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At least 1,171 records · Page 65

Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors

Targeted covalent inhibition represents one possible strategy to block the function of SARS-CoV-2 Main Protease (M PRO ), an enzyme that plays a critical role in the replication of the novel SARS-CoV-2. Toward the design of covalent inhibitors, we built a covalent inhibitor dataset using deep learning models followed by high throughput virtual screening of these candidates against M PRO . Two top-ranking inhibitors were selected for mechanistic investigations—one with an activated ester warhead that has a piperazine core and the other with an acrylamide warhead. Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. Simulations show that both candidates form more stable enzyme-inhibitor (E-I) complexes than the chosen NSP. It was found that both the NSP fragment and the activated ester inhibitor react with CYS145 of M PRO in a concerted manner, whereas the acrylamide inhibitor follows a stepwise mechanism. Most importantly, the reversible reaction and the subsequent hydrolysis reaction from E-I complexes are less probable when compared to the reactions with an NSP fragment, showing promise for these candidates to be the base for efficient M PRO inhibitors.

60 APPLIED LIFE SCIENCES↗

Connecting ground-state properties of 6 Li to each other and to scattering data

We examine the relationship between the asymptotic normalization coefficient (ANC) of 6 Li and other low-energy observables in the α–deuteron system. Our analysis uses a set of calculations carried out within the ab initio no core shell model with continuum (NCSMC) using a variety of inter-nucleon interactions and basis sizes, and yielding 6 Li deuteron separation energies between 1.3 and 1.8 MeV (Hebborn et al 2022 Phys. Rev. Lett. 129 042503). These NCSMC calculations show that the square of the ANC is strongly correlated with the separation energy over this range. In this work, we investigate the origin of this correlation using the phenomenological R-matrix, a single-channel potential and a perturbative approach. We show that this correlation occurs because the depth of the α–deuteron central potential changes by only a small relative amount as the separation energy varies. We then investigate if the ANC can be accurately extracted from α–deuteron phase shifts in an ideal case in which low-energy data are available and there are no experimental errors. We find that both R-matrix and Coulomb-modified effective-range theory (CM-ERE) yield extracted ANCs close to, although not exactly equal to, the NCSMC value, provided the extrapolation is constrained by the known position of the bound-state pole and at least three terms are included in the fit function. The R-matrix approach converges faster than the CM-ERE as the number of parameters increases and is also more robust against the inclusion of low-energy and high-energy phase shift data. Finally, our study also shows that a naive quantification of uncertainties by comparing different truncations used in both theories is not accurate, and suggests the accuracy of ANCs extracted from phase shift data needs further investigation.

R-matrix↗

Solving the electronic structure problem for over 100000 atoms in real space

Using a real-space high-order finite-difference approach, we investigate the electronic structure of large spherical silicon nanoclusters. Within Kohn-Sham density functional theory and using pseudopotentials, we report the self-consistent field convergence of a system with over 100000 atoms: a Si 107,641 ⁢H 9,084 nanocluster with a diameter of 16 nm. Our approach uses Chebyshev-filtered subspace iteration to speed up the convergence of the eigenspace, and blockwise Hilbert space-filling curves to speed up sparse matrix-vector multiplications, all of which are implemented in the parsec code. For the largest system, we utilized 2048 nodes (114 688 cores) on the Frontera machine in the Texas Advanced Computing Center. Our quantitative analysis of the electronic structure shows how it gradually approaches its bulk counterpart as a function of nanocluster size. The band gap is enlarged due to quantum confinement in nanoclusters, but decreases as the system size increases, as expected. In conclusion, our work serves as a proof of concept for the capacity of the real-space approach in efficiently parallelizing very large calculations using high-performance computer platforms, which can straightforwardly be replicated in other systems with more than 10 5 atoms.

0-dimensional systems↗

Electromagnetic Modeling of Lattice Structures in Additively Manufactured Electric Machines

Recent advancements in metal additive manufacturing (AM) show great potential to revolutionize the design and manufacturing of electromagnetic components used in the field of electrical engineering. Lattice structures directly printed by AM processes typically offer better structural performance with reduced weight, such as high stiffness, surface area, elongation, energy absorption, and porosity, than the solid counterpart. This paper aims to study the electromagnetic modeling of lattice structures used in additively manufactured magnetic cores or windings for electric machines. Three dimensional (3D) electromagnetic finite element (FE) analysis with high performance computing (HPC) shows the highest fidelity in predicting the electromagnetic performance of designs with lattice structures by preserving complex geometry details. FE-based homogenization methods have also been explored to potentially speed up concept design. A case study based on an additively manufactured axial-flux permanent magnet machine with a Hilbert pattern stator validates the discussed electromagnetic modeling approaches.

Chung, Shi-Uk [ANSYS, Inc.]↗

Self-Cooling Multiferroic Magnetic Devices

Increasing switching frequency reduces magnetic volume, but conventional ferrites, used from tens to hundreds of kilohertz, cannot sustain the temperature and frequency ranges demanded by current and emerging wide bandgap and ultrawide bandgap devices. Here, this work presents a novel magnetic material architecture combining nanocrystalline magnetic material and multiferroic layers for megahertz power conversion. The high saturation flux density of nanocrystalline alloys supports miniaturization but is traditionally constrained by excessive losses above 10 kHz. A revolutionary multiferroic material with solid-state cooling via caloric materials is defined that will enable the next generation of magnetic devices for wide-bandgap-integrated designs. This letter highlights the fundamental physics behind this capability alongside early development of a finite element analysis for the multiferroic-based magnetic device using ANSYS, showing that the core achieves more uniform thermal distribution and reduces peak temperature by 9 ° C compared to conventional ferrites.

Soft magnetic materials↗

Setup and verification of a SCALE/KENO platform for generic FHR benchmark calculations

The work presented in this article is preliminary to downstream analysis of a generic fluoride salt-cooled high-temperature reactor (gFHR) core performed by the University of Tennessee in collaboration with Kairos Power (KP). A Monte Carlo transport model of the publicly available gFHR equilibrium core is developed in SCALE/KENO with multigroup energy treatment. Several output quantities of interest are used to verify the simulations against a benchmark model developed by KP using the continuous energy Monte Carlo code Serpent 2. Good agreement is seen in flux and fission rate profiles with a maximum relative difference of 1.4% and 2.8% respectively. Furthermore, an effective multiplication factor bias of 44 pcm was observed between the two simulations. The fuel temperature reactivity coefficient calculated with SCALE is within uncertainty to the reference model. This verification acts as a publicly reproducible benchmark for the gFHR in SCALE/KENO. A simplified depletion model is also presented where a single fuel pebble is depleted to discharge burnup through the equilibrium core while the equilibrium core is assumed to be invariant. This method produces results that intercept the equilibrium core concentrations in every case, however, an interesting artifact of this particular depletion model is uncovered. The phenomenon is shown to be a fundamental feature of the differential rate equations and inspires questions about how this system behaves when the time evolution of the equilibrium core is considered. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data

The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, carbohydrates, lipids, lignins, hydrocarbons, phytochemicals and other compounds. Thus, there is a growing demand for informatics tools to analyze FT-MS data that will aid investigators seeking to understand the availability of carbon compounds to biotic and abiotic oxidation and to compare fundamental chemical properties of complex samples across groups. We present ftmsRanalysis, an R package which provides an extensive collection of data formatting and processing, filtering, visualization, and sample and group comparison functionalities. The package provides a suite of plotting methods and enables expedient, flexible and interactive visualization of complex datasets through functions which link to a powerful and interactive visualization user interface, Trelliscope. Example analysis using FT-MS data from a soil microbiology study demonstrates the core functionality of the package and highlights the capabilities for producing interactive visualizations.

97 MATHEMATICS AND COMPUTING↗

Potential use of ceramic coating as a thermal insulation on cooled turbine hardware

An analysis was made to determine the potential benefits of using a ceramic thermal insulation coating of calcia-stabilized zirconia on cooled engine parts. The analysis was applied to turbine vanes of a high temperature and high pressure core engine and a moderate temperature and low pressure research engine. Measurements made during engine operation showed that the coating substantially reduced vane metal wall temperatures. Evaluation of the durability of the coating on turbine vanes and blades in a furnace and engine were encouraging.

Liebert, C. H.↗

Experimental clean combustor program: Noise study

Under a Noise Addendum to the NASA Experimental Clean Combustor Program (ECCP) internal pressure fluctuations were measured during tests of JT9D combustor designs conducted in a burner test rig. Measurements were correlated with burner operating parameters using an expression relating farfield noise to these parameters. For a given combustor, variation of internal noise with operating parameters was reasonably well predicted by this expression but the levels were higher than farfield predictions and differed significantly among several combustors. For two burners, discharge stream temperature fluctuations were obtained with fast-response thermocouples to allow calculation of indirect combustion noise which would be generated by passage of the temperature inhomogeneities through the high pressure turbine stages of a JT9D turbofan engine. Using a previously developed analysis, the computed indirect combustion noise was significantly lower than total low frequency core noise observed on this and several other engines.

Sofrin, T. G.↗

Comments on the Venus rotation pole

Possible orientations of the Venus rotation pole as a function of planetary oblateness are calculated, taking into account the variation of the orbital inclination and motion of the nodal line produced by long-term planetary perturbations and assuming the obliquity to be fully damped. If the obliquity is stabilized against solar tides by core-mantle viscous coupling, a fully damped obliquity is the expected state. An analysis of earth-based radar data from 1964 to 1977 yields a pole position which lies near damped pole positions of small oblateness, no more than about 10 to the 6th. Possible implications of this result are considered.

Ward, W. R.↗

The Geopotential Research Mission - Mapping the near earth gravity and magnetic fields

The Geopotential Research Mission (GRM), NASA's low-level satellite system designed to measure the gravity and magnetic fields of the earth, and its objectives are described. The GRM will consist of two, Shuttle launched, satellite systems (300 km apart) that will operate simultaneously at a 160 km circular-polar orbit for six months. Current mission goals include mapping the global geoid to 10 cm, measuring gravity-field anomalies to 2 mgal with a spatial resolution of 100 km, detecting crustal magnetic anomalies of 100 km wavelength with 1 nT accuracy, measuring the vectors components to + or - 5 arc sec and 5 nT, and computing the main dipole or core field to 5 nT with a 2 nT/year secular variation detection. Resource analysis and exploration geology are additional applications considered.

Taylor, P. T.↗

Inverting travel times with a triplication

A method based on the use of constrained spline fits is used to overcome the difficulties arising when body-wave data in the form of T-delta are reduced to the tau-p form in the presence of cusps. In comparison with unconstrained spline fits, the method proposed here tends to produce much smoother models which lie approximately in the middle of the bounds produced by the extremal method. The method is noniterative and, therefore, computationally efficient. The method is applied to the lunar seismic data, where at least one triplication is presumed to occur in the P-wave travel-time curve. It is shown, however, that because of an insufficient number of data points for events close to the antipode of the center of the lunar network, the present analysis is not accurate enough to resolve the problem of a possible lunar core.

Jarosch, H. S.↗

Continuum radiation from active galactic nuclei: A statistical study

The physics of the continuum spectrum of active galactic nuclei (AGNs) was examined using a large data set and rigorous statistical methods. A data base was constructed for 469 objects which include radio selected quasars, optically selected quasars, X-ray selected AGNs, BL Lac objects, and optically unidentified compact radio sources. Each object has measurements of its radio, optical, X-ray core continuum luminosity, though many of them are upper limits. Since many radio sources have extended components, the core component were carefully selected out from the total radio luminosity. With survival analysis statistical methods, which can treat upper limits correctly, these data can yield better statistical results than those previously obtained. A variety of statistical tests are performed, such as the comparison of the luminosity functions in different subsamples, and linear regressions of luminosities in different bands. Interpretation of the results leads to the following tentative conclusions: the main emission mechanism of optically selected quasars and X-ray selected AGNs is thermal, while that of BL Lac objects is synchrotron; radio selected quasars may have two different emission mechanisms in the X-ray band; BL Lac objects appear to be special cases of the radio selected quasars; some compact radio sources show the possibility of synchrotron self-Compton (SSC) in the optical band; and the spectral index between the optical and the X-ray bands depends on the optical luminosity.

Isobe, T.↗

Early Archean spherule beds of possible impact origin from Barberton, South Africa: A detailed mineralogical and geochemical study

The Barberton Greenstone belt is a 3.5- to 3.2-Ga-old formation situated in the Swaziland Supergroup near Barberton, northeast Transvaal, South Africa. The belt includes a lower, predominantly volcanic sequence, and an upper sedimentary sequence (e.g., the Fig Tree Group). Within this upper sedimentary sequence, Lowe and Byerly identified a series of different beds of spherules with diameters of around 0.5-2 mm. Lowe and Byerly and Lowe et al. have interpreted these spherules to be condensates of rock vapor produced by large meteorite impacts in the early Archean. We have collected a series of samples from drill cores from the Mt. Morgan and Princeton sections near Barberton, as well as samples taken from underground exposures in the Sheba and Agnes mines. These samples seem much better preserved than the surface samples described by Lowe and Byerly and Lowe et al. Over a scale of just under 30 cm, several well-defined spherule beds are visible, interspaced with shales and/or layers of banded iron formation. Some spherules have clearly been deposited on top of a sedimentary unit because the shale layer shows indentions from the overlying spherules. Although fresher than the surface samples (e.g., spherule bed S-2), there is abundant evidence for extensive alteration, presumably by hydrothermal processes. In some sections of the cores sulfide mineralization is common. For our mineralogical and petrographical studies we have prepared detailed thin sections of all core and underground samples (as well as some surface samples from the S-2 layer for comparison). For geochemical work, layers with thicknesses in the order of 1-5 mm were separated from selected core and underground samples. The chemical analyses are being performed using neutron activation analysis in order to obtain data for about 35 trace elements in each sample. Major elements are being determined by XRF and plasma spectrometry. To clarify the history of the sulfide mineralization, sulfur isotopic compositions are being determined.

Koeberl, Christian↗

Interlaminar stress analysis at the skin-stiffener interface of a grid-stiffened composite panel

Results are presented of an analysis of the interlaminar stress components at the skin-wrap, skin-core, and wrap-core interfaces for an advanced-concept stiffened panel using a global/local finite element procedure. The procedure consists of a global model of two-dimensional shell elements that is used to design a grid-stiffened panel with blade-type stiffeners, a local model of three-dimensional solid elements that is used to compute interlaminar stress components, and a scheme devised to assign displacement boundary conditions for the local model that are derived from displacement and rotation data of a few nodes of the global model. The interlaminar stresses for this panel design were found to be well below typical tensile normal and shearing strengths of a graphite-epoxy material.

Wiggenraad, J. F. M.↗

Raman Study of Uncoated and p-BN/SiC-Coated Hi-Nicalon Fiber-Reinforced Celsian Matrix Composites: Distribution and Nanostructure of Different Phases - Part 1

Hi-Nicalon fiber reinforced celsian matrix composites were characterized by Raman spectroscopy and imaging, using several laser wavelengths. Composite #1 is reinforced by as-received fibers while coatings of p-BN and SiC protect the fibers in composite #2. The matrix contains traces of the hexagonal phase of celsian, which is concentrated in the neighborhood of fibers in composite #1. Some free silicon was evident in the coating of composite #2 which might involve a {BN + SiC yields BNC + Si} "reaction" at the p-BN/SiC interface. Careful analysis of C-C peaks revealed no abnormal degradation of the fiber core in the composites.

Gouadec, Gwenael↗

The Conference Proceedings of the 2003 Air Transport Research Society (ATRS) World Conference, Volume 5

The UNO Aviation Institute Monograph Series began in 1994 as a key component of the education outreach and information transfer missions of the Aviation Institute and the NASA Nebraska Space Grant & EPSCoR Programs. The series is an outlet for aviation materials to be indexed and disseminated through an efficient medium. Publications are welcome in all aspects of aviation. Publication formats may include, but are not limited to, conference proceedings, bibliographies, research reports, manuals, technical reports, and other documents that should be archived and indexed for future reference by the aviation and world wide communities. The Conference proceedings of the 2003 Air Transport Research Society (ATRS) world conference, volume 5 is presented. The topics include: 1) The Temporal Configuration of Airline Networks in Europe; 2) Determination and Applications of Environmental Costs at Different Sized Airports-Aircraft Noise and Engine Emissions; 3) Cost Effective Measures to Reduce CO2 Emissions in the Air Freight Sector; 4) An Assessment of the Sustainability of Air Transport System: Quantification of Indicators; 5) Regulation, Competition and Network Evolution in Aviation; 6) Regulation in the Air: Price and Frequency Cap; 7) Industry Consolidation and Future Airline Network Structures in Europe; 8) Application of Core Theory to the U.S. Airline Industry; 9) Air Freight Transshipment Route Choice Analysis; 10) A Fuzzy Approach of the Competition on Air Transport Market; and 11) Developing Passenger Demand Models for International Aviation from/to Egypt: A Case Study of Cairo Airport and Egyptair.

Bowen, Brent↗