BINA

3583 articles

75 publishers

Join mailing list

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.

Show more

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.

Show more

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?

Show more

Jan 2023 • bioRxiv

IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data

Ayelet Peres, William D Lees, Oscar L Rodriguez, Noah Y Lee, Pazit Polak, Ronen Hope, Meirav Kedmi, Andrew M Collins, Mats Ohlin, Steven H Kleinstein, Corey Watson, Gur Yaari

In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles as well as a novel method to infer individual genotypes. We demonstrate the strength of the two by comparing their outcomes to other genotype inference methods and validated the genotype approach with independent genomic long read data. The naming scheme is compatible with current annotation tools and pipelines. Analysis results can be converted from the proposed naming scheme to the nomenclature determined by the International Union of Immunological Societies (IUIS). Both the naming scheme and the genotype procedure are implemented in a freely available R package (PIgLET). To allow researchers to explore further the approach on real data and to adapt it for their future uses, we also created an interactive website (https://yaarilab.github.io/IGHV_reference_book).

Show more

Jan 2023 • arXiv preprint arXiv:2301.06100

Instability in the quantum restart problem

Ruoyu Yin, Eli Barkai

We study optimal restart times for the quantum first hitting time problem. Using a monitored one-dimensional lattice quantum walk with restarts, we find an instability absent in the corresponding classical problem. This instability implies that a small change in parameters can lead to a rather large change of the optimal restart time. We show that the optimal restart time versus a control parameter, exhibits sets of staircases and plunges. The plunges, are due to the mentioned instability, which in turn is related to the quantum oscillation of the first hitting time probability, in the absence of restarts. Furthermore, we prove that there are only two patterns of the staircase structures, dependent on the parity of the distance between the target and source in units of lattice constant.

Show more

Jan 2023 • Langmuir

Biotin Binding Hardly Affects Electron Transport Efficiency across Streptavidin Solid-State Junctions

Sudipta Bera, Sharada Govinda, Jerry A Fereiro, Israel Pecht, Mordechai Sheves, David Cahen

The electron transport (ETp) efficiency of solid-state protein-mediated junctions is highly influenced by the presence of electron-rich organic cofactors or transition metal ions. Hence, we chose to investigate an interesting cofactor-free non-redox protein, streptavidin (STV), which has unmatched strong binding affinity for an organic small-molecule ligand, biotin, which lacks any electron-rich features. We describe for the first time meso-scale ETp via electrical junctions of STV monolayers and focus on the question of whether the rate of ETp across both native and thiolated STV monolayers is influenced by ligand binding, a process that we show to cause some structural conformation changes in the STV monolayers. Au nanowire-electrode–protein monolayer–microelectrode junctions, fabricated by modifying an earlier procedure to improve the yields of usable junctions, were employed for ETp measurements. Our …

Show more

Jan 2023 • iScience

Temporal Synchronization Elicits Enhancement of Binocular Vision Functions

Auria Eisen-Enosh, Nairouz Farah, Uri Polat, Yossi Mandel

Integration of information over the central nervous system is an important neural process that affects our ability to perceive and react to the environment. The visual system is required to continuously integrate information arriving from two different sources (the eyes) to create a coherent percept with high spatiotemporal precision. Although this neural integration of information is assumed to be critical for visual performance, it can be impaired under some pathological or developmental conditions. Here we took advantage of a unique developmental condition, amblyopia (“lazy eye”), which is characterized by an impaired temporal synchronization between the two eyes, to meticulously study the effect of synchronization on the integration of binocular visual information. We measured the eyes’ asynchrony and compensated for it (with millisecond temporal resolution) by providing time-shifted stimuli to the eyes. We found …

Show more

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.

Show more

Jan 2023 • Polymer-Based Nanoscale Materials for Surface Coatings, 1-18, 2023

Introduction to coatings and surface preparation

Sayan Ganguly, Shlomo Margel

In this chapter, we would like to discuss polymer coating's know-how, which is a method of modifying surface qualities in order to satisfy operating requirements in a number of technological applications. In addition to adhesion and barrier capabilities, polymer coatings have also been used to improve scratch and abrasion resistance, solvent resistance, wettability, noncytotoxicity, and other features. For the manufacture of protective organic coatings a number of different techniques have been devised and used. A careful selection of polymer, coating process, and manufacturing conditions can result in high-performance coatings with improved attributes when applied correctly. Polymer coatings have recently been shown to be effective and widely used in a variety of applications, including solar cells, batteries, separation techniques, diodes, corrosion defense, packaging, and heathcare applications.

Show more

Jan 2023 • Genome Research

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

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

Crohn's disease (CD) is a chronic relapsing–remitting inflammatory disorder of the gastrointestinal tract that is characterized by altered innate and adaptive immune function. Although massively parallel sequencing studies of the T cell receptor repertoire identified oligoclonal expansion of unique clones, much less is known about the B cell receptor (BCR) repertoire in CD. Here, we present a novel BCR repertoire sequencing data set from ileal biopsies from pediatric patients with CD and controls, and identify CD-specific somatic hypermutation (SHM) patterns, revealed by a machine learning (ML) algorithm trained on BCR repertoire sequences. Moreover, ML classification of a different data set from blood samples of adults with CD versus controls identified that V gene usage, clusters, or mutation frequencies yielded excellent results in classifying the disease (F1 > 90%). In summary, we show that an ML algorithm …

Show more

Jan 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 …

Show more

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.

Show more

Jan 2023 • Polymer-Based Nanoscale Materials for Surface Coatings, 1-18, 2023

Introduction to coatings and surface preparation

Sayan Ganguly, Shlomo Margel

In this chapter, we would like to discuss polymer coating's know-how, which is a method of modifying surface qualities in order to satisfy operating requirements in a number of technological applications. In addition to adhesion and barrier capabilities, polymer coatings have also been used to improve scratch and abrasion resistance, solvent resistance, wettability, noncytotoxicity, and other features. For the manufacture of protective organic coatings a number of different techniques have been devised and used. A careful selection of polymer, coating process, and manufacturing conditions can result in high-performance coatings with improved attributes when applied correctly. Polymer coatings have recently been shown to be effective and widely used in a variety of applications, including solar cells, batteries, separation techniques, diodes, corrosion defense, packaging, and heathcare applications.

Show more

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 …

Show more

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.

Show more

Jan 2023 • bioRxiv

In vitro cellular reprogramming to model gonad development and its disorders

Nitzan Gonen, Caroline Eozenou, Richard Mitter, Andreia Bernardo, Almira Chervova, Emmanuel Frachon, Pierre-Henri Commère, Inas Mazen, Samy Gobaa, Kenneth McElreavey, Robin Lovell-Badge, Anu Bashamboo

During embryonic development, mutually antagonistic signaling cascades determine gonadal fate toward a testicular or ovarian identity. Errors in this process result in disorders of sex development (DSDs), characterized by discordance between chromosomal, gonadal, and anatomical sex. The absence of an appropriate, accessible in vitro system is a major obstacle in understanding mechanisms of sex-determination/DSDs. Here, we describe protocols for differentiation of mouse and human pluripotent cells toward gonadal progenitors. Transcriptomic analysis reveals that the in vitro–derived murine gonadal cells are equivalent to embryonic day 11.5 in vivo progenitors. Using similar conditions, Sertoli-like cells derived from 46,XY human induced pluripotent stem cells (hiPSCs) exhibit sustained expression of testis-specific genes, secrete anti-Müllerian hormone, migrate, and form tubular structures. Cells derived …

Show more

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 …

Show more

Jan 2023 • The Journal of Physical Chemistry B

Correction to “Monte Carlo Diffusion-Enhanced Photon Inference: Distance Distributions and Conformational Dynamics in Single-Molecule FRET”

Antonino Ingargiola, Shimon Weiss, Eitan Lerner

The Supporting Information is available free of charge at https://pubs. acs. org/doi/10.1021/acs. jpcb. 2c09011. A thorough description of additional MC-DEPI simulations of different conditions that yield the same FRET histograms and a full description of the methods used in this work as well as an appendix thoroughly describing the loss function used in this work for the fitting procedure (PDF)

Show more

Jan 2023 • Nano Letters

A RuCoBO Nanocomposite for Highly Efficient and Stable Electrocatalytic Seawater Splitting

Le-Wei Shen, Yong Wang, Jiang-Bo Chen, Ge Tian, Kang-Yi Xiong, Christoph Janiak, David Cahen, Xiao-Yu Yang

Efficient and stable electrocatalysts are critically needed for the development of practical overall seawater splitting. The nanocomposite of RuCoBO has been rationally engineered to be an electrocatalyst that fits these criteria. The study has shown that a calcinated RuCoBO-based nanocomposite (Ru2Co1BO-350) exhibits an extremely high catalytic activity for H2 and O2 production in alkaline seawater (overpotentials of 14 mV for H2 evolution and 219 mV for O2 evolution) as well as a record low cell voltage (1.466 V@10 mA cm–2) and long-term stability (230 h @50 mA cm–2 and @100 mA cm–2) for seawater splitting. The results show that surface reconstruction of Ru2Co1BO-350 occurs during hydrogen evolution reaction and oxygen evolution reaction, which leads to the high activity and stability of the catalyst. The reconstructed surface is highly resistant to Cl– corrosion. The investigation suggests that a new …

Show more

Jan 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 …

Show more

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 …

Show more

logo
Articali

Powered by Articali

TermsPrivacy