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At least 145 records · Page 8

High-resolution bandpass x-ray imaging with crystal reflectors: Overcoming geometric aberrations

The imaging problem of a specular reflector is revisited. Retaining terms through the second order in the reflector surface expansion, we derive the form of the aberration-limiting aperture for arbitrary magnification, assuming no bandwidth limitations. A permissible relative aperture size of the reflector is limited by a set relative aberration tolerance and scales with the tangent of the central glancing angle of incidence. These limiting aberrations become practically insignificant near backscattering. The results extend to x-ray diffracting crystals in symmetric Bragg geometry shaped as an ellipsoid of revolution. This geometry permits polychromatic imaging for hard x-rays over a bandwidth defined by the accepted range of Bragg angles, thereby suppressing aberrations of higher orders. We assess ellipsoidal crystal imagers using ray tracing simulations for two high-magnification designs with Bragg angles far from and close to backscattering. Finally, in both cases, the ellipsoidal crystals produce images of higher quality compared to those formed by equivalent toroidal crystal imagers.

Bragg reflection↗

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net

Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step in the cryo-EM-based structure determination. However, existing methods trained on a limited amount of cryo-EM data still cannot accurately pick protein particles from noisy cryo-EM images. The general foundational artificial intelligence–based image segmentation model such as Meta’s Segment Anything Model (SAM) cannot segment protein particles well because their training data do not include cryo-EM images. Here, we present a novel approach (CryoSegNet) of integrating an attention-gated U-shape network (U-Net) specially designed and trained for cryo-EM particle picking and the SAM. The U-Net is first trained on a large cryo-EM image dataset and then used to generate input from original cryo-EM images for SAM to make particle pickings. CryoSegNet shows both high precision and recall in segmenting protein particles from cryo-EM micrographs, irrespective of protein type, shape and size. On several independent datasets of various protein types, CryoSegNet outperforms two top machine learning particle pickers crYOLO and Topaz as well as SAM itself. The average resolution of density maps reconstructed from the particles picked by CryoSegNet is 3.33 Å, 7% better than 3.58 Å of Topaz and 14% better than 3.87 Å of crYOLO. It is publicly available at https://github.com/jianlin-cheng/CryoSegNet

59 BASIC BIOLOGICAL SCIENCES↗

Enabling the Acquisition of Electron Beam-Induced Current (EBIC) Images in Conventional SEM and STEM Instruments

Electron beam-induced current (EBIC) imaging is a well-established scanning electron microscope (SEM) technique used to analyze the behavior of microelectronic devices including solar cells. Recently, the application of EBIC imaging in an aberration-corrected scanning transmission electron microscope (STEM) has been demonstrated and offers great potential for the in situ study of electronic materials, correlating charge transport properties to atomic structural and elemental information. Here, this work presents two ways to implement EBIC imaging in conventional SEM and STEM systems: one relying on the instrument's inherent scanning and imaging electronics and the other involving third-party systems usually available in electron microscopes. The implementation of lock-in EBIC in systems equipped with a fast beam blanker is also described. In addition, this work shows and discusses the different mechanisms at play in EBIC imaging and their dependence on beam energy, sample impedance, and electrical measurement configuration, providing researchers with the basic information needed to apply the technique to their research.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Imaging surface topography with coherent x-ray reflectivity: Theory, kinematics, and simulations

A theoretical formalism is described for understanding coherent x-ray reflectivity (CXR) from the surface of a semi-infinite crystal having a variable surface topography, described by the height profile ℎ(𝑥,𝑦). The surface topography is imaged as a complex “effective density,” obtained from the phasing and inversion of the coherent x-ray reflectivity data, measured through a rocking scan centered at a vertical momentum transfer 𝑄$^{0}_{𝑧}$ and a vertical range Δ⁢𝑄 𝑧 . The formalism predicts that the effective density has an amplitude with a maximum located at the surface height for each position within the surface plane. The phase of the effective density has a lateral variation that is controlled by the surface height and a vertical variation that reflects a combination of the interfacial structure and specific choice of measurement conditions. This understanding enables direct observation of nanometer-scale interfacial topography, i.e., ℎ⁡(𝑥,𝑦)⁢𝑐 𝑠 (where 𝑐 𝑠 is the vertical substrate lattice parameter) with Å-scale sensitivity to surface height. Numerical simulations illustrate and confirm the theoretical results. These results show how the interpretation of the interfacial density phase obtained by CXR data inversion (i.e., surface topography with respect to a flat surface) is conceptually similar to that previously known for Bragg coherent diffraction imaging (BCDI) measurements of isolated nanoparticles (i.e., lattice displacements with respect to an ideal crystal lattice). This suggests that CXR can be thought of as a form of dark field imaging with respect to the bright field BCDI approach. An implication of these results is that interfacial imaging may bypass some of the significant challenges associated with BCDI imaging of multiple particles having different orientations.

X-ray imaging↗

Characterization of latent image of electron beam resist via critical-dimension resonant soft X-ray scattering

Metrology plays a crucial role in semiconductor manufacturing by providing accurate and precise measurement and characterization of critical parameters. With the development of high-resolution extreme ultraviolet lithography (EUVL) processes, critical dimensions are shrinking to sub-10 nm. Resist materials encounter the challenge of providing heightened sensitivity and a handle on exacerbating stochastic variations. A comprehensive understanding of the chemical profile of the latent image is pivotal for mitigating stochastic effects and optimizing pattern quality. However, the subtle differences in chemistry between the exposed and unexposed regions of the resists make it extremely challenging to characterize the latent images with sub-nanometer precision. Here, we develop the metrology with critical-dimension resonant soft X-ray scattering (CD-RSoXS) to probe the chemical profiles of latent images stored in resist after exposure. The combination of absorption spectroscopy and enhanced scattering contrast makes it possible to characterize the subtle structural and chemical variations in the latent image. Moreover, the results of the measurements are compared with the simulations with a finite element method–based Maxwell solver to extract a detailed profile of the latent and developed images. We demonstrate that the CD-RSoXS technique can provide valuable insights into the high spatial resolution and local chemical sensitivity simultaneously, which is crucial to understanding the resolution limits and stochastic effects in EUVL processes.

36 MATERIALS SCIENCE↗

Neural Posterior Estimation for Cataloging Astronomical Images with Spatially Varying Backgrounds and Point Spread Functions

Neural posterior estimation (NPE), a type of amortized variational inference, is a computationally efficient means of constructing probabilistic catalogs of light sources from astronomical images. To date, NPE has not been used to perform inference in models with spatially varying covariates. However, ground-based astronomical images exhibit spatially varying sky backgrounds and point spread functions (PSFs), and accounting for this variation is essential for constructing accurate catalogs of imaged light sources. In this work, we introduce a novel NPE-based cataloging method that trains an inference network with semisynthetic astronomical images generated using PSFs and backgrounds sampled from the Sloan Digital Sky Survey. In experiments with semisynthetic images, we evaluate the method on key cataloging tasks: light source detection, star/galaxy separation, and flux measurement. A “generalist” inference network—trained with diverse PSFs and backgrounds—performs as well as a “specialist” network even when both are evaluated on the specialist’s particular PSF/background combination. This result suggests that a single NPE network can generalize across spatial variations, eliminating the need for retraining on each observational condition.

astronomy image processing↗

A review of quantum imaging methods and enabling technologies

The field of quantum imaging has recently seen an explosion of new methods and techniques. At the heart of most quantum imaging approaches are three enabling technologies: the source of the quantum light, the detectors that turn sensing into imaging, and the method by which the quantum nature of light is leveraged to improve the desired measurement. This review addresses the dominant and emerging technologies in each of these components as well as details concerning the implementations of various quantum imaging methods.

36 MATERIALS SCIENCE↗

A comparative analysis of YOLOv8 and U-Net image segmentation approaches for transmission electron micrographs of polycrystalline thin films

Metallic thin films offer a platform to experimentally study the dynamics of microstructural evolution, but the required transmission electron microscopy (TEM)-based imaging generates complex images that are challenging to segment and quantify. This work provides a comparative analysis of a new YOLOv8 model and an established U-Net model for bright-field TEM images of polycrystals, employing a framework leveraging physical observables to evaluate performance against two hand-traced benchmark datasets. This methodology obviates the comparison of large, diversely structured, and manually labeled datasets that are required to assess performance on a per-image/per-pixel basis. It is found that the YOLOv8 model, adapted for real-time instance segmentation, has up to 43× faster inferencing (NVIDIA GeForce RTX 4090) compared to U-Net and reconstructs hand-traced grain size distributions (GSDs) with excellent fidelity, finding mean diameter within 3% for grains near an optimal magnification; for grains that deviate from the optimal pixel-diameter, the size of small- (large)-diameter grains is systematically over- (under)-estimated. This is partially mitigated by including scale-aware augmentations during training. Moreover, when the bias is corrected post-inference by a rigid shift in distribution, the YOLOv8 model reproduces ground truth GSDs with exceptional fidelity, with statistical tests indicating <5% probability that the distributions are distinct. Based on ground truth data, calibration curves pertaining to this shift can be constructed for a given model. This issue is not present in the U-Net model’s results, indicating that for quantitative measurements where the true size of objects is of interest, special procedures must be implemented for YOLO-based models.

36 MATERIALS SCIENCE↗

Quantifying leaf symptoms of sorghum charcoal rot in images of field‐grown plants using deep neural networks

Abstract Charcoal rot of sorghum (CRS) is a significant disease affecting sorghum crops, with limited genetic resistance available. The causative agent, Macrophomina phaseolina (Tassi) Goid, is a highly destructive fungal pathogen that targets over 500 plant species globally, including essential staple crops. Utilizing field image data for precise detection and quantification of CRS could greatly assist in the prompt identification and management of affected fields and thereby reduce yield losses. The objective of this work was to implement various machine learning algorithms to evaluate their ability to accurately detect and quantify CRS in red‐green‐blue images of sorghum plants exhibiting symptoms of infection. EfficientNet‐B3 and a fully convolutional network emerged as the top‐performing models for image classification and segmentation tasks, respectively. Among the classification models evaluated, EfficientNet‐B3 demonstrated superior performance, achieving an accuracy of 86.97%, a recall rate of 0.71, and an F1 score of 0.73. Of the segmentation models tested, FCN proved to be the most effective, exhibiting a validation accuracy of 97.76%, a recall rate of 0.68, and an F1 score of 0.66. As the size of the image patches increased, both models’ validation scores increased linearly, and their inference time decreased exponentially. This trend could be attributed to larger patches containing more information, improving model performance, and fewer patches reducing the computational load, thus decreasing inference time. The models, in addition to being immediately useful for breeders and growers of sorghum, advance the domain of automated plant phenotyping and may serve as a foundation for drone‐based or other automated field phenotyping efforts. Additionally, the models presented herein can be accessed through a web‐based application where users can easily analyze their own images.

Gonzalez, Emmanuel M.↗

Development of 52Mn Labeled Trastuzumab for Extended Time Point PET Imaging of HER2

Abstract Purpose Due to their long circulation time in the blood, monoclonal antibodies (mAbs) such as trastuzumab, are usually radiolabeled with long-lived positron emitters for the development of agents for Positron Emission Tomography (PET) imaging. Manganese-52 ( 52 Mn, t 1/2 = 5.6 d, β + = 29.6%, E(β ave ) = 242 keV) is suitable for imaging at longer time points providing a complementary technique to Zirconium-89 ( 89 Zr, t 1/2 = 3.3 d, β + = 22.7%, E(β ave ) = 396 keV)) because of its long half-life and low positron energy. To exploit these properties, we aimed to investigate suitable bifunctional chelators that could be readily conjugated to antibodies and labeled with 52 Mn under mild conditions using trastuzumab as a proof-of-concept. Procedures Trastuzumab was incubated with S-2-(4-isothiocyanatobenzyl)-1,4,7,10-tetraazacyclododecane tetraacetic acid (p-SCN-Bn-DOTA), 1-Oxa-4,7,10-tetraazacyclododecane-5-S-(4-isothiocyantobenzyl)-4,7,10-triacetic acid (p-SCN-Bn-Oxo-DO3A), and 3,6,9,15-tetraazabicyclo[9.3.1] pentadeca-1(15),11,13-triene-4-S-(4-isothiocyanatobenzyl)-3,6,9-triacetic acid (p-SCN-Bn-PCTA) at a tenfold molar excess. The immunoconjugates were purified, combined with [ 52 Mn]MnCl 2 at different ratios, and the labeling efficiency was assessed by iTLC. The immunoreactive fraction of the radiocomplex was determined through a Lindmo assay. Cell studies were conducted in HER2 + (BT474) and HER2- (MDA-MB-468) cell lines followed by in vivo studies. Results Trastuzumab-Oxo-DO3A was labeled within 30 min at 37 °C with a radiochemical yield (RCY) of 90 ± 1.5% and with the highest specific activity of the chelators investigated of 16.64 MBq/nmol. The labeled compound was purified with a resulting radiochemical purity of > 98% and retained a 67 ± 1.2% immunoreactivity. DOTA and PCTA immunoconjugates resulted in < 50 ± 2.5% (RCY) with similar specific activity. Mouse serum stability studies of [ 52 Mn]Mn-Oxo-DO3A-trastuzumab showed 95% intact complex for over 5 days. Cell uptake studies showed higher uptake in HER2 + (12.51 ± 0.83% /mg) cells compared to HER2- (0.85 ± 0.10%/mg) cells. PET images of mice bearing BT474 tumors showed high tumor uptake that was consistent with the biodistribution (42.02 ± 2.16%ID/g, 14 d) compared to MDA-MB-468 tumors (2.20 ± 0.80%ID/g, 14 d). Additionally, both models exhibited low bone uptake of < 1% ID/g. Conclusion The bifunctional chelator p-SCN-Bn-Oxo-DO3A is promising for the development of 52 Mn radiopharmaceuticals as it was easily conjugated, radiolabeled at mild conditions, and illustrated stability for a prolonged duration both in vitro and in vivo . High-quality PET/CT images of [ 52 Mn]Mn-Oxo-DO3A-trastuzumab were obtained 14 d post-injection. This study illustrates the potential of [ 52 Mn]Mn-Oxo-DO3A for the evaluation of antibodies using PET imaging.

Omweri, James M.↗

Comparison of automated chemical-guided segmentation and human annotation of soil organic matter in X-ray microcomputed tomography imaging in contrasted soil types

Soil organic matter (OM) formation and persistence is strongly influenced by the spatial distribution of organic substrates and microscale soil heterogeneity by dictating OM accessibility to microorganisms. However, traditional size and/or density fractionation techniques disrupt aggregate architecture, eliminating spatial information needed to fully understand intra-aggregate OM distribution. To quantify three-dimensional OM spatial distribution and automate segmentation in X-ray microcomputed tomography (µCT) imaging without human annotation bias, we developed an iodine gas vapor (I2) based staining workflow that eliminates labor-intensive manual annotation while maintaining segmentation accuracy, using aggregates from four taxonomically diverse soils (Xerofluvent, Haploxeroll Sphagnofibrist, Palehumult) with an 8-fold range of soil organic carbon. Human annotation of 10 µCT slices by the experienced and inexperienced annotators resulted in variations up to 3% in the Dice similarity coefficient (DSC), reflecting a degree of inherent subjectivity of manual labeling. Such inconsistencies are expected to compound as the number of manually annotated slices increases. Dual-energy µCT imaging at 33.1 keV (below the iodine (I) K-edge) and 33.2 keV (above the I K-edge) was used to resolve aggregate microstructure following I2 staining. The automated image subtraction pipeline identified OM regions by the I Kedge induced brightness increases, achieving DSC values of 0.58–0.83 relative to an experienced annotator. Sensitivity analyses revealed that the reconstruction alpha value—optimized via the open-source tool TomocuPy—and the 3D registration slice count were the primary determinants of accuracy, providing a novel benchmark for dual-energy soil imaging. The pipeline without GPU acceleration achieved 9.6 to 43.2 times faster than manual annotation. Using GPU-accelerated image post-processing and affine transformation matrices, the pipeline successfully segmented OM elements for large-scale datasets (3232×3232 pixel, 2048 slices) within ~5200 s from raw file acquisition to segmented output. The high-throughput approach enables the quantification of OM spatial distribution across diverse and heterogeneous soil.

Soil microbial biomass↗

X‑ray Coherent Diffractive Imaging of Large Helium Nanodroplets Doped with Small Molecules

We report the first X-ray coherent diffractive imaging experiment on molecule-doped helium nanodroplets. It complements previous work, where we reported single-shot X-ray coherent diffractive imaging studies of Xe dopant clusters formed in 4He and 3He droplets. These noble gas clusters were used to visualize the impact of rotational excitation of the droplets on the spatial distribution of atomic dopants within the droplets, and to study the differences and connections between quantum and classical droplet rotational motion. Here, we expand our studies to the molecular dopants CF4, CHF3, CH3CN, and SF6, imaged with 1.5 keV photons. We find multiple Bragg spots in the diffraction patterns of molecule-doped droplets with radii of approximately 600 nm, which provide evidence that molecules form elongated clusters with preferential alignment along the angular momentum axis of the 4He droplets, in agreement with our previous results on the aggregation of Xe clusters on quantum vortices. Real-space reconstructions of molecular dopant cluster density profiles are obtained for droplets with smaller radii of approximately 300 nm. The diffuse images suggest the formation of low-density, potentially porous, molecular clusters upon aggregation at T = 0.4 K in 4He droplets. In the normal fluid 3He droplets, molecules aggregate into loose clusters on the droplets' equator, similar to previous observations for Xe atoms. Time-of-flight mass spectra reveal that the doped helium nanodroplet moieties fragment extensively into constituent atomic ions, producing only a small fraction of molecular fragment ions. The findings are discussed in the context of previously proposed schemes to use He droplets as potential tamper materials for ultrafast X-ray imaging experiments.

Feinberg, AlexandraJ↗

Initial Stage of Nanoscale Imaging in Positive Tone Extreme UV Photoresists: The Influence of the Polymer Sequence

Photolithographic patterning using extreme ultraviolet (EUV, 92.5 eV) light is a radiolytic process that initially forms electrons, radical cations, anions, and neutral radicals in the polymeric photoresist matrix. These species may participate in the chemical reactions that define the ultimate resolution of the printed image, and their concentrations and nanometer-scale stochastic variations in their formation influence printed image quality. Proposals have been made that polymer chain uniformity may be advantageous in reducing stochastics due to spatial inhomogeneities, and this aspect of radiolysis is examined in this work. We have simulated the initial subpicosecond stages of the imaging process for a series of photoresist films that are identical in composition but vary in their polymer chain structures. We use detailed, physically accurate stochastic reaction-diffusion calculations to evaluate the influence of defined sequence and random copolymer structures on radiolytic spur formation, i.e., a cluster of species formed by electron-polymer interactions that defines the initial spatial characteristic of the imaging process. Predictions of electron thermalization in the present work are shown to be consistent with the literature, indicating that our overall computational approach for ultrafast nanoscale processes is sound. The computational results show that the polymer sequence has no significant effect on the spur composition. This suggests that any potential imaging improvements to be gained by sequence control must originate from postimaging lithographic process steps.

Absorption↗

Quantum Light Imaging of the Plant Root─Rhizobacteria─System Using iLOV Fluorescence

It has been demonstrated recently that the use of specific quantum states of light for two-photon microscopy can lead to a substantial reduction of the intensity of light needed for the imaging of biological objects. This opens new ways to better understand the delicate mechanisms of the interactions of living organisms in the rhizosphere on an extended time scale without optical damage or alteration of their native behavior. Herein, we report a successful realization of entangled two-photon excited fluorescence microscopy of wheat plant roots and a set of biological samples, including purified iLOV protein, bacterial cells expressing iLOV, and combination of these under an extremely low excitation intensity. The entangled two-photon coupling strength of iLOV was modeled using electronic structure calculations which demonstrated that the FMN chromophore in the iLOV protein has an entangled two-photon absorption (ETPA) cross section that is large enough for imaging using weak quantum light for fluorescence excitation. Successful imaging of plant-associated Pantoea sp. YR343 cells expressing iLOV validates the feasibility of using iLOV as a molecular label for characterizing plant-microbe interactions based on entangled photon imaging. In conclusion, the results demonstrate the advantageous use of entangled photon imaging under noninvasive and nondestructive conditions.

Varnavksi, Oleg [Univ. of Michigan, Ann Arbor, MI ↗

AI-enabled Lorentz microscopy for quantitative imaging of nanoscale magnetic spin textures

The manipulation and control of nanoscale magnetic spin textures are of rising interest as they are potential foundational units in next-generation computing paradigms. Achieving this requires a quantitative understanding of the spin texture behavior under external stimuli using in situ experiments. Lorentz transmission electron microscopy (LTEM) enables real-space imaging of spin textures at the nanoscale, but quantitative characterization of in situ data is extremely challenging. Here, we present an AI-enabled phase-retrieval method based on integrating a generative deep image prior with an image formation forward model for LTEM. Our approach uses a single out-of-focus image for phase retrieval and achieves significantly higher accuracy and robustness to noise compared to existing methods. Furthermore, our method is capable of isolating sample heterogeneities from magnetic contrast, as shown by application to simulated and experimental data. This approach allows quantitative phase reconstruction of in situ data and can also enable near real-time quantitative magnetic imaging.

36 MATERIALS SCIENCE↗

Ultrafast nano-imaging and nano-spectroscopy

Ultrafast pump–probe nano-imaging combines scanning probe-based optical near-field microscopy with ultrafast spectroscopy to enable imaging with deep sub-wavelength spatial resolution, femtosecond temporal resolution and simultaneous spectral resolution. Ultrafast nano-imaging has gained increased attention for its ability to provide far-from-equilibrium excitation and excited-state contrast. With coherent and nonlinear probing, coupled electron, spin and lattice dynamics on elementary timescale and length scale can be resolved. Through nano-movies, ultrafast nano-imaging visualizes correlated quantum dynamics underlying the properties of solid-state materials, semiconductors, molecular electronic, photonic, photovoltaic and other functional materials. With nanometre spatial resolution, this method probes elementary dynamic processes across multiple length scales that are otherwise obscured in conventional ultrafast spectroscopy in which heterogeneities are spatially averaged. Furthermore, this Primer describes the theoretical background and experimental implementation of ultrafast nano-imaging; signal interpretation and modelling; representative examples and a perspective for the future development of the field.

Microscopy↗

Development of a true single line of sight 3D hot-spot imaging for the National Ignition Facility

High resolution 3D self-emission x-ray imaging during inertial confinement fusion capsule implosion enables the measurement of the shape of the hotspot. While current 3D imaging capabilities use multiple lines of sight to perform image reconstruction, it would be highly desirable to use only one line of sight, as this would significantly reduce the number of windows in the target hohlraum and decrease their impacts on implosion symmetry. Such a goal is achievable using the zone plate coded imaging technique developed by N. M. Ceglio [Proc. SPIE 0106, 55-62 (1977)]. It consists of fielding a visible light Fresnel zone plate on shot to record a shadowgraph. Here, the image can then be reconstructed either by printing the shadowgraph on a transparent film and shining a suitable wavelength light through it or by numerical reconstruction. A new approach using numerical reconstruction is presented, and it relaxes the constraint by an order of magnitude on the optic design, thus enabling an easier fabrication process, as it allows a scaling-up of the optic dimensions. The design, fabrication process, and testing with an x-ray source of a prototype is presented. The reconstruction of an ~14.5 × 17 μm 2 broadband x-ray source was successful and shows that the performances are in line with expectation with an at least 5 mm axial resolution.

47 OTHER INSTRUMENTATION↗

Enhanced imaging of electronic hot spots using quantum squeezed light

Detecting electronic hot spots is important for understanding the heat dissipation and thermal management of electronic and semiconductor devices. Optical thermoreflective imaging is being used to perform precise temporal and spatial imaging of heat on wires and semiconductor materials. We apply quantum squeezed light to perform thermoreflective imaging on micro-wires, surpassing the shot-noise limit of classical approaches. We obtain a far-field temperature sensing accuracy of 42 mK after 50 ms of averaging and show that a 256×256 pixel image can be constructed with such sensitivity in 10 min. We can further obtain single-shot temperature sensing of 1.6 K after only 10 μs of averaging, enabling a dynamical study of heat dissipation. Not only do the quantum images provide accurate spatiotemporal information about heat distribution but also the measure of quantum correlation provides additional information, inaccessible by classical techniques, which can lead to a better understanding of the dynamics. We apply the technique to both aluminum and niobium microwires and discuss the applications of the technique in studying electron dynamics at low temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗