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Feb 2023 • Physical Review Letters

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 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.

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Feb 2023 • Physical Review E

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 in one dimension. When we coarse-grain, ie, bin the particle positions using bin sizes that are 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 as 2 D* t, 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 (BG) factor e− V (x)/k B T, the latter being nonnormalizable. 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 …

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Feb 2023

CRISPR-Cas9 RAG2 Correction Via Coding Sequence Replacement to Preserve Endogenous Gene Regulation and Locus Structure

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

RAG2-SCID is a primary immunodeficiency caused by mutations in Recombination-activating gene 2 (RAG2), a gene intimately involved in the process of lymphocyte maturation and function. ex-vivo manipulation of a patient’s own hematopoietic stem and progenitor cells (HSPCs) using CRISPR-Cas9/rAAV6 gene editing could provide a therapeutic alternative to the only current treatment, allogeneic hematopoietic stem cell transplantation (HSCT). Here we show a first-of-its-kind RAG2 correction strategy that replaces the entire endogenous coding sequence (CDS) to preserve the critical endogenous spatiotemporal gene regulation and locus architecture. Expression of the corrective transgene led to successful development into CD3+ TCRαβ+ and CD3+ TCRγδ+ T cells and promoted the establishment of highly diverse TRB and TRG repertoires in an in-vitro T-cell differentiation platform. We believe that a CDS replacement technique to correct tightly regulated genes, like RAG2, while maintaining critical regulatory elements and conserving the locus structure could bring safer gene therapy techniques closer to the clinic.

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Feb 2023 • The Journal of Physical Chemistry B

Experimental data confirm carrier-cascade model for solid-state conductance across proteins

Eszter Papp, Gábor Vattay, Carlos Romero-Muñiz, Linda A Zotti, Jerry A Fereiro, Mordechai Sheves, David Cahen

The finding that electronic conductance across ultrathin protein films between metallic electrodes remains nearly constant from room temperature to just a few degrees Kelvin has posed a challenge. We show that a model based on a generalized Landauer formula explains the nearly constant conductance and predicts an Arrhenius-like dependence for low temperatures. A critical aspect of the model is that the relevant activation energy for conductance is either the difference between the HOMO and HOMO–1 or the LUMO+1 and LUMO energies instead of the HOMO–LUMO gap of the proteins. Analysis of experimental data confirms the Arrhenius-like law and allows us to extract the activation energies. We then calculate the energy differences with advanced DFT methods for proteins used in the experiments. Our main result is that the experimental and theoretical activation energies for these three different proteins …

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Feb 2023 • Pharmaceutics 15 (2), 686, 2023

Bioimaging probes based on magneto-fluorescent nanoparticles

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.

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Feb 2023 • Batteries 9 (2), 110, 2023

Recent Progress in Solid Electrolytes for All-Solid-State Metal (Li/Na)–Sulfur Batteries

Ravindra Kumar Bhardwaj, David Zitoun

Background:This is an early access version, the complete PDF, HTML, and XML versions will be available soon.

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Feb 2023 • Nanophotonics

Digital laser-induced printing of MoS2

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 …

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Feb 2023 • Nanophotonics

Digital laser-induced printing of MoS2

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 …

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Feb 2023 • arXiv preprint arXiv:2202.03640

Designing exceptional-point-based graphs yielding topologically guaranteed quantum search

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.

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Feb 2023 • IEEE Transactions on Applied Superconductivity

Effect of magnetic fields on superconducting microwave coplanar resonators

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.

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Feb 2023 • Frontiers in Microbiology

Comparative genomics of Bacillus cereus sensu lato spp. biocontrol strains in correlation to in-vitro phenotypes and plant pathogen antagonistic capacity

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.

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Feb 2023 • Angewandte Chemie (International ed. in English)

Peptide Bond Formation in the Protonated Serine Dimer Following Vacuum UV Photon‐Induced Excitation

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.

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Feb 2023 • Solid State Nuclear Magnetic Resonance

Selective excitation with recoupling pulse schemes uncover properties of disordered mineral phases in bone-like apatite grown with bone proteins

Irina Matlahov, Alex Kulpanovich, Taly Iline-Vul, Merav Nadav-Tsubery, Gil Goobes

Bone construction has been under intensive scrutiny for many years using numerous techniques. Solid-state NMR spectroscopy helped unravel key characteristics of the mineral structure in bone owing to its capability of analyzing crystalline and disordered phases at high-resolution. This has invoked new questions regarding the roles of persistent disordered phases in structural integrity and mechanical function of mature bone as well as regarding regulation of early events in formation of apatite by bone proteins which interact intimately with the different mineral phases to exert biological control.Here, spectral editing tethered to standard NMR techniques is employed to analyze bone-like apatite minerals prepared synthetically in the presence and absence of two non-collagenous bone proteins, osteocalcin and osteonectin. A 1H spectral editing block allows excitation of species from the crystalline and disordered …

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Feb 2023 • arXiv preprint arXiv:2302.00726

Quantum engines and refrigerators

Loris Maria Cangemi, Chitrak Bhadra, Amikam Levy

Engines are systems and devices that convert one form of energy into another, typically into a more useful form that can perform work. In the classical setup, physical, chemical, and biological engines largely involve the conversion of heat into work. This energy conversion is at the core of thermodynamic laws and principles and is codified in textbook material. In the quantum regime, however, the principles of energy conversion become ambiguous, since quantum phenomena come into play. As with classical thermodynamics, fundamental principles can be explored through engines and refrigerators, but, in the quantum case, these devices are miniaturized and their operations involve uniquely quantum effects. Our work provides a broad overview of this active field of quantum engines and refrigerators, reviewing the latest theoretical proposals and experimental realizations. We cover myriad aspects of these devices, starting with the basic concepts of quantum analogs to the classical thermodynamic cycle and continuing with different quantum features of energy conversion that span many branches of quantum mechanics. These features include quantum fluctuations that become dominant in the microscale, non-thermal resources that fuel the engines, and the possibility of scaling up the working medium's size, to account for collective phenomena in many-body heat engines. Furthermore, we review studies of quantum engines operating in the strong system-bath coupling regime and those that include non-Markovian phenomena. Recent advances in thermoelectric devices and quantum information perspectives, including quantum measurement …

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Feb 2023 • npj Quantum Information

Fundamental quantum limits of magnetic nearfield measurements

Chen Mechel, Jonathan Nemirovsky, Eliahu Cohen, Ido Kaminer

Major advances in the precision of magnetic measurements bring us closer to quantum detection of individual spins at the single-atom level. On the quest for reducing both classical and quantum measurement noise, it is intriguing to look forward and search for precision limits arising from the fundamental quantum nature of the measurement process itself. Here, we present the limits of magnetic quantum measurements arising from quantum information considerations, and apply these limits to a concrete example of magnetic force microscopy (MFM). We show how such microscopes have a fundamental limit on their precision arising from the theory of imperfect quantum cloning, manifested by the entanglement between the measured system and the measurement probe. We show that counterintuitively, increasing the probe complexity decreases both the measurement noise and back action, and a judicious design …

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Feb 2023 • Angewandte Chemie (International ed. in English)

Peptide Bond Formation in the Protonated Serine Dimer Following Vacuum UV Photon‐Induced Excitation

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.

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Feb 2023 • Biomass Conversion and Biorefinery

Biomass-derived Carbon dots and their coated surface as a potential antimicrobial agent

R Blessy Pricilla, Moorthy Maruthapandi, Arulappan Durairaj, Ivo Kuritka, John HT Luong, Aharon Gedanken

Carbon dots (CDs) with an average diameter of 6.3 nm were synthesized from the medicinal seed extract of Syzygium cumini L. using one-pot hydrothermal synthesis. The prepared CDs exhibited excitation-dependent emission characteristics with photoluminescence (PL) emission maxima at an excitation of 340 nm. The CDs at 500 µg/mL displayed antimicrobial activities against four common pathogens. Both Staphylococcus aureus and S. epidermidis were completely eradicated by CDs within 12 h, compared to 24 h for Escherichia coli and Klebsiella pneumonia. The release of various oxygen species (ROS) was postulated to play a critical role in bacterial eradication. The CDs decorated on cotton fabric by ultrasonication also displayed good antibacterial activities against the above bacteria. The finding opens a plausible use of CDs in biomedical textiles with potent antimicrobial properties against both Gram …

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Feb 2023 • Biosensors 13 (3), 304, 2023

Magnetite-Based Biosensors and Molecular Logic Gates: From Magnetite Synthesis to Application

Nataliia Dudchenko, Shweta Pawar, Ilana Perelshtein, Dror Fixler

In the last few decades, point-of-care (POC) sensors have become increasingly important in the detection of various targets for the early diagnostics and treatment of diseases. Diverse nanomaterials are used as building blocks for the development of smart biosensors and magnetite nanoparticles (MNPs) are among them. The intrinsic properties of MNPs, such as their large surface area, chemical stability, ease of functionalization, high saturation magnetization, and more, mean they have great potential for use in biosensors. Moreover, the unique characteristics of MNPs, such as their response to external magnetic fields, allow them to be easily manipulated (concentrated and redispersed) in fluidic media. As they are functionalized with biomolecules, MNPs bear high sensitivity and selectivity towards the detection of target biomolecules, which means they are advantageous in biosensor development and lead to a more sensitive, rapid, and accurate identification and quantification of target analytes. Due to the abovementioned properties of functionalized MNPs and their unique magnetic characteristics, they could be employed in the creation of new POC devices, molecular logic gates, and new biomolecular-based biocomputing interfaces, which would build on new ideas and principles. The current review outlines the synthesis, surface coverage, and functionalization of MNPs, as well as recent advancements in magnetite-based biosensors for POC diagnostics and some perspectives in molecular logic, and it also contains some of our own results regarding the topic, which include synthetic MNPs, their application for sample preparation, and the …

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Feb 2023 • Cold Spring Harbor Protocols

Probing acoustic communication during fly reproductive behaviors

Anne C von Philipsborn, Galit Shohat-Ophir, Carolina Rezaval

During reproduction, male and female flies use wing vibration to generate different acoustic signals. Males produce a courtship song before copulation that is easily recognized by unilateral wing vibration. In copula, females produce a distinct sound pattern (copulation song) with both wings. Sexual rejection of immature virgins and aggressive encounters between males are also accompanied by sound pulses generated by wing flicks. Fly song has frequency ranges audible to the human ear and can be directly listened to after appropriate amplification. When displayed in an oscillogram, audio recordings can be mapped on wing-movement patterns and thus provide a fast and precise method to sample and quantify motor behaviors with high temporal resolution. After recording different fly sounds, their effect on behavior can be tested in playback experiments.

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Feb 2023 • ImmunoInformatics

AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets

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 …

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Feb 2023 • arXiv preprint arXiv:2302.00650

Multipartite entanglement detection via correlation minor norm

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.

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