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Dec 2023 • Genome Research

A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls

Modi Safra, Lael Werner, Pazit Polak, Ayelet Peres, Naomi Salamon, Michael Schvimer, Batia Weiss, Iris Barshack, Dror S Shouval, Gur Yaari

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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 • 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 • Advanced Optical Materials

Optical Properties and Ultrafast Near‐Infrared Localized Surface Plasmon Dynamics in Naturally p‐Type Digenite Films

Andrea Villa, Madina Telkhozhayeva, Fabio Marangi, Eti Teblum, Aaron M Ross, Mirko Prato, Luca Andena, Roberto Frassine, Francesco Scotognella, Gilbert Daniel Nessim

Copper chalcogenides are materials characterized by intrinsic doping properties, allowing them to display high carrier concentrations due to their defect‐heavy structures, independent of the preparation method. Such high doping enables these materials to display plasmonic resonances, tunable by varying their stoichiometry. Here, plasmonic dynamics is studied in drop‐cast Cu9S5 (digenite) nanocrystals (NCs) film using ultrafast pump–probe spectroscopy. The NCs are synthesized by thermal annealing of copper foil using chemical vapor deposition (CVD), followed by sonication and drop‐casting of the isolated few‐layered flakes on different substrates. The samples display a broad localized surface plasmon resonance (LSPR) in the near‐infrared (NIR), peaking at 2100 nm. The free carrier response is further confirmed by fitting the linear absorption with a Drude–Lorentz effective medium approximation model …

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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 • arXiv preprint arXiv:2210.10935

Brownian particles in periodic potentials: Coarse-graining versus fine structure

Lucianno Defaveri, Eli Barkai, David A Kessler

We study the motion of an overdamped particle connected to a thermal heat bath in the presence of an external periodic potential. When the coarse-graining is larger than the periodicity of the potential, the packet of spreading particles, all starting from a common origin, converges to a normal distribution centered at the origin with a mean-squared displacement that grows like , with an effective diffusion constant that is smaller than that of a freely diffusing particle. We examine the interplay between this coarse-grained description and the fine structure of the density, which is given by the Boltzmann-Gibbs factor , the latter being non-normalizable. We explain this result and construct a theory of observables using the Fokker-Planck equation. These observables are classified as those that are related to the BG fine structure, like the energy or occupation times, while others, like the positional moments, for long times, converge to those of the large-scale description. Entropy falls into a special category as it has a coarse-grained and a fine structure description. The basic thermodynamic formula is extended to this far from equilibrium system. The ergodic properties are also studied using tools from infinite ergodic theory.

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Oct 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 development of 'beyond-Li' batteries and supercapacitors 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 electrochemical performance and stability. Significant attention was given to the cathodes' protons storage mechanism. In-situ …

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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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Sep 2023 • arXiv preprint arXiv:2109.04237

Study of entanglement via a multi-agent dynamical quantum game

Bar Y Peled, Amit Te'eni, 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 mimicking 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 …

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Sep 2023 • arXiv preprint arXiv:2209.11760

Dynamic cloaking of a diamond-shaped hole in elastic plate

Kun Tang, Eitam Luz, David Amram, Luna Kadysz, Sebastien Guenneau, Patrick Sebbah

Invisibility cloaks for flexural waves have been mostly examined in the continuous-wave regime, while invisibility is likely to deteriorate for short pulses. Here, we propose the practical realization of a unidirectional invisibility cloak for flexural waves based on an area-preserving coordinate transformation. Time-resolved experiments reveal how the invisibility cloak deviates a pulsed plane-wave from its initial trajectory, and how the initial wavefront perfectly recombines behind the cloak, leaving the diamond-shaped hole invisible, notwithstanding the appearance of a forerunner. Three-dimensional full-elasticity simulations support our experimental observations.

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Sep 2023 • arXiv preprint arXiv:2209.00480

Coherence and realism in the Aharonov-Bohm effect

Ismael L Paiva, Pedro R Dieguez, Renato M Angelo, Eliahu Cohen

The Aharonov-Bohm effect is a fundamental topological phenomenon with a wide range of applications. It consists of a charge encircling a region with a magnetic flux in a superposition of wavepackets having their relative phase affected by the flux. In this work, we analyze this effect using an entropic measure known as realism, originally introduced as a quantifier of a system's degree of reality and mathematically related to notions of global and local quantum coherence. More precisely, we look for observables that lead to gauge-invariant realism associated with the charge before it completes its loop. We find that the realism of these operators has a sudden change when the line connecting the center of both wavepackets crosses the solenoid. Moreover, we consider the case of a quantized magnetic field source, pointing out similarities and differences between the two cases. Finally, we discuss the implications of these results to the understanding of the effect.

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Sep 2023 • arXiv preprint arXiv:2209.03872

Observation of coherent oscillations in the association of dimers from a thermal gas of ultracold atoms

Roy Elbaz, Yaakov Yudkin, P Giannakeas, Jan-Michael Rost, Chris H Greene, Lev Khaykovich

We report the observation of coherent oscillations in conversion efficiency of molecules formed from a thermal gas of ultracold atoms. Finite thermal energy of the gas causes loss of coherence when a broad continuum is resonantly coupled to a discrete bound state. Restoration of the coherence can be achieved through non-adiabatic transitions of the dressed molecular energy level that are induced by a strong modulation pulse with fast envelope dynamics. Conditions to observe coherent oscillations are verified, and control of their properties is demonstrated. The main experimental findings are supported by theoretical modeling and numerical calculations.

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Aug 2023 • arXiv preprint arXiv:2208.08154

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

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

A thorough understanding of biological species and of emerging nanomaterials requires, among others, their in-depth characterization with optical techniques capable of nano-resolution. Nanoscopy techniques based on tip-enhanced optical effects have gained over the past years tremendous interest given their potential to probe various optical properties with resolutions depending on 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 techniques (TEN) still largely rely on probes that are not specifically developed for such applications, but for Atomic Force Microscopy. This cages their potential in many regards, e.g. in terms of signal-to-noise ratio, attainable image quality, or extent of applications. In this article we place first steps towards next-gen TEN, demonstrating the fabrication and modelling of specialized TEN probes with known optical properties. The proposed framework is highly flexible and can be easily adjusted to be of o benefit to various types of TEN techniques, for which probes with known optical properties could potentially enable faster and more accurate imaging via different routes, such as direct signal enhancement or novel signal modulation strategies. We consider that the reported development can pave the way for a vast number of novel TEN imaging protocols and applications, given the many advantages that it offers.

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Aug 2023 • arXiv preprint arXiv:2208.11008

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 motivation to the growing interest garnered by this model. True chaotic behaviour 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, i.e., 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, SVD, which filters out these sample to sample fluctuations, the Thouless energy becomes parametrically much larger, essentially of order of the band width. It is shown that the SYK model in non-self-averaging even in the thermodynamic limit which must be taken into account in considering its short time properties.

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Jul 2023 • Fuel

Design of three-dimensional hexagonal petal-like nickel-copper cobaltite//luffa sponge-derived activated carbon electrode materials for high-performance solid-state supercapattery

Sengodan Prabhu, Moorthy Maruthapandi, Arulappan Durairaj, S Arun Kumar, John HT Luong, Rajendran Ramesh, Aharon Gedanken

Three-dimensional porous nanostructured materials are considered superior materials for energy storage applications due to their high storage capability. A nickel copper-cobalt oxide (NCC) composite with a uniform 3-D porous nanostructure (positive electrode materials) and luffa sponge-derived activated carbon (LPAC) with honeycomb-like structure (negative electrode materials) were synthesized by a simple hydrothermal and chemical method. A sample of the nickel-copper cobalt oxide-5 (NCC-5) nanocomposite reached a high specific capacitance of 1048 F/g at the current density of 0.5 A/g. The NCC-5 nanocomposite sample shows a retention capacity of 93 % after 10,000 charge and discharge cycles with 95 % of Coulombic efficiency (CE). The LPAC illustrates a remarkable specific capacitance of 909 F/g at 1 A/g of current density, compared to the best literature value of 400 F/g. The full-cell NCC-5//LPAC …

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Jul 2023 • Nature Communications 14 (1), 1462, 2023

B cell class switch recombination is regulated by DYRK1A through MSH6 phosphorylation

Liat Stoler-Barak, Ethan Harris, Ayelet Peres, Hadas Hezroni, Mirela Kuka, Amalie Grenov, Neta Gurwicz, Meital Kupervaser, Bon Ham Yip, Matteo Iannacone, Gur Yaari, John Crispino, Ziv Shulman

B cell class switch recombination is regulated by DYRK1A through MSH6 phosphorylation | Research Square Research Square Browse Preprints COVID-19 Preprints Protocols Videos Journals Tools & Services Overview Digital Editing Professional Editing Badges Research Promotion Your Cart About Preprint Platform In Review Editorial Policies FAQ Our Team Advisory Board Blog Sign In Submit a Preprint Cite Share Download PDF Article B cell class switch recombination is regulated by DYRK1A through MSH6 phosphorylation Liat Stoler-Barak, Ethan Harris, Ayelet Peres, Hadas Hezroni, and 9 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/10.21203/rs.3.rs-1779641/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Nature Portfolio Version 1 posted 05 Jul, 2022 You are reading this latest preprint version Abstract Protection from viral infections depends …

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May 2023 • arXiv preprint arXiv:2205.08563

Majorana-Weyl cones in ferroelectric superconductors

Hennadii Yerzhakov, Roni Ilan, Efrat Shimshoni, Jonathan Ruhman

Topological superconductors are predicted to exhibit outstanding phenomena, including non-abelian anyon excitations, heat-carrying edge states, and topological nodes in the Bogoliubov spectra. Nonetheless, and despite major experimental efforts, we are still lacking unambiguous signatures of such exotic phenomena. In this context, the recent discovery of coexisting superconductivity and ferroelectricity in lightly doped and ultra clean SrTiO opens new opportunities. Indeed, a promising route to engineer topological superconductivity is the combination of strong spin-orbit coupling and inversion-symmetry breaking. Here we study a three-dimensional parabolic band minimum with Rashba spin-orbit coupling, whose axis is aligned by the direction of a ferroelectric moment. We show that all of the aforementioned phenomena naturally emerge in this model when a magnetic field is applied. Above a critical Zeeman field, Majorana-Weyl cones emerge regardless of the electronic density. These cones manifest themselves as Majorana arcs states appearing on surfaces and tetragonal domain walls. Rotating the magnetic field with respect to the direction of the ferroelectric moment tilts the Majorana-Weyl cones, eventually driving them into the type-II state with Bogoliubov Fermi surfaces. We then consider the consequences of the orbital magnetic field. First, the single vortex is found to be surrounded by a topological halo, and is characterized by two Majorana zero modes: One localized in the vortex core and the other on the boundary of the topological halo. For a finite density of vortices forming close enough to the upper critical field, these halos …

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May 2023 • arXiv preprint arXiv:2205.01974

Restart expedites quantum walk hitting times

Ruoyu Yin, Eli Barkai

Classical first-passage times under restart are used in a wide variety of models, yet the quantum version of the problem still misses key concepts. We study the quantum first detected passage time under restart protocol using a monitored quantum walk. The restart strategy eliminates the problem of dark states, i.e. cases where the particle is not detected at all, while maintaining the ballistic propagation which is important for fast search. We find profound effects of quantum oscillations on the restart problem, namely a type of instability of the mean detection time, and optimal restart times that form staircases, with sudden drops as the rate of sampling is modified. In the absence of restart and in the Zeno limit, the detection of the walker is not possible and we examine how restart overcomes this well-known problem, showing that the optimal restart time becomes insensitive to the sampling period.

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Mar 2023 • ACS Omega

In Situ Coatings of Polymeric Films with Core Polystyrene, Core–Shell Polystyrene/SiO2, and Hollow SiO2 Micro/Nanoparticles and Potential Applications

Sharon Hayne, Shlomo Margel

In many industrial settings, films of polymers such as polypropylene (PP) and polyethylene terephthalate (PET) require surface treatment due to poor wettability and low surface energy. Here, a simple process is presented to prepare durable thin coatings composed of polystyrene (PS) core, PS/SiO2 core–shell, and hollow SiO2 micro/nanoparticles onto PP and PET films as a platform for various potential applications. Corona-treated films were coated with a monolayer of PS microparticles by in situ dispersion polymerization of styrene in ethanol/2-methoxy ethanol with polyvinylpyrrolidone as stabilizer. A similar process on untreated polymeric films did not yield a coating. PS/SiO2 core–shell coated microparticles were produced by in situ polymerization of Si(OEt)4 in ethanol/water onto a PS-coated film, creating a raspberry-like morphology with a hierarchical structure. Hollow porous SiO2-coated microparticles onto …

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Mar 2023 • Nature

RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer

Amina Jbara, Kuan-Ting Lin, Chani Stossel, Zahava Siegfried, Haya Shqerat, Adi Amar-Schwartz, Ela Elyada, Maxim Mogilevsky, Maria Raitses-Gurevich, Jared L Johnson, Tomer M Yaron, Ofek Ovadia, Gun Ho Jang, Miri Danan-Gotthold, Lewis C Cantley, Erez Y Levanon, Steven Gallinger, Adrian R Krainer, Talia Golan, Rotem Karni

Pancreatic ductal adenocarcinoma (PDA) is characterized by aggressive local invasion and metastatic spread, leading to high lethality. Although driver gene mutations during PDA progression are conserved, no specific mutation is correlated with the dissemination of metastases–. Here we analysed RNA splicing data of a large cohort of primary and metastatic PDA tumours to identify differentially spliced events that correlate with PDA progression. De novo motif analysis of these events detected enrichment of motifs with high similarity to the RBFOX2 motif. Overexpression of RBFOX2 in a patient-derived xenograft (PDX) metastatic PDA cell line drastically reduced the metastatic potential of these cells in vitro and in vivo, whereas depletion of RBFOX2 in primary pancreatic tumour cell lines increased the metastatic potential of these cells. These findings support the role of RBFOX2 as a potent metastatic suppressor in …

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Mar 2023 • Ultrasonics Sonochemistry, 106364, 2023

Sonochemistry of Molten Gallium

Vijay Bhooshan Kumar, Aharon Gedanken, Ze'ev Porat


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