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At least 91 records · Page 5

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Coarse-grained modeling can be used to explore general theories that are independent of specific chemical detail. In this paper, we present cg_openmm, a Python-based simulation framework for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics of cooperative secondary structures. cg_openmm facilitates the building of coarse-grained topology and random starting configurations, setup of GPU-accelerated replica exchange molecular dynamics simulations with the OpenMM software package, and features a suite of postprocessing thermodynamic and structural analysis tools. In particular, native contact analysis, heat capacity calculations, and free energy of folding calculations are used to identify and characterize cooperative folding transitions and stable secondary structures. In this work, we demonstrate the capabilities of cg_openmm on a simple 1–1 Lennard-Jones coarse-grained model, in which each residue contains 1 backbone and 1 side-chain bead. By scanning both nonbonded and bonded force-field parameter spaces at the coarse-grained level, we identify and characterize sets of parameters which result in the formation of stable helices through cooperative folding transitions. Furthermore, we show that the geometries and stabilities of these helices can be tuned by manipulating the force-field parameters.

36 MATERIALS SCIENCE↗

Large inverse Faraday effect for Rydberg states of free atoms and isolated donors in semiconductors

We report on the induction of magnetization in Rydberg systems by means of the inverse Faraday effect and propose the appearance of the effect in two such systems: Rydberg atoms proper and shallow dopants in semiconductors. Rydberg atoms are characterized by a large orbital radius. This large radius gives such excited states a large angular moment, which when driven with circularly polarized light translates to a large effective magnetic field $\mathscr{B}$ eff . We calculate this effect to generate effective magnetic fields of O⁡(1⁢ µ⁢T)×($\frac{ω}{1THz}$) -1 ⁢ ($\frac{\mathscr{I}}{10Wcm^{-2}}$)⁢n 4 in the Rydberg states of atoms such as Rb and Cs for off-resonant photon beams with frequency ω and intensity $\mathscr{I}$ expressed in units of the denominators and n the principal quantum number. Additionally, terahertz spectroscopy of phosphorus-doped silicon reveals a large cross section for excitation of shallow dopants to Rydberg-like states, which even for small n have the potential to be driven similarly with circularly polarized light to produce an even larger magnetization. Our theoretical calculations estimate $\mathscr{B}$ eff as O⁡(10 2 T) for Si:P with a beam intensity of 10 8 Wcm -2 .

36 MATERIALS SCIENCE↗

Vertical profiles of trace gas and aerosol properties over the eastern North Atlantic: variations with season and synoptic condition

Abstract. Because of their extensive coverage, marine low clouds greatly impact the global climate. Presently, the response of marine low clouds to the changes in atmospheric aerosols remains a major source of uncertainty in climate simulations. One key contribution to this large uncertainty derives from the poor understanding of the properties and processes of marine aerosols under natural conditions and the perturbation by anthropogenic emissions. The eastern North Atlantic (ENA) is a region of persistent but diverse subtropical marine boundary layer (MBL) clouds, where cloud albedo and precipitation are highly susceptible to perturbations in aerosol properties. Here we examine the key processes that drive the cloud condensation nuclei (CCN) population in the MBL using comprehensive characterizations of aerosol and trace gas vertical profiles during the Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) field campaign. During ACE-ENA, a total of 39 research flights were conducted in the Azores: 20 during summer 2017 and 19 during winter 2018. During summer, long-range-transported aerosol layers were periodically observed in the lower free troposphere (FT), leading to elevated FT CCN concentrations (NCCN). Both biomass burning and pollution from North America contribute to submicron aerosol mass in these layers, with pollution likely the dominant contributor. In contrast, long-range transported continental emissions have a much weaker influence on the aerosol properties in the ENA during the winter season. While the entrainment of FT air is a major source of particle number in the MBL for both seasons, on average it does not serve as a direct source of CCN in the MBL because the average FT NCCN is the same or even lower than that in the MBL. The particle number flux due to FT entrainment is dominated by pre-CCN (particles that are too small to form cloud droplets under typical conditions, i.e., particles with sizes below the Hoppel minimum) due to the elevated Npre-CCN in the lower FT. Once these pre-CCN are entrained into the MBL, they can grow and reach CCN size range through condensational growth, representing an indirect and major source of MBL CCN in the ENA. The impact of synoptic conditions on the aerosol properties is examined. Under pre-front and post-front conditions, shallow convective activity often leads to a deep and decoupled boundary layer. Coalescence scavenging and evaporation of drizzle below clouds lead to reduced NCCN and larger accumulation-mode particle sizes in the upper cloud-containing decoupled layer, indicating that surface measurements overestimate the NCCN relevant to the formation of MBL clouds under decoupled conditions.

54 ENVIRONMENTAL SCIENCES↗

Quarterly Management Document – FY22, 3rd Quarter, Multi-pass Hybrid Laser Arc Welding of Alloy 740H

During the 3rd quarter of FY22, progress was made on modeling and simulation of deep penetration laser welding of Alloy 740H. Advances in the modeling of residual stress development arising from the calculated temperature field of the solidifying weld pool were made to understand the development of solidification cracking. Additionally, preliminary modeling of the temperature field within the weld pool of a wobbling laser heat source was performed. The maximum temperature of the weld pool was found to vary with time. These result will allow modeling of deep penetration laser welding using a wobbling laser to mitigate weld defects and cracking. Also, additional characterization of hybrid laser arc welds indicated that these welds were not defect-free as originally thought and the current HLA welds would not be acceptable under criteria outlined in the ASME Boiler and Pressure Vessel Code, Section IX. Therefore, additional welding trails with variation of the welding parameters and HLA welding configurations are required to produce welds acceptable under the Section IX criteria. It was shown that considerable reduction of HLAW defects had been achieved with each successive welding campaign. Therefore additional variation of HLAW parameters may still yield the desired defect-free welds, however, options for alternate HLAW configurations as well as plate preheating are outlined as contingency plans to obtain suitable welds. These additional (unplanned) HLAW trial may prevent subsequent milestones from being achieved within the original budget.

36 MATERIALS SCIENCE↗

Revealing room temperature ferromagnetism in exfoliated Fe 5 GeTe 2 flakes with quantum magnetic imaging

Van der Waals (vdW) material Fe 5 GeTe 2 , with its long-range ferromagnetic ordering near room temperature, has significant potential to become an enabling platform for implementing novel spintronic and quantum devices. To pave the way for applications, it is crucial to determine the magnetic properties when the thickness of Fe 5 GeTe 2 reaches the few-layers regime. However, this is highly challenging due to the need for a characterization technique that is local, highly sensitive, artifact-free, and operational with minimal fabrication. Prior studies have indicated that Curie temperature T C can reach up to close to room temperature for exfoliated Fe 5 GeTe 2 flakes, as measured via electrical transport; there is a need to validate these results with a measurement that reveals magnetism more directly. Here, we investigate the magnetic properties of exfoliated thin flakes of vdW magnet Fe 5 GeTe 2 via quantum magnetic imaging technique based on nitrogen vacancy centers in diamond. Through imaging the stray fields, we confirm room-temperature magnetic order in Fe 5 GeTe 2 thin flakes with thickness down to 7 units cell. The stray field patterns and their response to magnetizing fields with different polarities is consistent with previously reported perpendicular easy-axis anisotropy. Furthermore, we perform imaging at different temperatures and determine the Curie temperature of the flakes at ≈300 K. These results provide the basis for realizing a room-temperature monolayer ferromagnet with Fe 5 GeTe 2 . This work also demonstrates that the imaging technique enables rapid screening of multiple flakes simultaneously as well as time-resolved imaging for monitoring time-dependent magnetic behaviors, thereby paving the way towards high throughput characterization of potential two-dimensional (2D) magnets near room temperature and providing critical insights into the evolution of domain behaviors in 2D magnets due to degradation.

2D magnet↗

The Value of Watching How Materials Grow: A Multimodal Case Study on Halide Perovskites

Material synthesis is one of the most important aspects in humankinds’ endeavor to discover and create new materials for energy applications. One strategy to tailor materials with desired functions in a rational way is by knowing how functions relate to structure, synthetic variables, arrangement of atoms and molecules, and how functions evolve during synthesis. In order to accelerate materials synthesis, discovery, and optimization by 10 times it is the right time now to integrate computational tools, synthesis, and characterization. One particular barrier to realizing this concept is the understanding of when and how phases form in real time during synthesis, which is challenging to asses by existing theoretical frameworks. In addition, transient or metastable phases with positive free energy above the lowest-free energy ground state can be revealed by such real time (in situ) measurements. Metastable materials are ubiquitous in condensed matter and can show superior properties compared to their equilibrium form. This work discusses the value of emerging multimodal in situ characterizations exemplified on hybrid halide perovskites. Finally, the ways in which the implementation of in situ measurements can advance the materials science synthesis field as well as their role to enable close-loop feedback control and autonomous synthesis are discussed.

36 MATERIALS SCIENCE↗

An ML-based terrestrial data fusion and augmentation framework to enable advanced understanding of the terrestrial carbon and water interactions

Soil moisture is essential to the terrestrial carbon and water cycles and land–atmosphere interactions. There are various types of soil moisture data, and each type has the distinct spatiotemporal strengths and limitations, depending on the diverse applications and retrieval methodologies of different data types (Li et al., in review; The PNNL-82151 FY23 Report). However, the limitations of different soil moisture data in terms of accuracy and spatiotemporal coverage hinder our ability to further understand the soil moisture dynamics across scales. To have a gap free soil moisture data product with a fine spatiotemporal coverage and vertical profiles, we train extreme gradient boosting (XGBoost) models by using (1) in-situ soil moisture measurements from the International Soil Moisture Network (ISMN), (2) soil moisture from the ECMWF reanalysis (ERA) at the 9 km and sub-daily spatiotemporal resolution, (3) the Daymet meteorological fields, and (4) data products that characterize surface conditions, including soil texture, organic content, topography, vegetation type, and rooting depth. We use the trained XGBoost models that have consistent performance across seven soil layers, i.e., 0–5 cm, 5–10 cm, 10–20 cm, 20–40 cm, 40–60 cm, 60–100 cm, and 100–200 cm, and the gridded model predictors to generate a soil moisture data at the 1 km and daily spatiotemporal resolution for the Continental United States (CONUS) from 2001–2020. This dataset can be broadly used for Earth system model benchmark, monitoring extreme weathers, making informed decisions regarding agriculture, water resource management, climate change mitigation, and ecosystem preservation.

58 GEOSCIENCES↗

Multimodality in the Search for New Physics in Pulsar Timing Data and the Case of Kination-amplified Gravitational-wave Background from Inflation

We investigate the kination-amplified inflationary gravitational-wave background (GWB) interpretation of the signal recently reported by various pulsar timing array (PTA) experiments. Kination is a post-inflationary phase in the expansion history dominated by the kinetic energy of some scalar field, characterized by a stiff equation of state w = 1. Within the inflationary GWB model, we identify two modes that can fit the current data sets (NANOGrav and EPTA) with equal likelihood: the kination-amplification (KA) mode and the ordinary, no-kination-amplification (no-KA) mode. The multimodality of the likelihood motivates a Bayesian analysis with nested sampling. We analyze the free spectra of current PTA data and mock free spectra constructed with higher signal-to-noise ratios using nested sampling. The analysis of the mock spectrum designed to be consistent with the best fit to the NANOGrav 15 yr (NG15) data successfully reveals the expected bimodal posterior for the first time while excluding the reheating mode that appears in the fit to the current NG15 data, making a case for our correct and comprehensive treatment of potential multimodal posteriors arising from future PTA data sets. The resultant Bayes factor is $\mathcal{B}$ $\equiv$ Z no–KA /Z KA = 2.9 ± 1.9, indicating comparable statistical significance between the two modes. Given the theoretical model-building challenges of producing highly blue-tilted primordial tensor spectra, the KA mode has the advantage of requiring less blue primordial spectra, compared with the no-KA mode. The synergy between future cosmic microwave background polarization, pulsar timing, and laser interferometer measurements of gravitational waves will help resolve the ambiguity implied by the multimodal posterior in PTA-only searches.

Cosmology↗

Upper-Hybrid Waves Driven by Meandering Electrons Around Magnetic Reconnection X Line

Magnetic reconnection is a fundamental process in collisionless space plasma environment, and plasma waves relevant to the kinetic interactions can have a significant impact on the multiscale behavior of reconnection. Here, we present Magnetospheric Multiscale (MMS) observations during an encounter of an X line of symmetric magnetic reconnection in the magnetotail. The X line is characterized by reversals of ion and electron jets and electromagnetic fields, agyrotropic electron velocity distribution functions (VDFs), and an electron-scale current sheet. MMS observe large-amplitude nonlinear upper-hybrid (UH) waves on both sides of the neutral line, and the wave amplitudes have highly localized distribution along the normal direction. Here, the inbound meandering electrons drive the UH waves, releasing the free energy stored from the reconnection electric field along the meandering trajectories. The interaction between the meandering electrons and the UH waves may modify the balance of the reconnection electric field around the X line.

58 GEOSCIENCES↗

Topological solitonic macromolecules

Being ubiquitous, solitons have particle-like properties, exhibiting behaviour often associated with atoms. Bound solitons emulate dynamics of molecules, though solitonic analogues of polymeric materials have not been considered yet. Here we experimentally create and model soliton polymers, which we call “polyskyrmionomers”, built of atom-like individual solitons characterized by the topological invariant representing the skyrmion number. With the help of nonlinear optical imaging and numerical modelling based on minimizing the free energy, we reveal how topological point defects bind the solitonic quasi-atoms into polyskyrmionomers, featuring linear, branched, and other macromolecule-resembling architectures, as well as allowing for encoding data by spatial distributions of the skyrmion number. Application of oscillating electric fields activates diverse modes of locomotion and internal vibrations of these self-assembled soliton structures, which depend on symmetry of the solitonic macromolecules. Our findings suggest new designs of soliton meta matter, with a potential for the use in fundamental research and technology.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Shielded magnetic small-angle neutron scattering for characterization of radioactive samples

The development of a Pb-shielded fixture for the execution of a small-angle neutron scattering (SANS)-based workflow for interrogation of highly irradiated nuclear materials has been explored. The Pb shielding was specially designed to reduce the detected radioactivity from the specimen during SANS experiments, and the overall configuration is termed shielded magnetic SANS (SM-SANS). Two FeCrAl-based alloys, C35M and 125YF, were examined with the SM-SANS technique using a free-form size distribution locally monodisperse model in both the as-received and irradiated states. Quantitative values derived from the free-form size distribution were compared with atom probe tomography experiments. Microstructural and compositional parameters determined using the two characterization techniques were complements of each other. The results demonstrate that the SM-SANS technique is an effective means of characterizing nanoscale clustering in irradiated material systems and provides new avenues for investigating radioactive material microstructures.

FeCrAl↗

Quantum Chemistry Calculations for Metabolomics

A primary goal of metabolomics and exposomics studies is to fully characterize the small molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversi-ty present within the metabolome and exposome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials (“standards”), which are not available for most molecules. Computational quantum chemis-try methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alter-native route for building reference libraries, i.e., in silico libraries for “standards-free” identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solu-tion. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectros-copy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics and exposomics studies. We expect this review will inspire researchers in the field of small molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.

Metabolism↗

Three-dimensional high-content imaging of unstained soft tissue with subcellular resolution using a laboratory-based X-ray microscope

With increasing interest in studying biological systems across spatial scales—from centimeters down to nanometers—histology continues to be the gold standard for tissue imaging at cellular resolution, providing an essential bridge between macroscopic and nanoscopic analysis. However, its inherently destructive and two-dimensional nature limits its ability to capture the full three-dimensional complexity of tissue architecture. Here, we show that phase-contrast X-ray microscopy can enable three-dimensional virtual histology with subcellular resolution. This technique provides direct quantification of electron density without restrictive assumptions, allowing for direct characterization of cellular nuclei in a standard laboratory setting. By combining high spatial resolution and soft tissue contrast, with automated segmentation of cell nuclei, we demonstrated virtual Hematoxylin and Eosin (H&E) staining using machine learning-based style transfer, yielding volumetric datasets compatible with existing histopathological analysis tools. Furthermore, by integrating electron density and the sensitivity to nanometric features of the dark field contrast channel, we achieve stain-free, high-content imaging capable of distinguishing nuclei and extracellular matrix.

3D virtual histology↗

Anomalies in the electromagnetic response and peculiarities of the domain structure in the magnetic Weyl semimetal Co 3⁢ Sn 2 ⁢S 2

In this paper, we present a comprehensive study of magnetic properties of Co 3 ⁢Sn 2 ⁢S 2 (CoSnS) crystals using macroscopic characterization and observations of the domain structure (DS) in a wide range of easy- and hard-axis fields (𝐻) and temperatures (𝑇). From macroscopic measurements, we derive temperature dependences of the basic magnetic parameters of the material [saturation magnetization 𝑀 𝑠 ⁡(𝑇), uniaxial anisotropy constant 𝐾⁡(𝑇), and exchange stiffness 𝐴⁡(𝑇)] and, based on them, calculate the thermodynamic magnetization 𝑀⁡(𝐻,𝑇) curves and DS parameters for pinning-free samples. We find important qualitative and quantitative differences between the theory and experiment defined by the efficient pinning of domain walls (DWs) in our samples. It turns out that, already at temperatures close to the ferromagnetic transition 𝑇 𝑐 , the DW dynamics falls into the heavy creep regime, resulting in a strong deferral of the DS adjustment into the equilibrium state. Here, we suggest that specific magnetic defects, responsible for pinning and causing field-tuned reproducible domain nucleation patterns observed in our high-quality samples, are pointlike. Recently found magnetic polarons formed around vacancies and impurities, which carry strong diamagnetic moments of spin-orbit nature and are intrinsic for CoSnS and expected in other Weyl semimetals, are a possible source of pinning yielding peculiar 𝑀⁡(𝐻,𝑇) response of CoSnS.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Computational general relativistic force-free electrodynamics: II. Characterization of numerical diffusivity

Scientific codes are an indispensable link between theory and experiment; in (astro-)plasma physics, such numerical tools are one window into the universe’s most extreme flows of energy. The discretization of Maxwell’s equations – needed to make highly magnetized (astro)physical plasma amenable to its numerical modeling – introduces numerical diffusion. It acts as a source of dissipation independent of the system’s physical constituents. Understanding the numerical diffusion of scientific codes is the key to classifying their reliability. It gives specific limits in which the results of numerical experiments are physical. We aim at quantifying and characterizing the numerical diffusion properties of our recently developed numerical tool for the simulation of general relativistic force-free electrodynamics by calibrating and comparing it with other strategies found in the literature. Our code correctly models smooth waves of highly magnetized plasma. We evaluate the limits of general relativistic force-free electrodynamics in the context of current sheets and tearing mode instabilities. We identify that the current parallel to the magnetic field (j ∥ ), in combination with the breakdown of general relativistic force-free electrodynamics across current sheets, impairs the physical modeling of resistive instabilities. We find that at least eight numerical cells per characteristic size of interest (e.g., the wavelength in plasma waves or the transverse width of a current sheet) are needed to find consistency between resistivity of numerical and of physical origins. High-order discretization of the force-free current allows us to provide almost ideal orders of convergence for (smooth) plasma wave dynamics. The physical modeling of resistive layers requires suitable current prescriptions or a sub-grid modeling for the evolution of j ∥ .

79 ASTRONOMY AND ASTROPHYSICS↗

Ptychography at the Linac Coherent Light Source in a parasitic geometry

X-ray free-electron lasers (FELs) are being recognized as a powerful tool in an ever-increasing number of research fields, but are very limited as to the number of experiments that they can support. This work shows that more beamtime could be made available by using `parasitic' geometries, where a secondary experiment uses the X-ray beam that the primary experiment does not utilize. The first successful ptychography experiment, a scanning coherent diffractive imaging technique, in a parasitic geometry at an X-ray FEL is demonstrated. Utilizing the CXI hutch at the Linac Coherent Light Source (LCLS), it is shown that the obtained data are of high quality and that characterizing the beam using ptychography can be much faster than traditional imprinting methods.

42 ENGINEERING↗

Large-volume CdZnTe bar detectors characterized by laser-induced transient currents

In this work, we studied the free-carrier transport properties and space-charge formation/polarization in a CdZnTe bar-shaped radiation detector using the Laser-Induced Transient Current technique. We found out that a steady-state space charge ranging from 8 x 10 8 to 2.1 x 10 9 cm -3 is formed throughout the detector at about 0.5 s following biasing. The measured current waveforms were modeled by Monte Carlo simulations after taking into account the electric and weighting fields inside the detector and shielding box. Modeling of the unpolarized waveforms revealed an exceptionally high electron mobility-lifetime product μ e τ e ≥0.095cm 2 V -1 . The observed formation of positive space charge in the biased detector and linear scaling of the current waveform shapes on applied bias revealed that the detector polarization is attributed to carrier injection at the anode. In conclusion, measurements in pulsed and DC bias in modified electrode geometry proved the surface-charge formation.

47 OTHER INSTRUMENTATION↗

Neutron Identification Capabilities in MicroBooNE Through the Application of Machine Learning with Blips

Neutrinos (ν) are subatomic particles first observed in 1956 by LANL physicists Clyde Cowan and Frederick Reines but first theorized by Wolfgang Pauli in 1930. Neutrinos are the least massive known particle and are classified as leptons with 3 flavors corresponding to their leptonic counterparts (electron, muon, and tau). We know that they are abundant, 65 billion neutrinos travel through your fingertip every second, and elusive, a single neutrino could fly through a lightyear of lead without interacting at all. Though, there is much still unknown and a better characterization of these “ghostly” particles can give us clues as to the matter/anti-matter asymmetry in the early universe and possible glimpses into new physics. To measure a particle that is extremely light and rarely interacting, physicists have developed an extremely sensitive detector known as a Liquid Argon Time Projection Chamber (LArTPC). The fiducial volume (or TPC) is bombarded with neutrinos, some of which interact with argon (Ar) atoms to produce particles that in turn excite and ionize the Ar. The products of these are free electrons which then drift through the TPC’s applied magnetic field towards a multi-plane wire readout system. The electrons’ charge is collected at this anode and the light from the initial interactions is collected by photomultiplier tubes (PMTs). In conjunction, these mechanisms allow LArTPCs to achieve millimeter spatial resolution and sub-MeV energy thresholds. The detector of interest in this study is the MicroBooNE Experiment at Fermilab. MicroBooNE is an above ground LArTPC with dimensions of approximately 10m × 2.5m × 2.3m, about the size of a school bus. Its purpose is to study neutrinos, so to improve rates of measured ν interactions, the detector is squarely in the path of the Booster Neutrino Beam (BNB) at Fermilab. A major challenge in neutrino studies is energy reconstruction, much of the neutrino’s original energy is lost in interactions that the detector is not sensitive to, often due to low-energy products. The initial goal of this analysis was to better identify neutrons, the main source of poor energy reconstruction in neutrino events. Because neutrons are neutral particles, like neutrinos, we can only directly measure the products of their interactions in LArTPCs. Most of these products are low-energy signals and while each one contributes a negligible amount of energy, collectively these signals make up most of the lost energy in each neutrino event. We define these signals as blips; point-like, isolated depositions of charge in the detector. Blips have MeV-scale energies and are the size of a single hit (charge deposition) or a cluster of a few hits on at least two wire planes. Blips are the principal detector features used to study low-energy physics; thus, they are the key to unlocking information not only about neutrons but gamma photons, supernova and solar neutrinos as well as helping us better identify certain particles. Therefore, this analysis strives to use blips for improved neutron identification (ID) and characterization.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗