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At least 1,585 records · Page 88

Chemical Genetic Analysis and Functional Characterization of Staphylococcal Wall Teichoic Acid 2-Epimerases Reveals Unconventional Antibiotic Drug Targets

Here we describe a chemical biology strategy performed in Staphylococcus aureus and Staphylococcus epidermidis to identify MnaA, a 2-epimerase that we demonstrate interconverts UDP-GlcNAc and UDP-ManNAc to modulate substrate levels of TarO and TarA wall teichoic acid (WTA) biosynthesis enzymes. Genetic inactivation of mnaA results in complete loss of WTA and dramatic in vitro β-lactam hypersensitivity in methicillin-resistant S. aureus (MRSA) and S. epidermidis (MRSE). Likewise, the β-lactam antibiotic imipenem exhibits restored bactericidal activity against mnaA mutants in vitro and concomitant efficacy against 2-epimerase defective strains in a mouse thigh model of MRSA and MRSE infection. Interestingly, whereas MnaA serves as the sole 2-epimerase required for WTA biosynthesis in S. epidermidis, MnaA and Cap5P provide compensatory WTA functional roles in S. aureus. We also demonstrate that MnaA and other enzymes of WTA biosynthesis are required for biofilm formation in MRSA and MRSE. We further determine the 1.9Å crystal structure of S. aureus MnaA and identify critical residues for enzymatic dimerization, stability, and substrate binding. Finally, the natural product antibiotic tunicamycin is shown to physically bind MnaA and Cap5P and inhibit 2-epimerase activity, demonstrating that it inhibits a previously unanticipated step in WTA biosynthesis. In summary, MnaA serves as a new Staphylococcal antibiotic target with cognate inhibitors predicted to possess dual therapeutic benefit: as combination agents to restore β-lactam efficacy against MRSA and MRSE and as non-bioactive prophylactic agents to prevent Staphylococcal biofilm formation.

59 BASIC BIOLOGICAL SCIENCES↗

Wellbore Microannulus Characterization and Modeling.

Subsurface geologic formations used for extracting resources such as oil and gas can subsequently be used as a storage reservoir for the common greenhouse gas CO 2 , a concept known as Carbon Capture and Storage (CCS). Pre-existing wellbores penetrate the reservoirs where supercritical CO 2 is to be injected. These wellbores can potentially be a pathway for contamination if CO 2 leaks through wellbore flaws to an overlying aquifer or the atmosphere. Characterizing wellbore integrity and providing zonal isolation by repairing these wellbore flaws is of critical importance to the long-term isolation of CO 2 and success of CCS. This research aims to characterize the microannulus region of the cement sheath-steel casing interface in terms of its compressibility and permeability. A mock-up of a wellbore system was used for lab-scale testing. Specimens, consisting of a cement sheath cast on a steel casing with microannuli, were subjected to confining pressures and casing pressures in a pressure vessel that allows simultaneous measurement of gas flow along the axis of the specimen. The flow was interpreted as the hydraulic aperture of the microannuli. Numerical models are used to analyze stress and displacement conditions along the casing-cement interface. These numerical results provide good agreement with closed-form elastic solutions. Numerical models incorporating flaws of varying dimensions along the casing-cement interface were then developed to describe the microannulus region. A joint model is used to describe the hydraulic aperture of the microannulus region, whose mechanical stiffness is altered in response to the imposed stress state across the joint interface. The aperture-stress behavior is based upon laboratory measurements of hydraulic aperture as a function of imposed stress conditions. This investigation found that microannulus permeability can satisfactorily be described by a joint model and that the constitutive model imposed in a numerical simulation can play a significant role in the solution behavior and agreement to experimental data. Recommendations for future work include an application of the joint model with a thermally active large-scale reservoir coupled with pore pressure caused by dynamic CO 2 injection and subsequent microannulus region affects.

03 NATURAL GAS↗

Flavor Dependence of Charged Pion Fragmentation Functions

We have measured the flavor dependence of multiplicities for π + and π - production in semi-inclusive deep-inelastic scattering (SIDIS) on proton and deuteron to explore a possible charge symmetry violation in fragmentation functions. The experiment used an electron beam with energies of 10.2 and 10.6 GeV at Jefferson Lab and the Hall-C spectrometers. The electron kinematics spanned the range 0.3 < x < 0.6, 2 < Q 2 < 5.5 GeV2, and 2.2 < W < 3.2 GeV. The pion fractional momentum range was 0.3 < z < 0.7, and the transverse momentum range was 0 < p T < 0.25 GeV/c. Assuming factorization and allowing for isospin breaking, the results can be described by two “favored” and two “unfavored” effective low p T fragmentation functions that are flavor-dependent. We find each pair converges to a common flavor-independent fragmentation function at the highest W, where factorization is most applicable.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Development of an Automated Software Reliability Tester for Digital I and C

Existing nuclear facilities are in the process of upgrading analog systems to new, software- based digital components; however, the qualification of these new systems has been a significant hurdle for their implementation in the United States. This paper describes the development of a Software Reliability Tester (SRT) that will provide a means to quantify the reliability and fault tolerance of digital instrumentation and control (I and C) systems used in nuclear facilities. The SRT is comprised of hardware and software that exercise digital equipment inputs and compare the outputs to expected values to quantify system reliability. Incorporation of fault injection techniques enables the SRT to evaluate the robustness of digital I and C in the presence of abnormal conditions. The integration of both quantitative reliability and fault tolerance measures will provide the nuclear industry with an automated and systematic approach to digital I and C qualification. This will enable safer, more reliable, and more cost effective implementations of a broad spectrum of digital I and C equipment in existing and next generation nuclear facilities. This paper includes a description of the design of the SRT, including software modules and the hardware interface. In addition, an example of using the SRT to automate functional testing of a digital timer relay is presented. The SRT described in this paper provides a means to conduct efficient and robust testing for a variety of digital devices. Future plans for the SRT include integrating fault injection testing so that devices can be evaluated in the presence of off-normal conditions. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Effect of ensemble generalization on the highest-occupied Kohn-Sham eigenvalue

There are several approximations to the exchange-correlation functional in density-functional theory, which accurately predict total energy-related properties of many-electron systems, such as binding energies, bond lengths, and crystal structures. Other approximations are designed to describe potential-related processes, such as charge transfer and photoemission. However, the development of a functional which can serve the two purposes simultaneously is a long-standing challenge. Trying to address it, we employ in the current work the ensemble generalization procedure proposed by Kraisler and Kronik [Phys. Rev. Lett. 110, 126403 (2013)]. Focusing on the prediction of the ionization potential via the highest occupied Kohn-Sham eigenvalue, we examine a variety of exchange-correlation approximations: the local spin-density approximation, semi-local generalized gradient approximations, and global and local hybrid functionals. Results for a test set of 26 diatomic molecules and single atoms are presented. We find that the aforementioned ensemble generalization systematically improves the prediction of the ionization potential, for various systems and exchange-correlation functionals, without compromising the accuracy of total energy-related properties. We specifically examine hybrid functionals. These depend on a parameter controlling the ratio of semi-local to non-local functional components. The ionization potential obtained with ensemble-generalized functionals is found to depend only weakly on the parameter value, contrary to common experience with non-generalized hybrids, thus eliminating one aspect of the so-called “parameter dilemma” of hybrid functionals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cosmological constraints on exotic injection of electromagnetic energy

We compute cosmic microwave background (CMB) anisotropy constraints on exotic forms of energy injection in electromagnetic (e.m.) channels over a large range of timescales. We show that these constraints are very powerful around or just after recombination, although CMB keeps some sensitivity e.g. to decaying species with lifetimes as long as 10{sup 25} s. These bounds are complementary to CMB spectral distortions and primordial nucleosynthesis ones, which dominate at earlier timescales, as we also review here. For the first time, we describe the effects of the e.m. energy injection on the CMB power spectra as a function of the injection epoch , using the lifetime of a decaying particle as proxy. We also identify a suitable on-the-spot approximation, that can be used to derive accurate constraints, and describe its differences with the most up-to-date treatment. Our results are of interest not only for early universe relics constituting (a fraction of) the dark matter, but also for other exotic injection of e.m. radiation. For illustration, we apply our formalism to: i) Primordial black holes of mass 10{sup 13.5} g ∼< M ∼< 10{sup 16.8} g, showing that the constraints are comparable to the ones obtained from gamma-ray background studies and even dominate below ∼ 10{sup 14} g. ii) To a peculiar mass-mixing range in the sterile neutrino parameter space, complementary to other astrophysical and laboratory probes. iii) Finally, we provide a first estimate of the room for improvement left for forthcoming 21 cm experiments, comparing it with the reach of proposed CMB spectral distortion (PiXiE) and CMB angular power spectrum (CORE) missions. We show that the best and most realistic opportunity to look for this signal (or to improve over current constraints) in the 21 cm probe is to focus on the Cosmic Dawn epoch, 15 ∼< z ∼< 30, where the qualitatively unambiguous signature of a spectrum in emission can be expected for models that evade all current constraints.

79 ASTRONOMY AND ASTROPHYSICS↗

Towards an accurate description of perovskite ferroelectrics: exchange and correlation effects

Using the van der Waals density functional with C09 exchange (vdW-DF-C09), which has been applied to describing a wide range of dispersion-bound systems, we explore the physical properties of prototypical ABO 3 bulk ferroelectric oxides. Surprisingly, vdW-DF-C09 provides a superior description of experimental values for lattice constants, polarization and bulk moduli, exhibiting similar accuracy to the modified Perdew-Burke-Erzenhoff functional which was designed specifically for bulk solids (PBEsol). The relative performance of vdW-DF-C09 is strongly linked to the form of the exchange enhancement factor which, like PBEsol, tends to behave like the gradient expansion approximation for small reduced gradients. These results suggest the general-purpose nature of the class of vdW-DF functionals, with particular consequences for predicting material functionality across dense and sparse matter regimes.

36 MATERIALS SCIENCE↗

COOL-LAMPS. VII. Quantifying Strong-lens Scaling Relations with 177 Cluster-scale Strong Gravitational Lenses in DECaLS

Abstract We estimate the Einstein-radius-enclosed total mass for 177 cluster-scale strong gravitational lenses identified by the ChicagO Optically selected Lenses Located At the Margins of Public Surveys (COOL-LAMPS) collaboration with lens redshifts ranging from 0.2 ⪅ z ⪅ 1.0 using the brightest-cluster-galaxy (BCG) redshift and an observable proxy for the Einstein radius. We constrain the Einstein-radius-enclosed luminosity and stellar mass by fitting parametric spectral energy distributions to aperture photometry from the Dark Energy Camera Legacy Survey (DECaLS) in the g -, r -, and z -band Dark Energy Camera filters. We find that the BCG redshift, enclosed total mass, and enclosed luminosity are strongly correlated and well described by a planar relationship in 3D space. We find that the enclosed total mass and stellar mass are correlated with a logarithmic slope of 0.50 0 − 0.031 + 0.029 , and the enclosed total mass and stellar-to-total mass fraction are correlated with a logarithmic slope of − 0.49 5 − 0.033 + 0.032 . In tandem with the small radii within which these slopes are constrained, this may suggest invariance in baryon conversion efficiency and feedback strength as a function of cluster-centric radii in galaxy clusters. Additionally, the correlations described here should have utility in ranking strong-lensing candidates in upcoming imaging surveys—such as Rubin/Legacy Survey of Space and Time—in which an algorithmic treatment of strong lenses will be needed due to the sheer volume of data these surveys will produce.

Mork, Simon D. (ORCID:0000000255739131)↗

Modeling the Infrared Reverberation Response of the Circumnuclear Dusty Torus in AGNs: The Effects of Cloud Orientation and Anisotropic Illumination

The obscuring circumnuclear torus of dusty molecular gas is one of the major components of active galactic nuclei (AGN). The torus can be studied by analyzing the time response of its infrared (IR) dust emission to variations in the AGN continuum luminosity, a technique known as reverberation mapping. The IR response is the convolution of the AGN ultraviolet/optical light curve with a transfer function that contains information about the size, geometry, and structure of the torus. Here, we describe a new computer model that simulates the reverberation response of a clumpy torus. Given an input optical light curve, the code computes the emission of a 3D ensemble of dust clouds as a function of time at selected IR wavelengths, taking into account light travel delays. We present simulated dust emission responses at 3.6, 4.5, and 30 μ m that explore the effects of various geometrical and structural properties, dust cloud orientation, and anisotropy of the illuminating radiation field. We also briefly explore the effects of cloud shadowing (clouds are shielded from the AGN continuum source). Example synthetic light curves have also been generated, using the observed optical light curve of the Seyfert 1 galaxy NGC 6418 as input. The torus response is strongly wavelength-dependent, due to the gradient in cloud surface temperature within the torus, and because the cloud emission is strongly anisotropic at shorter wavelengths. Anisotropic illumination of the torus also significantly modifies the torus response, reducing the lag between the IR and optical variations.

79 ASTRONOMY AND ASTROPHYSICS↗

Jet fragmentation transverse momentum distributions in pp and p-Pb collisions at $ \sqrt{s}$, $\sqrt{s_{\mathrm{NN}}}$ = 5.02 TeV

Jet fragmentation transverse momentum ( j T ) distributions are measured in proton-proton (pp) and proton-lead (p-Pb) collisions at s NN = 5 . 02 TeV with the ALICE experiment at the LHC. Jets are reconstructed with the ALICE tracking detectors and electromagnetic calorimeter using the anti- k T algorithm with resolution parameter R = 0 . 4 in the pseudorapidity range |η| < 0 . 25. The j T values are calculated for charged particles inside a fixed cone with a radius R = 0 . 4 around the reconstructed jet axis. The measured j T distributions are compared with a variety of parton-shower models. Herwig and P ythia 8 based models describe the data well for the higher j T region, while they underestimate the lower j T region. The j T distributions are further characterised by fitting them with a function composed of an inverse gamma function for higher j T values (called the “wide component”), related to the perturbative component of the fragmentation process, and with a Gaussian for lower j T values (called the “narrow component”), predominantly connected to the hadronisation process. The width of the Gaussian has only a weak dependence on jet transverse momentum, while that of the inverse gamma function increases with increasing jet transverse momentum. For the narrow component, the measured trends are successfully described by all models except for Herwig. For the wide component, Herwig and PYTHIA 8 based models slightly underestimate the data for the higher jet transverse momentum region. These measurements set constraints on models of jet fragmentation and hadronisation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Drosophila models to study causative genes for human rare intractable neurological diseases

Highlights: • Drosophila models targeting some ALS-causing genes are described. • Drosophila models targeting some CMT-causing genes are described. • Drosophila models targeting some Sotos syndrome-causing genes are described. • Genes and pathways that commonly interact with ALS- and/or CMT-causing genes are described. Drosophila is emerging as a convenient model for investigating human diseases. Functional homologues of almost 75% of human disease-related genes are found in Drosophila. Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disease that causes defects in motoneurons. Charcot-Marie-Tooth disease (CMT) is one of the most commonly found inherited neuropathies affecting both motor and sensory neurons. No effective therapy has been established for either of these diseases. In this review, after overviewing ALS, Drosophila models targeting several ALS-causing genes, including TDP-43, FUS and Ubiquilin2, are described with their genetic interactants. Then, after overviewing CMT, examples of Drosophila models targeting several CMT-causing genes, including mitochondria-related genes and FIG 4, are also described with their genetic interactants. In addition, we introduce Sotos syndrome caused by mutations in the epigenetic regulator gene NSD1. Lastly, several genes and pathways that commonly interact with ALS- and/or CMT-causing genes are described. In the case of ALS and CMT that have many causative genes, it may be not practical to perform gene therapy for each of the many disease-causing genes. The possible uses of the common genes and pathways as novel diagnosis markers and effective therapeutic targets are discussed.

60 APPLIED LIFE SCIENCES↗

An Ab Initio -Derived Force Field for Amorphous Silica Interfaces for Use in Molecular Dynamics Simulations

Here, we present a classical interatomic force field, silica-DDEC, to describe the interactions of amorphous and crystalline silica surfaces, parametrized using density functional theory-based charges. Charge schemes for silica surfaces were developed using the density-derived electrostatic and chemical (DDEC) method, which reproduces atomic charges of the periodic models as well as the electrostatic potential away from the atom sites. Lennard–Jones parameters were determined by requiring the correct description of (i) the amorphous silica density, coordination defects, and local coordination geometry, relative to experimental measurements, and (ii) water-silica interatomic distances compared with ab initio results. Deprotonated surface silanol sites are also described within the model based on DDEC charges. The result is a general electronic structure-derived model for describing fully flexible amorphous and crystalline silica surfaces and interactions of liquids with silica surfaces of varying structure and protonation state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Signatures of cysteine oxidation on muscle structural and contractile proteins are associated with physical performance and muscle function in older adults: Study of Muscle, Mobility and Aging (SOMMA)

Oxidative stress is considered a contributor to declining muscle function and mobility during aging; however, the underlying molecular mechanisms remain poorly described. We hypothesized that greater levels of cysteine (Cys) oxidation on muscle proteins are associated with decreased measures of mobility. Herein, we applied a novel redox proteomics approach to measure reversible protein Cys oxidation in vastus lateralis muscle biopsies collected from 56 subjects in the Study of Muscle, Mobility and Aging (SOMMA), a community-based cohort study of individuals aged 70 years and older. We tested whether levels of Cys oxidation on key muscle proteins involved in muscle structure and contraction were associated with muscle function (leg power and strength), walking speed, and fitness (VO 2 peak on cardiopulmonary exercise testing) using linear regression models adjusted for age, sex, and body weight. Higher oxidation levels of select nebulin Cys sites were associated with lower VO 2 peak, while greater oxidation of myomesin-1, myomesin-2, and nebulin Cys sites was associated with slower walking speed. Higher oxidation of Cys sites in key proteins such as myomesin-2, alpha-actinin-2, and skeletal muscle alpha-actin were associated with lower leg power and strength. We also observed an unexpected correlation (R = 0.48) between a higher oxidation level of eight Cys sites in alpha-actinin-3 and stronger leg power. Despite this observation, the results generally support the hypothesis that Cys oxidation of muscle proteins impairs muscle power and strength, walking speed, and cardiopulmonary fitness with aging.

59 BASIC BIOLOGICAL SCIENCES↗

Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases

Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair’s identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps.

59 BASIC BIOLOGICAL SCIENCES↗

Unusual Exchange Couplings and Intermediate Temperature Weyl State in Co 3 Sn 2 S 2

Understanding magnetism and its possible correlations to topological properties has emerged to the forefront as a difficult topic in studying magnetic Weyl semimetals. Co 3 Sn 2 S 2 is a newly discovered magnetic Weyl semimetal with a kagome lattice of cobalt ions and has triggered intense interest for rich fantastic phenomena. In this study, we report the magnetic exchange couplings of Co 3 Sn 2 S 2 using inelastic neutron scattering and two density functional theory (DFT) based methods: constrained magnetism and multiple-scattering Green’s function methods. Co 3 Sn 2 S 2 exhibits highly anisotropic magnon dispersions and linewidths below T C , and paramagnetic excitations above T C . The spin-wave spectra in the ferromagnetic ground state is well described by the dominant third-neighbor “across-hexagon” J d model. Our density functional theory calculations reveal that both the symmetry-allowed 120° antiferromagnetic orders support Weyl points in the intermediate temperature region, with distinct numbers and the locations of Weyl points. Our study highlights the important role Co 3 Sn 2 S 2 can play in advancing our understanding of kagome physics and exploring the interplay between magnetism and band topology.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Probing electronic wave functions of sodium-doped clusters: Dyson orbitals, anisotropy parameters, and ionization cross-sections

We apply high-level ab initio methods to describe the electronic structure of small clusters of ammonia and dimethylether (DME) doped with sodium, which provide a model for solvated electrons. We investigate the effect of the solvent and cluster size on the electronic states. We consider both energies and properties, with a focus on the shape of the electronic wave function and the related experimental observables such as photoelectron angular distributions. The central quantity in modeling photoionization experiments is the Dyson orbital, which describes the difference between the initial N-electron and final (N-1)-electron states of a system. Dyson orbitals enter the expression of the photoelectron matrix element, which determines total and partial photoionization cross-sections. We compute Dyson orbitals for the Na(NH3)n and Na(DME)m clusters using correlated wave functions (obtained with equation-of-motion coupled-cluster model for electron attachment with single and double substitutions) and compare them with more approximate Hartree-Fock and Kohn-Sham orbitals. As a result, we also analyze the effect of correlation and basis sets on the shapes of Dyson orbitals and the experimental observables.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Development and Demonstration of a Class 6 Range-Extended Electric Vehicle for Commercial Pickup and Delivery Operation: Preprint

Range-extended hybrids are an attractive option for medium- and heavy-duty commercial vehicle fleets because they offer the efficiency of an electrified powertrain with the driving range of a conventional diesel powertrain. The vehicle essentially operates as if it was purely electric for most trips, while ensuring that all commercial routes can be completed in any weather conditions or geographic terrain. Fuel use and point-source emissions can be significantly reduced, and in some cases eliminated, as many shorter routes can be fully electrified with this architecture. Under a U.S. Department of Energy (DOE)-funded project for Medium- and Heavy-Duty Vehicle Powertrain Electrification, Cummins has developed a plug-in hybrid electric Class 6 truck with a range-extending engine designed for pickup and delivery application. The National Renewable Energy Laboratory (NREL) assisted by developing representative workday drive cycles for Class 6 operation and an adapted cycle to enable vehicle track testing. A novel, automated driving system was utilized by Southwest Research Institute (SwRI) to improve the repeatability of the track testing conducted to quantify vehicle energy consumption. Cummins used a drivetrain model to design the hybrid control system for increased fuel savings. The control system functionality and fuel savings objective of 50% or more were confirmed by track testing described in this paper.

ADVANCED PROPULSION SYSTEMS↗

A full-angle Monte-Carlo scattering technique including cumulative and single-event Rutherford scattering in plasmas [Theory of cumulative large-angle collisions in plasmas]

Here, we describe and justify a full-angle scattering (FAS) method to faithfully reproduce the accumulated differential angular Rutherford scattering probability distribution function (pdf) of particles in a plasma. The FAS method splits the scattering events into two regions. At small angles it is described by cumulative scattering events resulting, via the central limit theorem, in a Gaussian-like pdf; at larger angles it is described by single-event scatters and retains a pdf that follows the form of the Rutherford differential cross-section. The FAS method is verified using discrete Monte-Carlo scattering simulations run at small timesteps to include each individual scattering event. We identify the FAS regime of interest as where the ratio of temporal/spatial scale-of-interest to slowing-down time/length is from 10 -3 to 0.3–0.7; the upper limit corresponds to Coulomb logarithm of 20–2, respectively. Two test problems, high-velocity interpenetrating plasma flows and keV-temperature ion equilibration, are used to highlight systems where including FAS is important to capture relevant physics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗