BINA

The immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-read SMRT sequencing to amplify VDJ-C sequences from F1 (BALB/c x C57BL/6) hybrid animals. Previously unreported strain variations were identified in the Ighm and Ighg2b genes, and analysis of VDJ rearrangements led to the inference of 278 germline IGHV alleles. 169 alleles are not present in the C57BL/6 genome reference sequence. To establish a set of expressed BALB/c IGHV germline gene sequences, we computationally retrieved IGHV haplotypes from the IgM dataset. Haplotyping led to the confirmation of 162 BALB/c IGHV gene sequences. A musIGHV398 pseudogene variant also appears to be present in the BALB/cByJ substrain, while a functional musIGHV398 gene is highly expressed in the BALB/cJ substrain. Only four of the BALB/c alleles were also observed in the C57BL/6 haplotype. The full set of inferred BALB/c sequences has been used to establish a BALB/c IGHV reference set, hosted at https://ogrdb.airr-community.org. We assessed whether assemblies from the Mouse Genome Project (MGP) are suitable for the determination of the genes of the IGH loci. Only 37 (43.5%) of the 85 confirmed IMGT-named BALB/c IGHV and 33 (42.9%) of the 77 confirmed non-IMGT IGHV were found in a search of the MGP BALB/cJ genome assembly. This suggests that Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data, but not currently-available genome assemblies …

CRISPR-Cas technology has revolutionized gene editing, but concerns remain due to its propensity for off-target interactions. This, combined with genotoxicity related to both CRISPR-Cas9-induced double-strand breaks and transgene delivery, poses a significant liability for clinical genome-editing applications. Current best practice is to optimize genome-editing parameters in preclinical studies. However, quantitative tools that measure off-target interactions and genotoxicity are costly and time-consuming, limiting the practicality of screening large numbers of potential genome-editing reagents and conditions. Here, we show that flow-based imaging facilitates DNA damage characterization of hundreds of human hematopoietic stem and progenitor cells per minute after treatment with CRISPR-Cas9 and recombinant adeno-associated virus serotype 6. With our web-based platform that leverages deep learning for …

Applying direct growth and deposition of optical surfaces holds great promise for the advancement of future nanophotonic technologies. Here, we report on a chemical vapor deposition (CVD) technique for depositing amorphous selenium (a-Se) spheres by desorption of selenium from Bi2Se3 and re-adsorption on the substrate. We utilize this process to grow scalable, large area Se spheres on several substrates and characterize their Mie-resonant response in the mid-infrared (MIR) spectral range. We demonstrate size-tunable Mie resonances spanning the 2–16 μm spectral range for single isolated resonators and large area ensembles. We further demonstrate strong absorption dips of up to 90% in ensembles of particles in a broad MIR range. Finally, we show that ultra-high-Q resonances arise in the case where Se Mie-resonators are coupled to low-loss epsilon-near-zero (ENZ) substrates. These findings …

The study of recurrences and revivals in quantum systems has attracted a great deal of interest because of its importance in the control of quantum systems and its potential use in developing new technologies. In this work, we introduce a protocol to induce full-state revivals in a huge class of quantum walks on a -dimensional lattice governed by a -dimensional coin system. The protocol requires two repeated interventions in the coin degree of freedom. We also present a characterization of the walks that admits such a protocol. Moreover, we modify the quantity known as P\'olya number, typically used in the study of recurrences in classical random walks and quantum walks, to create a witness of the first revival of the walk.

Transition-metal dichalcogenides (TMDCs) are unique layered materials with exotic properties. So, examining their structures holds tremendous importance. 2H-MoSe2 (analogous to MoS2; Gr. 6 TMDC) is a crucial optoelectronic material studied extensively using Raman spectroscopy. In this regard, low-frequency Raman (LFR) spectroscopy can probe this material’s structure as it reveals distinct vibration modes. Here, we focus on understanding the microstructural evolution of different 2H-MoSe2 morphologies and their layers using LFR scattering. We grew phase-pure 2H-MoSe2 (with variable microstructures) directly on a Mo foil using a two-furnace ambient-pressure chemical vapor deposition (CVD) system by carefully controlling the process parameters. We analyzed the layers of exfoliated flakes after ultrasonication and drop-cast 2H-MoSe2 of different layer thicknesses by choosing different concentrations of …

The global energy demand is expected to rise continuously in the foreseeable future, and this demand cannot be fulfilled with fossil fuels if the ambitious goals for global reduction in greenhouse gas emissions are to be met. 1, 2 Therefore, it is necessary to switch to energy production from sustainable energy sources such as solar and wind. 3, 4 These sources suffer from intermittent production, producing a surplus of energy at certain hours and seasons and little to none at others. Hence, large energy storage solutions are necessary in order to store the excess energy in peak times and compensate at the lowand down-times. 4, 5One of the most promising energy storage solutions today is chemical, in the form of hydrogen, which can be used with fuel cells to generate electricity or burned to generate heat, as well as being used in the chemical industry for various applications. 5 It can be easily produced with various …

Recent advances in focused ion beam (FIB) technology exploit accelerated helium or neon ions, rather than gallium, for maskless fabrication of superconducting nanocomponents. We present a study of the effect of the damage induced by the accelerated ions on the superconducting transition temperature, T c, of a patterned~ 85-nm-wide Nb wire, demonstrating a decrease of T c from~ 5.5 K in the wire patterned by He ions to~ 2.8 and 2.3 K exploiting Ne and Ga ions, respectively. In an effort to gain insight into the origin of these changes in T c, we performed Stopping and Range of Ions in Matter (SRIM) simulations to estimate the damage induced by each type of ion. The simulations show that the lateral distribution of the ion beam and the sputtering rate in using Ne or Ga are significantly larger than those caused by He, consistent with the changes in the measured electrical properties of the nanowire.

The sluggish kinetics of the anodic oxygen evolution reaction (OER) limit the overall efficiency of green hydrogen production. The proposed strategy to overcome this is to replace OER with other kinetically favorable anodic reactions like urea oxidation reaction (UOR). Herein, we develop an organometallic synthesis of nickel nitride nanoparticles supported on carbon (Ni3N–C) as the catalyst for both UOR and hydrogen evolution reaction (HER). A precious group metal-free electrolyzer based on Ni3N–C catalyst (as both anode and cathode) is implemented for the first time, and the urea electrolyzer cell has a 200 mV lower overpotential compared to that of the water electrolyzer.

Metasurfaces have seen a great evolution over the last few years, demonstrating a high degree of control over the amplitude, phase, polarization, and spectral properties of reflected or transmitted electromagnetic waves. Nevertheless, the inherent limitation of static metasurface realizations, which cannot be controlled after their fabrication, engages an ongoing pursuit for reconfigurable metasurfaces with profound tunability. In this paper, we mitigate this grand challenge by demonstrating a new method for free-space rapid optical tunability and modulation, utilizing a planar aluminum nanodisk metasurface coated with indium tin oxide (ITO) on a thin film of lithium niobate (LiNbO) with a chromium/gold (Cr/Au) substrate. Resonance coupling gives rise to an enhanced, confined electromagnetic field residing in the thin film, leading to a narrow and high contrast dip in reflectance of around 1.55 μm. The precise spectral …

We review the development of 'single' nanoparticle-based inorganic and organic voltage sensors which can eventually become a viable tool for 'non-genetic optogenetics'. The voltage sensing is accomplished with optical imaging at the fast temporal response and high spatial resolutions in a large field of view. Inorganic voltage nanosensors utilize the Quantum Confined Stark effect (QCSE) to sense local electric fields. Engineered nanoparticles achieve substantial single-particle voltage sensitivity (~2% Δ spectral Stark shift, up to ~30% ΔF/F per 160 mV) at room temperature due to enhanced charge separation. A dedicated home build fluorescence microscope records spectrally resolved images to measure QCSE induced spectral shift at the single-particle level. Biomaterial based surface ligands are designed and developed based on theoretical simulations. The hybrid nanobiomaterials satisfies anisotropic …

Correlated beams are important in classical and quantum communication as well as other technologies. However, classical amplifiers, which are essential for long transmission of correlated beams, degrade the correlation due to noise and due to the amplifier spectral response. We measure, with a novel high resolution single-shot measurement system, the impact of amplifiers on correlated beams. We develop a new method for analyzing the correlation between the signal and idler beams by choosing peaks in the pulses according to their power levels. We demonstrate how to tailor the correlation after the amplifier to obtain either higher or lower correlation. Our research may influence the future use of amplifiers in non-classical communication systems as well as the transmission of quantum information over long distances.

Physical interpretations of the time-symmetric formulation of quantum mechanics, due to Aharonov, Bergmann, and Lebowitz are discussed in terms of weak values. The most direct, yet somewhat naive, interpretation uses the time-symmetric formulation to assign eigenvalues to unmeasured observables of a system, which results in logical paradoxes, and no clear physical picture. A top-down ontological model is introduced that treats the weak values of observables as physically real during the time between pre- and post-selection (PPS), which avoids these paradoxes. The generally delocalized rank-1 projectors of a quantum system describe its fundamental ontological elements, and the highest-rank projectors corresponding to individual localized objects describe an emergent particle model, with unusual particles whose masses and energies may be negative or imaginary. This retrocausal top-down model leads to an intuitive particle-based ontological picture, wherein weak measurements directly probe the properties of these exotic particles, which exist whether or not they are actually measured

The functionality of a nanoscale silicon-based optoelectronic modulator is deeply analyzed while it appears that two competing processes, thermal and photonic, are occurring at the same time, and are preventing the optimization of the electro-optics coupling. While an incident illumination-beam first process is translated into photons, generating pairs of electrons–holes, a second process of thermal generation, creating phonons enables a loss of energy. Complementary studies, combining strong analytical models and numerical simulations, enabled to better understand this competition between photonic and thermal activities, in order to optimize the modulator. Moreover, in order to prevent unnecessary heating effects and to present a proposed solution, a picosecond pulsed laser is suggested and demonstrated as the ultimate solution so no energy will be wasted in heat, and still the photonic energy will be fully …

In recent years it became clear that the metallic regime of systems that exhibit a many body localization (MBL) behavior show properties which are quite different than the vanilla metallic region of the single particle Anderson regime. Here we show that the large scale energy spectrum of a canonical microscopical model featuring MBL, displays a non-universal behavior at intermediate scales, which is distinct from the deviation from universality seen in the single particle Anderson regime. The crucial step in revealing this behavior is a global unfolding of the spectrum performed using the singular value decomposition (SVD) which takes into account the sample to sample fluctuations of the spectra. The spectrum properties may be observed directly in the singular value amplitudes via the scree plot, or by using the SVD to unfold the spectra and then perform a number of states variance calculation. Both methods reveal an intermediate scale of energies which follow super Posissonian statistics.

Photodynamic therapy (PDT) and photothermal therapy (PTT) are promising therapeutic methods for cancer treatment; however, as single modality therapies, either PDT or PTT are still limited in their success rate. A dual application of both PDT and PTT, in a combined protocol, has gained immense interest. In this study, gold nanoparticles (AuNPs) are conjugated with a PDT agent, meso-tetrahydroxyphenylchlorin (mTHPC) photosensitizer, designed as nanotherapeutic agents that can activate a dual photodynamic/photothermal therapy. The AuNP-mTHPC complex is biocompatible, soluable, and photostable. PDT efficiency is high because of immediate reactive oxygen species (ROS) production upon mTHPC activation by the 650 nm laser which decreased mitochondrial membrane potential (∆ψm). Likewise, the AuNP-mTHPC complex is used as a photoabsorbing (PTA) agent for PTT, due to efficient plasmon absorption and excellent photothermal conversion characteristics of AuNPs under laser irradiation at 532 nm. Under the laser irradiation of a PDT/PTT combination, a twofold phototoxicity outcome follows, compared to PDT-only or PTT-only treatment. This indicates that PDT and PTT have synergistic effects together as a combined therapeutic method. Hence, applying our AuNP-mTHPC may be a potential treatment of cancer in the biomedical field.

Crucial metabolic functions of peroxisomes rely on a variety of peroxisomal membrane proteins (PMPs). While mRNA transcripts of PMPs were shown to be colocalized with peroxisomes, the process by which PMPs efficiently couple translation with targeting to the peroxisomal membrane remained elusive. Here, we combine quantitative electron microscopy with proximity-specific ribosome profiling and reveal that translation of specific PMPs occurs on the surface of peroxisomes in the yeast Saccharomyces cerevisiae. This places peroxisomes alongside chloroplasts, mitochondria, and the endoplasmic reticulum as organelles that use localized translation for ensuring correct insertion of hydrophobic proteins into their membranes. Moreover, the correct targeting of these transcripts to peroxisomes is crucial for peroxisomal and cellular function, emphasizing the importance of localized translation for cellular physiology.

This paper proposes a method for a scheme of spectral phase encoding with resolution of up to 10 MHz and addressability of 40GHz, for a typical wide-band optical data carrying signal, by means of optical instruments and prior knowledge about the signal. The setup includes an array of Fabri-Perot Interferometers (FPI) which bypass the grating limitations, and a phase-only spatial light modulator (SLM) to properly encode the diffracted light. Their arrangement along with the method of Optical Code Division Multiple Access (OCDMA) was simulated, and promised fine results for various encoding schemes.

RNA guided nucleases are regarded as the future genome editing technologies. As such, they need to meet strong safety margins. Two major challenges in incorporating CRISPR technologies into the clinical world are off-target activity and editing efficiency. The common way to tackle such issues is to measure the binding and cleavage kinetics of the CRISPR enzyme. This can be challenging since, for example, DNA is not released from the CAS9 protein post cleavage. Here a promising new microfluidic approach to characterizing Enzymatic Interaction and Function of CRISPR complexes on a microfluidic platform (EnzyMIF) is presented. The method can rapidly detect the kd, koff, km and kcat for various RNA guided nucleases. In this work, two single guide RNAs with significantly different in-cell cleavage efficiency, RAG2 and RAG1, are used as proof-of-concept. The EnzyMIF assay results provide biochemical …

Solid matrix-supported liquid metal nanoparticles have been drawing attention as a nanoadditive in the fabrication of electroconductive flexible and soft materials. The present work reports a facile, green, and sonochemical synthesis approach of gallium (Ga) nanoparticles embedded in reduced graphene oxide (RGO) under ambient conditions for the first time. The as-synthesized ultrasonic energy-irradiated RGO/Ga nanocomposite was studied using SEM, TEM, DSC, XRD, XPS, and solid-state NMR. Because of their electrical conductivity, RGO/Ga nanoparticles have been used as a conducting inclusion for a poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) matrix and coated on cotton fabrics to develop a smart e-textile for electromagnetic (EM) radiation-shielding application. In the X-band (8.2–12.4 GHz) frequency range, the nanocomposites’ EM interference-shielding efficiency was about …