaelis, Jaba Mitra, Gustavo G Moya Munoz, Robert Quast, Nicole Robb, Michael Sattler, Michael Schlierf, Jonathan Schneider, Tim Schroeder, Anna Sefer, Piau Siong Tan, Johann Thurn, Philip Tinnefeld, John van Noort, Shimon Weiss, Nicolas Wendler, Anders Barth, Claus AM Seidel, Don C Lamb, Thorben Cordes

Single-molecule FRET (smFRET) has become an established tool to study biomolecular structure and dynamics in vitro and in live cells. We performed a worldwide blind study involving 19 labs to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems that undergo distinct conformational changes, we obtained an uncertainty of the FRET efficiency of less than 0.06, corresponding to an interdye distance precision of less than 0.2 nm and accuracy of less than 0.5 nm. We further discuss the limits for detecting distance fluctuations with sensitivity down to less than 10% of the Foerster distance and provide guidelines on how to detect potential dye perturbations. The ability of smFRET experiments to simultaneously measure distances and avoid averaging of conformational dynamics slower than the fluorescence lifetime is unique for dynamic structural biology.

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Jan 2023 • Physical Review B

Sachdev-Ye-Kitaev model: Non-self-averaging properties of the energy spectrum

Richard Berkovits

The short time (large energy) behavior of the Sachdev-Ye-Kitaev model (SYK) is one of the main reasons for the growing interest garnered by this model. True chaotic behavior sets in at the Thouless time, which can be extracted from the energy spectrum. In order to do so, it is necessary to unfold the spectrum, ie, to filter out global tendencies. Using a simple ensemble average for unfolding results in a parametically low estimation of the Thouless energy. By examining the behavior of the spectrum as the distribution of the matrix elements is changed into a log-normal distribution, it is shown that the sample-to-sample level spacing variance determines this estimation of the Thouless energy. Using the singular value decomposition method, which filters out these global sample-to-sample fluctuations, the Thouless energy becomes parametrically much larger, essentially of the order of the band width. It is shown that the …

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Jan 2023 • Advanced Photonics Nexus

Toward augmenting tip-enhanced nanoscopy with optically resolved scanning probe tips

Jeremy Belhassen, Simcha Glass, Eti Teblum, George A Stanciu, Denis E Tranca, Zeev Zalevsky, Stefan G Stanciu, Avi Karsenty

A thorough understanding of biological species and emerging nanomaterials requires, among other efforts, their in-depth characterization through optical techniques capable of nanoresolution. Nanoscopy techniques based on tip-enhanced optical effects have gained tremendous interest over the past years, given their potential to obtain optical information with resolutions limited only by the size of a sharp probe interacting with focused light, irrespective of the illumination wavelength. Although their popularity and number of applications is rising, tip-enhanced nanoscopy (TEN) techniques still largely rely on probes that are not specifically developed for such applications, but for atomic force microscopy. This limits their potential in many regards, e.g., in terms of signal-to-noise ratio, attainable image quality, or extent of applications. We take the first steps toward next-generation TEN by demonstrating the fabrication …

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Jan 2023 • Nanomaterials 13 (3), 598, 2023

Recent Advances in the Spintronic Application of Carbon-Based Nanomaterials

Shweta Pawar, Hamootal Duadi, Dror Fixler

The term “carbon-based spintronics” mostly refers to the spin applications in carbon materials such as graphene, fullerene, carbon nitride, and carbon nanotubes. Carbon-based spintronics and their devices have undergone extraordinary development recently. The causes of spin relaxation and the characteristics of spin transport in carbon materials, namely for graphene and carbon nanotubes, have been the subject of several theoretical and experimental studies. This article gives a summary of the present state of research and technological advancements for spintronic applications in carbon-based materials. We discuss the benefits and challenges of several spin-enabled, carbon-based applications. The advantages include the fact that they are significantly less volatile than charge-based electronics. The challenge is in being able to scale up to mass production.

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Jan 2023 • International Journal of Molecular Sciences

Characterization of Continuous Transcriptional Heterogeneity in High-Risk Blastemal-Type Wilms’ Tumors Using Unsupervised Machine Learning

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

Wilms’ tumors are pediatric malignancies that are thought to arise from faulty kidney development. They contain a wide range of poorly differentiated cell states resembling various distorted developmental stages of the fetal kidney, and as a result, differ between patients in a continuous manner that is not well understood. Here, we used three computational approaches to characterize this continuous heterogeneity in high-risk blastemal-type Wilms’ tumors. Using Pareto task inference, we show that the tumors form a triangle-shaped continuum in latent space that is bounded by three tumor archetypes with “stromal”,“blastemal”, and “epithelial” characteristics, which resemble the un-induced mesenchyme, the cap mesenchyme, and early epithelial structures of the fetal kidney. By fitting a generative probabilistic “grade of membership” model, we show that each tumor can be represented as a unique mixture of three hidden “topics” with blastemal, stromal, and epithelial characteristics. Likewise, cellular deconvolution allows us to represent each tumor in the continuum as a unique combination of fetal kidney-like cell states. These results highlight the relationship between Wilms’ tumors and kidney development, and we anticipate that they will pave the way for more quantitative strategies for tumor stratification and classification.

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Jan 2023 • Energy Storage Materials

Zeolites as Multifunctional Additives Stabilize High-Voltage Li-Batteries Based on LiNi0. 5Mn1. 5O4 Cathodes, Mechanistic Studies

Sandipan Maiti, Hadar Sclar, Xiaohan Wu, Judith Grinblat, Michael Talianker, Aleksandr Kondrakov, Boris Markovsky, Doron Aurbach

The work reported herein discusses the improved electrochemical and thermal behavior of LiNi0.5Mn1.5O4 (LNMO) spinel cathodes via surface engineering using a series of zeolites. The limiting issues of these high voltage electrodes are phase transition during Li-ions intercalation/de-intercalation processes, weakening the active material's structure. Besides, it initiates harmful interfacial side reactions, including solution species oxidation and Ni & Mn dissolution, affecting their long-term cycling stability severely and detrimentally. Therefore, we propose a zeolite-based surface modification of LNMO involving a simple surface coating strategy that includes liquid-phase (ethanol) mixing followed by heat treatment at 200°C under nitrogen gas flow. The cathodes comprising LNMO coated with 2 wt% zeolites exhibited significantly improved cycling stability than the reference cathodes with the uncoated material …

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