BINA

3692 articles

75 publishers

Join mailing list

Sep 2023 • Nucleic Acids Research

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 T 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 strengths of the two by comparing their outcomes to other genotype inference methods. We validate 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 …

Show more

Sep 2023 • Nucleic Acids Research

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 T 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 strengths of the two by comparing their outcomes to other genotype inference methods. We validate 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 …

Show more

Sep 2023 • Energy Storage Materials, 103001, 2023

Reviewing Failure Mechanisms and Modification Strategies in Stabilizing High-Voltage LiCoO2 Cathodes beyond 4.55 V

Rajashree Konar, Sandipan Maiti, Netanel Shpigel, Doron Aurbach

Lithium cobalt oxide (LiCoO2 or LCO) is undoubtedly one of the best commercial cathode materials for Lithium-ion batteries (LIBs). High energy density, excellent cycle life, and long-term reliability make it most attractive for the growing electronics market. The working voltages in LCO have been raised to achieve greater energy density that can fulfill fast charging and portable electronics consumer needs. Yet, charging beyond 4.4V inevitably decreases the cathode stability, resulting in poor performance. Several factors cause operational issues in LCO at high voltages, particularly surface degradation, unfavorable side reactions, and irreversible phase transitions. These detrimental phenomena are aggravated by the increased charging voltage, leading to rapid capacity decay and early cell failure. Our review summarizes the failure mechanisms and mitigation strategies adopted recently to stabilize LCO at high …

Show more

Sep 2023 • Journal of Bacteriology 205 (10), e00166-23, 2023

The biofilm community resurfaces: new findings and post-pandemic progress

Jennifer L Greenwich, Derek Fleming, Ehud Banin, Susanne Häussler, Birthe V Kjellerup, Karin Sauer, Karen L Visick, Clay Fuqua

The ninth American Society for Microbiology Conference on Biofilms was convened in-person on 13–17 November 2022 in Charlotte, NC. As the first of these conferences since prior to the start of the COVID-19 pandemic, the energy among the participants of the conference was clear, and the meeting was a tremendous success. The mixture of >330 oral and poster presentations resoundingly embodied the vitality of biofilm research across a wide range of topics and multiple scientific disciplines. Special activities, including a pre-conference symposium for early career researchers, further enhanced the attendee experience. As a general theme, the conference was deliberately structured to provide high levels of participation and engagement among early career scientists.

Show more

Sep 2023 • Electrochimica Acta

Iron doped cobalt nickel layered double hydroxide supported on nickel foam as a robust electrocatalyst for highly efficient water oxidation in alkaline sea water

Akanksha Gupta, Hari Krishna Sadhanala, Aharon Gedanken

The seawater electrolysis is an economically favorable approach for water splitting application because seawater is one of the plentiful abundant natural resources on our earth. In water splitting pathway, the anodic half-cell reaction from seawater stills a challenging task due to anodic corrosion and the competitive chloride oxidation process. In the current study, we prepared flower-shaped porous nanorods of iron doped cobalt nickel layered double hydroxide supported on nickel foam (Fe0.05 CoNi LDH/NF), which require very less oxygen evolution reaction (OER) overpotential in 1M KOH (212 mV) and alkaline seawater (287 mV) to deliver 10 mAcm−2 current density and exhibited remarkable 14 h durability. At the same time, post treated sample reveals the better OER activity after chronopotentiometry analysis, because of superior conductivity and corrosion-resistance of the electrocatalyst. The doping of Fe …

Show more

Sep 2023 • arXiv preprint arXiv:2309.13126

Stretched-exponential relaxation in weakly-confined Brownian systems through large deviation theory

Lucianno Defaveri, Eli Barkai, David A Kessler

Stretched-exponential relaxation is a widely observed phenomenon found in glassy systems. It was previously modeled with non-Markovian dynamics reflecting a memory effect. Here, we study a Brownian particle under the influence of a confining, albeit weak, potential field that grows with distance as a sub-linear power law. We find that for this memoryless model, observables display stretched-exponential relaxation. The probability density function of the system is studied using a rate function ansatz. We obtain analytically the stretched-exponential exponent along with an anomalous power-law scaling of length with time. The rate function exhibits a point of nonanalyticity, indicating a dynamical phase transition. In particular, the rate function is double-valued both to the left and right of this point, leading to four different rate functions, depending on the choice of initial conditions and symmetry.

Show more

Sep 2023 • arXiv preprint arXiv:2309.05469

Invariant-based control of quantum many-body systems across critical points

Hilario Espinós, Loris Maria Cangemi, Amikam Levy, Ricardo Puebla, Erik Torrontegui

Quantum many-body systems are emerging as key elements in the quest for quantum-based technologies and in the study of fundamental physics. In this context, finding control protocols that allow for fast and high fidelity evolutions across quantum phase transitions is of particular interest. Ideally, such controls should be scalable with the system size and not require controllable and unwanted extra interactions. In addition, its performance should be robust against potential imperfections. Here we design an invariant-based control technique that ensures perfect adiabatic-like evolution in the lowest energy subspace of the many-body system, and is able to meet all these requirements -- tuning the controllable parameter according to the analytical control results in high-fidelity evolutions operating close to the speed limit, valid for any number particles. As such, Kibble-Zurek scaling laws break down, leading to tunable and much better time scaling behavior. We illustrate our findings by means of detailed numerical simulations in the transverse-field Ising and long-range Kitaev models and demonstrate the robustness against noisy controls and disorder.

Show more

Sep 2023 • Journal of Raman Spectroscopy

Enhancement of the E12g and A1g Raman modes and layer identification of 2H‐WS2 nanosheets with metal coatings

Bharathi Rajeswaran, Rajashree Konar, Rena Yitzhari, Gilbert Daniel Nessim, Yaakov Raphael Tischler

Raman spectroscopy in transition metal dichalcogenides (TMDCs) helps determine their structural information and layer dependency. Because it is non‐destructive and fast, it is an archetypal spectroscopic technique to investigate the structure and defects in TMDCs. In our earlier study, we used a metal‐dielectric coating to enhance Raman signal of WS2 because the Raman Spectra measured from WS2 coated on the standard Si/SiO2 was significantly lower. This metal‐dielectric coating allowed access to the otherwise unavailable E12g and A1g modes of WS2. In this study, we compare the Raman spectra of WS2 on a Si/SiO2 to that of metal layers (Au [200 nm] and Al [200 nm]). A significant enhancement in the Raman signal of 2‐3L WS2 is observed for both the Au and Al coatings. Although 200 nm Au coating enhances the Raman Signal better than the 10 nm Au coating, it does not resolve the other …

Show more

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.

Show more

Sep 2023 • Journal of Raman Spectroscopy

Enhancement of the E12g and A1g Raman modes and layer identification of 2H‐WS2 nanosheets with metal coatings

Bharathi Rajeswaran, Rajashree Konar, Rena Yitzhari, Gilbert Daniel Nessim, Yaakov Raphael Tischler

Raman spectroscopy in transition metal dichalcogenides (TMDCs) helps determine their structural information and layer dependency. Because it is non‐destructive and fast, it is an archetypal spectroscopic technique to investigate the structure and defects in TMDCs. In our earlier study, we used a metal‐dielectric coating to enhance Raman signal of WS2 because the Raman Spectra measured from WS2 coated on the standard Si/SiO2 was significantly lower. This metal‐dielectric coating allowed access to the otherwise unavailable E12g and A1g modes of WS2. In this study, we compare the Raman spectra of WS2 on a Si/SiO2 to that of metal layers (Au [200 nm] and Al [200 nm]). A significant enhancement in the Raman signal of 2‐3L WS2 is observed for both the Au and Al coatings. Although 200 nm Au coating enhances the Raman Signal better than the 10 nm Au coating, it does not resolve the other …

Show more

Sep 2023 • Electrochimica Acta

Advanced impedance analysis of direct quinone fuel cells using distribution of relaxation times

Yan Yurko, Lior Elbaz

The need for new, reliable, and sustainable energy sources led to the development of new types of fuel cells. Fuel cells that rely on liquid hydrogen carriers may be the ultimate solution to the expensive hydrogen logistics issues. In this category, direct quinone fuel cells (DQFCs) are a promising new technology that solves many of the issues of traditional fuel cells. As a new technology, DQFCs need to be studied thoroughly to reach their full potential. Here, we use a distribution of relaxation times (DRT) analysis to analyze the impedance data of DQFCs, to gain a better understanding of the system. We systematically changed the operating parameters and attributed the changes in the DRT spectra to the physical processes they correspond to. The four main peaks observed in the DRT measurements were assigned to oxygen reduction reaction (ORR), quinone diffusion resistance, proton diffusion in the membrane …

Show more

Sep 2023 • Journal of The Electrochemical Society

The Effect of Chlorides on the Performance of DME/Mg [B (HFIP) 4] 2 Solutions for Rechargeable Mg Batteries

Ben Dlugatch, Janina Drews, Ran Attias, Bar Gavriel, Adar Ambar, Timo Danner, Arnulf Latz, Doron Aurbach

One of the major issues in developing electrolyte solutions for rechargeable magnesium batteries is understanding the positive effect of chloride anions on Mg deposition-dissolution processes on the anode side, as well as intercalation-deintercalation of Mg 2+ ions on the cathode side. Our previous results suggested that Cl− ions are adsorbed on the surface of Mg anodes and Chevrel phase Mg x Mo 6 S 8 cathodes. This creates a surface add-layer that reduces the activation energy for the interfacial Mg ions transportation and related charge transfer, as well as promotes the transport of Mg 2+ from the solution phase to the Mg anode surface and into the cathodes' host materials. Here, this work further examines the effect of adding chlorides to the state-of-the-art Mg [B (HFIP) 4] 2/DME electrolyte solution, specifically focusing on reversible magnesium deposition, as well as the performance of Mg cells with …

Show more

Sep 2023 • Applied Physics Letters

Super-resolution reconstruction of structured illumination microscopy based on pixel reassignment

Xing Liu, Xiang Fang, Yunze Lei, Jiaoyue Li, Sha An, Juanjuan Zheng, Ying Ma, Haiyang Ma, Zeev Zalevsky, Peng Gao

In this work, we report a pixel reassignment based super-resolution reconstruction algorithm for structured illumination microscopy (entitled PR-SIM). PR-SIM provides a twofold theoretical resolution enhancement by reassigning the pixels in raw SIM images with respect to the center of each illumination fringe and applying further deconvolution. By comparing with frequency domain based algorithms, PR-SIM is more immune to fringe distortion and, hence, it is more suited for large-field SIM in that it processes the raw images locally. Meanwhile, the reconstruction speed of PR-SIM can be enhanced by skipping empty regions in the image and further enhanced by employing GPU-base parallel calculation. Overall, we can envisage that the PR-SIM can be extended for other illumination modulation based microscopic techniques.

Show more

Sep 2023 • Superconductor Science and Technology

Dendritic flux avalanches in superconducting hybrid structures

Michal Wasserman, Avner Shaulov, Amos Sharoni, Yosef Yeshurun

Magneto-optical imaging was employed to study dendritic flux avalanches in metal/superconductor and superconductor/superconductor hybrid structures over an extended range of magnetic field ramping rates. Our results in Cu/NbN show that the previously reported suppression of dendritic flux avalanches in metal coated superconducting films is limited to low ramping rates; as the ramping rate increases, the metal coating becomes less and less effective. A more complex behavior is exhibited in superconductor/superconductor hybrid structures. Our measurement in NbN partially coated with Nb, reveal three distinctive types of dendritic avalanches: those propagating in only one layer, either as regular dendrites in the uncoated NbN or as surface dendrites in the Nb layer, and hybrid dendrites that propagate in both the Nb and NbN layers simultaneously. These three types of dendrites are distinguished by their …

Show more

Sep 2023 • Journal of The Electrochemical Society

Understanding the Positive Effect of LATP in Polymer Electrolytes in All-Solid-State Lithium Batteries

Ortal Breuer, Gayathri Peta, Yuval Elias, Hadas Alon-Yehezkel, Yu-Ting Weng, Miryam Fayena-Greenstein, Nae-Lih Wu, Mikhael D Levi, Doron Aurbach

Composite solid electrolytes with ceramic particles dispersed in a polymer matrix are considered a correct choice for all-solid-state batteries. These electrolytes balance the high ionic conductivity of superionic-ceramic conductors and the elasticity of polymers. Here, Li|| LiFePO 4 batteries with 30 wt% of LATP embedded in PEO 20: LiTFSI show superior performance at elevated temperature. After∼ 150 cycles, cells retained 84% of their original capacity compared to only 51% for batteries with no additive. At 5 C cells demonstrate 43% higher capacity. In symmetric cells with blocking and non-blocking electrodes and all-solid-state batteries LATP lowers the impedance of the electrode-electrolyte interface ensuring cycling stability. LATP improves performance by stabilization of the cathode-electrolyte interface, apparently the major contributor to the cell impedance.

Show more

Sep 2023 • Superconductor Science and Technology

Dendritic flux avalanches in superconducting hybrid structures

M Wasserman, A Shaulov, A Sharoni, Y Yeshurun

Magneto-optical imaging was employed to study dendritic flux avalanches in metal/superconductor and superconductor/superconductor hybrid structures over an extended range of magnetic field ramping rates. Our results in Cu/NbN show that the previously reported suppression of dendritic flux avalanches in metal coated superconducting films is limited to low ramping rates; as the ramping rate increases, the metal coating becomes less and less effective. A more complex behavior is exhibited in superconductor/superconductor hybrid structures. Our measurement in NbN partially coated with Nb, reveal three distinctive types of dendritic avalanches: those propagating in only one layer, either as regular dendrites in the uncoated NbN or as surface dendrites in the Nb layer, and hybrid dendrites that propagate in both the Nb and NbN layers simultaneously. These three types of dendrites are distinguished by their …

Show more

Sep 2023 • 2023 48th International Conference on Infrared, Millimeter, and Terahertz …, 2023

Novel split-well resonant-phonon terahertz quantum cascade laser supporting clean four-level system.

S Levy, N Lander Gower, S Piperno, SJ Addamane, JL Reno, A Albo

We present a novel terahertz quantum cascade laser (THz QCL) scheme supporting a clean four-level system, ‘four’ being the number of the active laser states, as verified by the negative differential resistance (NDR) observed all the way up to room temperature. In this study, we analyze and discuss the temperature performance of this new design. Experimental as well as theoretical work was performed to analyze the effects of the doping density as well as the impact of the different scattering mechanisms.

Show more

Sep 2023 • arXiv preprint arXiv:2309.13197

X-ray Parametric Down Conversion at the APS Synchrotron

NJ Hartley, D Hodge, T Buckway, R Camacho, P Chow, E Christie, A Gleason, S Glenzer, A Halavanau, AM Hardy, C Recker, S Sheehan, S Shwartz, H Tarvin, M Ware, J Wunschel, Y Xiao, RL Sandberg, G Walker

We present measurements of X-ray Parametric Down Conversion at the Advanced Photon Source synchrotron facility. We use an incoming pump beam at 22 keV to observe the simultaneous, elastic emission of down-converted photon pairs generated in a diamond crystal. The pairs are detected using high count rate silicon drift detectors with low noise. Production by down-conversion is confirmed by measuring time-energy correlations in the detector signal, where photon pairs within an energy window ranging from 10 to 12 keV are only observed at short time differences. By systematically varying the crystal misalignment and detector positions, we obtain results that are consistent with the constant total of the down-converted signal.

Show more

Sep 2023 • Journal of Physics B: Atomic, Molecular and Optical Physics

Vacuum UV studies of protonated serine clusters

Ori Licht, Maria Nihamkin, Mirit Anaby, Patrick Rousseau, Alexandre Giuliani, Aleksandar Milosavljevic, Raj Singh, Vy Nguyen, Laurent Nahon, Yoni Toker

In a recent work, we have shown that photon absorption can cause a chemical bond to be created between the two monomers within a protonated serine dimer, a process known as intra-cluster bond formation (ICBF), despite this process not occurring following thermal excitation via low energy collision-induced dissociation (LE-CID). Here we show further evidence for non-statistical photon-induced dissociation (PID) of the protonated serine dimer. In addition we discuss LE-CID and PID studies of the protonated serine octamer, showing that in this case as well, PID leads to non-statistical fragmentation and to the formation of two bonds between three neighboring monomers.

Show more

Sep 2023 • Journal of The Electrochemical Society

The Effect of Chlorides on the Performance of DME/Mg [B (HFIP) 4] 2 Solutions for Rechargeable Mg Batteries

Ben Dlugatch, Janina Drews, Ran Attias, Bar Gavriel, Adar Ambar, Timo Danner, Arnulf Latz, Doron Aurbach

One of the major issues in developing electrolyte solutions for rechargeable magnesium batteries is understanding the positive effect of chloride anions on Mg deposition-dissolution processes on the anode side, as well as intercalation-deintercalation of Mg2+ ions on the cathode side. Our previous results suggested that Cl- ions are adsorbed on the surface of Mg anodes and Chevrel phase MgxMo6S8 cathodes. This creates a surface add-layer that reduces the activation energy for the interfacial Mg ions transportation and related charge transfer, as well as promotes the transport of Mg2+ from the solution phase to the Mg anode surface and into the cathodes' host materials. Here, this work further examines the effect of adding chlorides to the state-of-the-art Mg[B(HFIP)4]2/DME electrolyte solution, specifically focusing on reversible magnesium deposition, as well as the performance of Mg cells with benchmark …

Show more

Sep 2023 • 2023 IEEE 33rd International Workshop on Machine Learning for Signal …, 2023

Utilizing Perturbation of Atoms’ Positions for Equivariant Pre-Training in 3D Molecular Analysis

Tal Kiani, Avi Caciularu, Shani Zev, Dan Thomas Major, Jacob Goldberger


logo
Articali

Powered by Articali

TermsPrivacy