Feb 2023 • Physical Review Letters
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 hitting time with restart using a monitored quantum walk. The restart strategy eliminates the problem of dark states, ie, cases where the particle evades detection, while maintaining the ballistic propagation which is important for a 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.
Show moreFeb 2023 • Physical Review Research
Gal Amit, Yonathan Japha, Tomer Shushi, Ron Folman, Eliahu Cohen
Cold atoms hold much promise for the realization of quantum technologies, but still encounter many challenges. In this work we show how the fundamental Casimir-Polder force, by which atoms are attracted to a surface, may be temporarily suppressed by utilizing a specially designed quantum potential, which is familiar from the hydrodynamic or Bohmian reformulations of quantum mechanics. We show that when harnessing the quantum potential via suitable atomic wave-packet engineering, the absorption by the surface can be dramatically reduced. As a result, the probing time of the atoms as sensors can increase. This is proven both analytically and numerically. Furthermore, an experimental scheme is proposed for achieving the required shape for the atomic wave packet. All these may assist existing applications of cold atoms in metrology and sensing and may also enable prospective ones. Finally, these …
Show moreFeb 2023 • Nature communications
Xuan Trung Nguyen, Katrin Winte, Daniel Timmer, Yevgeny Rakita, Davide Raffaele Ceratti, Sigalit Aharon, Muhammad Sufyan Ramzan, Caterina Cocchi, Michael Lorke, Frank Jahnke, David Cahen, Christoph Lienau, Antonietta De Sio
Coupling electromagnetic radiation with matter, e.g., by resonant light fields in external optical cavities, is highly promising for tailoring the optoelectronic properties of functional materials on the nanoscale. Here, we demonstrate that even internal fields induced by coherent lattice motions can be used to control the transient excitonic optical response in CsPbBr3 halide perovskite crystals. Upon resonant photoexcitation, two-dimensional electronic spectroscopy reveals an excitonic peak structure oscillating persistently with a 100-fs period for up to ~2 ps which does not match the frequency of any phonon modes of the crystals. Only at later times, beyond 2 ps, two low-frequency phonons of the lead-bromide lattice dominate the dynamics. We rationalize these findings by an unusual exciton-phonon coupling inducing off-resonant 100-fs Rabi oscillations between 1s and 2p excitons driven by the low-frequency …
Show moreFeb 2023 • Frontiers in Microbiology
Maya Moshe, Chhedi Lal Gupta, Rakeshkumar Manojkumar Jain, Noa Sela, Dror Minz, Ehud Banin, Omer Frenkel, Eddie Cytryn
Bacillus cereus sensu lato (Bcsl) strains are widely explored due to their capacity to antagonize a broad range of plant pathogens. These include B. cereus sp. UW85, whose antagonistic capacity is attributed to the secondary metabolite Zwittermicin A (ZwA). We recently isolated four soil and root-associated Bcsl strains (MO2, S−10, S-25, LSTW-24) that displayed different growth profiles and in-vitro antagonistic effects against three soilborne plant pathogens models: Pythium aphanidermatum (oomycete) Rhizoctonia solani (basidiomycete), and Fusarium oxysporum (ascomycete). To identify genetic mechanisms potentially responsible for the differences in growth and antagonistic phenotypes of these Bcsl strains, we sequenced and compared their genomes, and that of strain UW85 using a hybrid sequencing pipeline. Despite similarities, specific Bcsl strains had unique secondary metabolite and chitinase-encoding genes that could potentially explain observed differences in in-vitro chitinolytic potential and anti-fungal activity. Strains UW85, S-10 and S-25 contained a (~500 Kbp) mega-plasmid that harbored the ZwA biosynthetic gene cluster. The UW85 mega-plasmid contained more ABC transporters than the other two strains, whereas the S-25 mega-plasmid carried a unique cluster containing cellulose and chitin degrading genes. Collectively, comparative genomics revealed several mechanisms that can potentially explain differences in in-vitro antagonism of Bcsl strains toward fungal plant pathogens.
Show moreFeb 2023 • Nanophotonics
Adamantia Logotheti, Adi Levi, Doron Naveh, Leonidas Tsetseris, Ioanna Zergioti
Due to their atomic-scale thickness, handling and processing of two-dimensional (2D) materials often require multistep techniques whose complexity hampers their large-scale integration in modern device applications. Here we demonstrate that the laser-induced forward transfer (LIFT) method can achieve the one-step, nondestructive printing of the prototypical 2D material MoS2. By selecting the optimal LIFT experimental conditions, we were able to transfer arrays of MoS2 pixels from a metal donor substrate to a dielectric receiver substrate. A combination of various characterization techniques has confirmed that the transfer of intact MoS2 monolayers is not only feasible, but it can also happen without incurring significant defect damage during the process. The successful transfer of MoS2 shows the broad potential the LIFT technique has in the emerging field of printed electronics, including printed devices based …
Show moreFeb 2023 • IEEE Transactions on Applied Superconductivity
A Roitman, A Shaulov, Y Yeshurun
Coplanar microwave resonators made of NbN and YBa 2 Cu 3 O 7-δ show similar behavior under the influence of magnetic field. In particular, the two resonators exhibit marked difference between zero-field-cooled (ZFC) and field-cooled (FC) measurements, which is attributed to the presence of screening currents in ZFC but not in FC measurements.
Show moreFeb 2023 • Angewandte Chemie (International ed. in English)
Ori Licht, Dario Barreiro-Lage, Patrick Rousseau, Alexandre Giuliani, Aleksandar Milosavljevic, Avinoam Isaak, Yitzhak Mastai, Amnon Albeck, Raj Singh, Vy Nguyen, Laurent Nahon, Lara Martinez, Sergio Díaz-Tendero, Yoni Toker
Possible routes for intra-cluster bond formation (ICBF) in protonated serine dimers have been studied. We found no evidence of ICBF following low energy collision induced dissociation (in correspondence with previous works), however, we do observe clear evidence for ICBF following photon absorption in the eV range. Moreover, the comparison of photon induced dissociation measurements of the protonated serine dimer to those of a protonated serine dipeptide provides evidence that ICBF, in this case, involves peptide bond formation (PBF). The experimental results are supported by {\it ab initio} molecular dynamics and exploration of several excited state potential energy surfaces, unravelling a pathway for PBF following photon absorption. The combination of experiments and theory provides insight into the PBF mechanisms in clusters of amino acids, and reveals the importance of electronic excited states reached upon UV/VUV light excitation.
Show moreFeb 2023 • ImmunoInformatics
William D Lees, Scott Christley, Ayelet Peres, Justin T Kos, Brian Corrie, Duncan Ralph, Felix Breden, Lindsay G Cowell, Gur Yaari, Martin Corcoran, Gunilla B Karlsson Hedestam, Mats Ohlin, Andrew M Collins, Corey T Watson, Christian E Busse, The AIRR Community
Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but …
Show moreFeb 2023 • Biophysical Journal
Debjit Roy, Xavier Michalet, Kiran Bharadwaj, Evan W Miller, Yijie Wang, Arjun Deb, Michael A Wayne, Claudio Bruschini, Edoardo Charbon, Mahbanoo Vakili, Robert Gunsalus, Robert T Clubb, Shimon Weiss
While great progress has been achieved in developing optical methods for measuring fast changes in membrane potential (like action potentials) in excitable cells, less progress has been made in precise (and calibrated) measurements of steady state resting membrane potentials (RMPs) and small changes in RMPs (in excitable or non-excitable cells). In excitable cells, small changes in RMPs are associated with multiple physiological processes such as sub-threshold events in neuronal signaling and in synaptic plasticity. They also play an important role in cell differentiation and proliferation of cardiomyocytes. In non-excitable cells, such as bacterial colonies, RMP changes play important roles in intercellular communication, coordination, metabolism, and stress response. Accurate and precise recordings of minute RMP changes require noise-immune optical tools. We have been developing an RMP (calibrated …
Show moreFeb 2023 • Pharmaceutics 15 (2), 686, 2023
Sayan Ganguly, Shlomo Margel
Novel nanomaterials are of interest in biology, medicine, and imaging applications. Multimodal fluorescent-magnetic nanoparticles demand special attention because they have the potential to be employed as diagnostic and medication-delivery tools, which, in turn, might make it easier to diagnose and treat cancer, as well as a wide variety of other disorders. The most recent advancements in the development of magneto-fluorescent nanocomposites and their applications in the biomedical field are the primary focus of this review. We describe the most current developments in synthetic methodologies and methods for the fabrication of magneto-fluorescent nanocomposites. The primary applications of multimodal magneto-fluorescent nanoparticles in biomedicine, including biological imaging, cancer treatment, and drug administration, are covered in this article, and an overview of the future possibilities for these technologies is provided.
Show moreFeb 2023 • Nanophotonics
Adamantia Logotheti, Adi Levi, Doron Naveh, Leonidas Tsetseris, Ioanna Zergioti
Due to their atomic-scale thickness, handling and processing of two-dimensional (2D) materials often require multistep techniques whose complexity hampers their large-scale integration in modern device applications. Here we demonstrate that the laser-induced forward transfer (LIFT) method can achieve the one-step, nondestructive printing of the prototypical 2D material MoS2. By selecting the optimal LIFT experimental conditions, we were able to transfer arrays of MoS2 pixels from a metal donor substrate to a dielectric receiver substrate. A combination of various characterization techniques has confirmed that the transfer of intact MoS2 monolayers is not only feasible, but it can also happen without incurring significant defect damage during the process. The successful transfer of MoS2 shows the broad potential the LIFT technique has in the emerging field of printed electronics, including printed devices based …
Show moreFeb 2023 • Cold Spring Harbor Protocols
Anne C von Philipsborn, Galit Shohat-Ophir, Carolina Rezaval
Courtship behaviors in Drosophila melanogaster are innate and contain highly stereotyped but also experience-and state-dependent elements. They have been the subject of intense study for more than 100 years. The power of Drosophila as a genetic experimental system has allowed the dissection of reproductive behaviors at a molecular, cellular, and physiological level. As a result, we know a great deal about how flies perceive sensory cues from potential mates, how this information is integrated in higher brain centers to execute reproductive decisions, and how state and social contexts modulate these responses. The simplicity of the assay has allowed for its broad application. Here, we introduce methods for studying male and female innate reproductive behaviors as well as their plastic responses.
Show moreFeb 2023 • Batteries 9 (2), 110, 2023
Ravindra Kumar Bhardwaj, David Zitoun
Background:This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Show moreFeb 2023 • arXiv preprint arXiv:2202.03640
Quancheng Liu, David A Kessler, Eli Barkai
We design monitored quantum walks with the aim of optimizing state transfer and target search. We show how to construct walks with the property that all the eigenvalues of the non-Hermitian survival operator, describing the mixed effect of unitary dynamics and the back-action of measurement, coalesce to zero, corresponding to an exceptional point whose degree is the size of the Hilbert space. Generally, this search is guaranteed to succeed in a bounded time for any initial condition. It also performs better than the classical random walk search or quantum search on typical graphs. For example, a crawler can be designed such that, starting on a node of the graph, the walker is detected on any of the nodes with probability one at predetermined times. It also allows perfect quantum state transfer from one node of the system to any other, with or without monitoring. Interestingly, this crawler is described as a massless Dirac quasi-particle.
Show moreFeb 2023 • arXiv preprint arXiv:2302.00650
Rain Lenny, Amit Te'eni, Bar Y Peled, Avishy Carmi, Eliahu Cohen
Entanglement is a uniquely quantum resource giving rise to many quantum technologies. It is therefore important to detect and characterize entangled states, but this is known to be a challenging task, especially for multipartite mixed states. The correlation minor norm (CMN) was recently suggested as a bipartite entanglement detector employing bounds on the quantum correlation matrix. In this paper we explore generalizations of the CMN to multipartite systems based on matricizations of the correlation tensor. It is shown that the CMN is able to detect and differentiate classes of multipartite entangled states. We further analyze the correlations within the reduced density matrices and show their significance for entanglement detection. Finally, we employ matricizations of the correlation tensor for introducing a measure of global quantum discord.
Show moreFeb 2023 • Results in Surfaces and Interfaces
Naftali Kanovsky, Taly Iline-Vul, Shlomo Margel
Superhydrophobic surfaces are receiving increasing attention due to their real-world applications. However, these surfaces suffer from a lack of durability and complicated synthetic processes. This research uses a combination of a simple in-situ coating process between oxygen-activated polypropylene films and unreacted silane monomers. The in-situ process uses a modified Stöber method with the addition of the surfactant cetyltrimethylammonium bromide (CTAB) which aggregates silica (SiO 2) particles in a basic aqueous solution. This resulted in a layer of covalently bonded hierarchical coating of individual and aggregated SiO 2 “flakes” and particles. These coatings were found to have at least double the surface roughness than samples prepared without CTAB with superhydrophilic properties due to their high surface roughness and hydrophilic surface chemical groups. A second layer of fluorocarbon silane …
Show moreJan 2023 • arXiv preprint arXiv:2301.01581
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 moreJan 2023 • bioRxiv
Hadar Bootz-Maoz, Ariel Simon, Sara Del Mare-Roumani, Yifat Bennet, Danping Zheng, Sivan Amidror, Eran Elinav, Nissan Yissachar
The intestinal epithelial barrier facilitates homeostatic host-microbiota interactions and immunological tolerance. However, mechanistic dissections of barrier dynamics following luminal stimulation pose a substantial challenge. Here, we describe an ex-vivo intestinal permeability assay, X-IPA, for quantitative analysis of gut permeability dynamics at the whole-tissue level. We demonstrate that specific gut microbes and metabolites induce rapid, dose-dependent increases to gut permeability, thus providing a powerful approach for precise investigation of barrier functions.
Show moreJan 2023 • JOURNAL OF PHYSICAL CHEMISTRY B
Antonino Ingargiola, Shimon Weiss, Eitan Lerner
Jan 2023 • arXiv preprint arXiv:2301.06100
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 moreJan 2023 • bioRxiv
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).
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