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DOE OSTI2015

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Two-stage crash process in resistive drift ballooning mode driven ELM crash

We report a two-stage crash process in edge localized mode (ELM) driven by resistive drift-ballooning modes (RDBMs) numerically simulated in a full annular torus domain with a scale-separated four-field reduced MHD (RMHD) model using the BOUT++ framework. In the early nonlinear phase, the small first crash is triggered by linearly unstable RDBMs, and m/n=2/1 magnetic islands are nonlinearly excited by nonlinear coupling of RDBMs as well as their higher harmonics. Here, m is the poloidal mode number, n is the toroidal mode number, the q = 2 rational surface exists near the pressure gradient peak, and q is the safety factor. Simultaneously, middle-n RDBM turbulence develops but is poloidally localized around X-points of the magnetic islands, leading to the small energy loss. The second large crash occurs in the late nonlinear phase. Higher harmonics of m/n=2/1 magnetic islands well develop around the q = 2 surface via nonlinear coupling and make the magnetic field stochastic by magnetic island overlapping. Turbulence heat transport develops at X-points of higher harmonics of m/n=2/1 magnetic islands, resulting in the turbulence spreading in the poloidal direction. The large second crash is triggered when the turbulence covers the whole poloidal region so that the magnetic island generation and magnetic field stochastization before the large crash can be interpreted as ELM precursors. It is concluded that the ELM trigger is attributed to the turbulent spreading in the poloidal direction in synchronization with the magnetic field stochastization and the crash is driven by E × B convection rather than the conventional Rechester–Rosenbluth anomalous electron heat transport.

Seto, H. (ORCID:0000000259278643)↗

DOE OSTI2015

Dense and half-dense NiZnCo ferrite ceramics: Their respective relevance for antenna downsizing, according to their dielectric and magnetic properties at microwave frequencies

Spinel ferrite Ni{sub 0.5}Zn{sub 0.3}Co{sub 0.2}Fe{sub 1.98}O{sub 4−x} nanoparticles were synthesized by co-precipitation method, and samples were realized by moulding and annealing at key temperatures (T{sub M} = 800 °C, 900 °C, 1050 °C, determined beforehand through shrinkage measurements) going with calcining and sintering processes. Annealing at 800 °C and 900 °C led to half-dense ceramics (porosity ∼50 vol. %), whereas bulky ferrite was obtained after annealing at 1050 °C. Elemental analysis, X-ray diffraction and ion chromatography analysis were performed. Complex dielectric permittivity (ε*) and magnetic permeability (μ*) were investigated up to 6 GHz. With increasing T{sub M}, a decreasing amount of Fe{sup 2+} was observed, going with increasing sample density. Coupled effects of the Fe{sup 2+} concentration and of the porosity, both on dielectric and magnetic properties, were chiefly investigated and discussed. The materials show almost constant permittivities (ε′ = 5.0, 6.0, and 14.8 for T{sub M} = 800 °C, 900 °C and 1050 °C, respectively). The bulk value at f = 1 GHz (ε′ = 14.8) can be interpreted well according to Shannon's theory. The permittivities of the half-dense ceramics are discussed on the basis of Bruggeman's Effective Medium Theory. The materials annealed at 800 °C and 900 °C show almost constant magnetic permeabilities in the frequency range from 0.2 to 1 GHz (μ′ = 3.4 and 6.0 for T{sub M} = 800 °C and 900 °C). The observed permeability behavior is typical of monodomain particles, except for the sample annealed at 1050 °C, for which domain wall contribution to μ* is suspected because of non-negligible losses at low frequency (μ″ = 1.3–1.8 at f < 0.3 GHz). This finding is supported by estimations of the upper and lower values for the critical grain size, on the basis of Brown–Van der Zaag's theory. Facing bulk ceramics, and in view of using Ni{sub 0.5}Zn{sub 0.3}Co{sub 0.2}Fe{sub 1.98}O{sub 4−x} ferrite as substrate for antenna miniaturization, the electromagnetic properties of half-dense ceramics materials seem to be very competitive at frequencies beyond 0.2 GHz, and up to 0.7–0.8 GHz.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Magneto-Structural Combined Dimensional and Topology Optimization of Interior Permanent Magnet Synchronous Machine Rotors

A magneto-structural combined dimensional and topology optimization approach for interior permanent magnet synchronous machine (IPMSM) rotor design is proposed using the Solid Isotropic Material Penalization (SIMP) density-based topology optimization method. This method optimizes the location and dimensions of the permanent magnets (PMs) embedded in the rotor, while simultaneously optimizing the lamination flux barriers using topology optimization.To allow for the location and dimensions of the PMs to change while retaining the same number of mesh elements and connectivity, the mesh must be deformed. Mesh deformation is accomplished using a Laplace smoothing technique. To increase the range of PM displacement and size changes, the non-PM areas of the rotor design domain are divided into sub-regions along whose boundaries the mesh nodes are redistributed also using a Laplace smoothing algorithm. Three examples of IPMSM rotor optimizations are presented to demonstrate the proposed approach.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2020

Macroscale Control of Reactivity using 3D Printed Materials with Intrinsic Catalytic Properties

The morphology of heterogeneous catalysts can impact their performance. However, standard manufacturing methods like extrusion or pelleting offer little options for tailoring catalyst shape. Herein, stereolithographic 3D printing is used to produce catalysts with controlled topologies to enhance their performance. A series of magnetic stir-bar compartments (SBC) were 3D printed and tested as catalysts for sucrose hydrolysis. The SBC were printed using acrylic acid (AA) and 1,6-hexanediol diacrylate (HDDA) as acid sites and hydrophobic crosslinking domains, respectively. Variations in the number and tilt direction of the SBC blades produced significant changes in their apparent catalytic activities. These changes resulted from differences in the fraction of active surface effectively interacting with the reactants in solution, as revealed by computational fluid dynamics simulations. Moreover, varying HDDA:AA ratios in SBC regulated reactant-surface interactions to control catalytic activity. Overall, 3D printing catalysts enables quick performance optimization by simultaneously controlling macroscopic structure and molecular composition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Benchmarking collective effects of electron interactions in a wiggler with OPAL-FEL

OPAL-FEL is a recently developed tool for the modeling of particle accelerators containing wigglers or undulators. It extends the well established 3D electrostatic particle-tracking code OPAL, by merging it with the finite-difference time-domain electromagnetic solver MITHRA. We present results of two benchmark cases where OPAL-FEL simulations are compared to experimental results. Both experiments concern electron beamlines where the longitudinal phase space is modulated with a short magnetic wiggler. Good agreement was found in both the space charge and radiation dominated regimes.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

Multiplexed profiling of transcriptional regulators in plant cells

Transcriptional regulators play key roles in plant growth, development and environmental responses; however, understanding how their regulatory activity is encoded at the protein level has been hindered by a lack of multiplexed large-scale methods to characterize protein libraries in planta. Here we present enrichment of nuclear trans-elements reporter assay in plants with sequencing (ENTRAP-seq), a high-throughput method that introduces protein-coding libraries into plant cells to drive a nuclear magnetic sorting-based reporter, enabling multiplexed measurement of regulatory activity from thousands of protein variants. Using ENTRAP-seq and machine learning, we screen 1,495 plant viruses and identify hundreds of putative transcriptional regulatory domains found in structural proteins and enzymes not associated with gene regulation. In addition, we combine ENTRAP-seq with machine-guided design to engineer the activity of a plant transcription factor in a semirational fashion. Our findings demonstrate how scalable protein function assays deployed in planta will enable the characterization of natural and synthetic coding diversity in plants.

Alamos, Simon↗

DOE OSTI2019

Intense intermittent radiation at the plasma frequency on EAST

Intense intermittent radiation has been observed regularly in EAST plasmas herein. The duration of radiation bursts is with a characterization time of a few microseconds. The radiation is very intense, with an equivalent radiation temperature higher than the electron cyclotron emission by a few orders of magnitude. An electron density threshold exists to terminate the bursts, and it is strongly dependent on the toroidal magnetic field. The radiation frequency $f$ is at the plasma frequency, and the frequency bandwidth $Δf$ is very narrow (~1.5 MHz FWHM, $Δf /f$ ~3 × 10 –5 ). The fine structure of the spectrum in the frequency domain has been observed, and the frequency spacing is around 3 MHz. The cavity modes model is capable of explaining the radiation frequency and the frequency spacing. However, a quantitative and complete description of this phenomenon is still lacking.

&#969 pe bursts↗

DOE OSTI2017

Growth and structural characterization of large superconducting crystals of La 2 - x Ca 1 + x Cu 2 O 6

Large crystals of La 2 - x Ca 1 + x Cu 2 O 6 (La-Ca-2126) with x = 0:10 and 0.15 have been grown and converted to bulk superconductors by high-pressure oxygen annealing. The superconducting transition temperature, T c , is as high as 55 K; this can be raised to 60 K by post-annealing in air. Here we present structural and magnetic characterizations of these crystals using neutron scattering and muon spin rotation techniques. While the as-grown, non-superconducting crystals are single phase, we nd that the superconducting crystals contain 3 phases forming coherent domains stacked along the c axis: the dominant La-Ca-2126 phase, very thin (1.5 unit-cell) intergrowths of La 2 CuO 4 , and an antiferromagnetic La 8 Cu 8 O 20 phase. We propose that the formation and segregation of the latter phases increases the Ca concentration of the La-Ca-2126, thus providing the hole-doping that supports superconductivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Atomic-scale visualization of topological spin textures in the chiral magnet MnGe

Peeking into magnetic textures Topological spin textures hold promise as robust carriers of information and have been observed in bulk materials with a specific crystal structure. One of these materials, manganese germanide (MnGe), exhibits unusual textures in bulk form. Repicky et al . used spin-polarized scanning tunneling microscopy to study surface magnetism in thin films of MnGe. Achieving high spatial resolution, the researchers observed stripe-like features consistent with a helical state. In regions where the film was slightly curved due to strain, the intersection of domain walls led to characteristic closed patterns that could be manipulated with current/voltage pulses. —JS

Science & Technology - Other Topics↗

DOE OSTI2018

Effects of Laser-Cutting and Spark Erosion Techniques and Heat Treatment on the Magnetic Properties of Grain-Oriented Transformer Steels

Spark erosion and laser-cutting processes were examined in terms of their effects on the magnetic properties of grain-oriented electrical steels at working frequencies. The maximum permeability value in each case was considered a reference to determine the quantitative effect of cutting and eroding methods as well as the effects of heat treatment. To minimize the deterioration that appears after the piercing process is implemented, the specimens were subjected to heat treatment at the most appropriate temperature. The influence of stress-relief annealing could be observed throughout the domain refinement on the surface by using magneto-optical Kerr microscopy. Additionally, it was clearly seen that the domain contrast at the cut edge of the spark-eroded sample was more uniform than that provided by laser cutting upon applying a high AC-field amplitude.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Electromagnetic wave attenuation measurements in a ring-shaped inductively coupled air plasma

An aerocraft with the surface, inlet and radome covered large-area inductive coupled plasma (ICP) can attenuate its radar echo effectively. The shape, thickness, and electron density (N{sub e}) distribution of ICP are critical to electromagnetic wave attenuation. In the paper, an air all-quartz ICP generator in size of 20 × 20 × 7 cm{sup 3} without magnetic confinement is designed. The discharge results show that the ICP is amorphous in E-mode and ring-shaped in H-mode. The structure of ICP stratifies into core region and edge halo in H-mode, and its width and thickness changes from power and pressure. Such phenomena are explained by the distribution of RF magnetic field, the diffusion of negative ions plasma and the variation of skin depth. In addition, the theoretical analysis shows that the N{sub e} achieves nearly uniform within the electronegative core and sharply steepens in the edge. The N{sub e} of core region is diagnosed by microwave interferometer under varied conditions (pressure in range of 10–50 Pa, power in 300–700 W). Furthermore, the electromagnetic wave attenuation measurements were carried out with the air ICP in the frequencies of 4–5 GHz. The results show that the interspaced ICP is still effective to wave attenuation, and the wave attenuation increases with the power and pressure. The measured attenuation is approximately in accordance with the calculation data of finite-different time-domain simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Thermal transport across nanoscale damage profile in sapphire irradiated by swift heavy ions

In this work, we studied the degradation of thermal conductivity in single crystal sapphire (α-Al 2 O 3 ) irradiated by 167 MeV Xe swift heavy ions (SHIs) over the multiple fluences in the range of 10 12 –10 14 ions/cm 2 . Thermal conductivity was measured primarily in the cross-plane direction using a noncontact ultrafast optical pump-probe technique called picosecond time domain thermoreflectance (TDTR). Multiple samples with variable ion fluences allowed us to probe distinct regions resulting from different regimes of microstructure evolution caused by electronic energy loss. By tuning the penetration depth of the thermal waves using different modulation frequencies, two regions with distinct conductivities were identified and the values of which were found to be consistent with phonon-mediated thermal transport models while the microstructure was confirmed by electron microscopy characterization. These damaged regions were determined to be a several micrometer thick ion track region and several tens of nanometer-thick amorphous layer present only above 5.0 × 10 13 ions/cm 2 . These results demonstrate the applicability of TDTR to resolve thermal transport behavior in SHI irradiated oxides having nonhomogeneous damage profile on a nanometer scale. The presented approach facilitates future studies aiming at resolving the impact of distinct damage resulting from electronic and nuclear stopping regimes under irradiation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Multivariate Machine Learning Models of Nanoscale Porosity from Ultrafast NMR Relaxometry

Abstract Nanoporous materials are of great interest in many applications, such as catalysis, separation, and energy storage. The performance of these materials is closely related to their pore sizes, which are inefficient to determine through the conventional measurement of gas adsorption isotherms. Nuclear magnetic resonance (NMR) relaxometry has emerged as a technique highly sensitive to porosity in such materials. Nonetheless, streamlined methods to estimate pore size from NMR relaxometry remain elusive. Previous attempts have been hindered by inverting a time domain signal to relaxation rate distribution, and dealing with resulting parameters that vary in number, location, and magnitude. Here we invoke well‐established machine learning techniques to directly correlate time domain signals to BET surface areas for a set of metal‐organic frameworks (MOFs) imbibed with solvent at varied concentrations. We employ this series of MOFs to establish a correlation between NMR signal and surface area via partial least squares (PLS), following screening with principal component analysis, and apply the PLS model to predict surface area of various nanoporous materials. This approach offers a high‐throughput, non‐destructive way to assess porosity in c.a. one minute. We anticipate this work will contribute to the development of new materials with optimized pore sizes for various applications.

Fricke, Sophia N.↗

DOE OSTI2024

Multivariate Machine Learning Models of Nanoscale Porosity from Ultrafast NMR Relaxometry

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Discovery of very high energy γ-ray emission from the blazar 1ES 0033+595 by the MAGIC telescopes

The number of known very high energy (VHE) blazars is ~50, which is very small in comparison to the number of blazars detected in other frequencies. This situation is a handicap for population studies of blazars, which emit about half of their luminosity in the γ-ray domain. Moreover, VHE blazars, if distant, allow for the study of the environment that the high-energy γ-rays traverse in their path towards the Earth, like the extragalactic background light (EBL) and the intergalactic magnetic field (IGMF), and hence they have a special interest for the astrophysics community. In this papaer, we present the first VHE detection of 1ES 0033+595 with a statistical significance of 5.5σ. The VHE emission of this object is constant throughout the MAGIC observations (2009 August and October), and can be parametrized with a power law with an integral flux above 150 GeV of (7.1 ± 1.3) × 10 -12 photons cm -2 s -1 and a photon index of (3.8 ± 0.7). We model its spectral energy distribution (SED) as the result of inverse Compton scattering of synchrotron photons. For the study of the SED, we used simultaneous optical R-band data from the KVA telescope, archival X-ray data by Swift as well as INTEGRAL, and simultaneous high-energy (HE, 300 MeV–10 GeV) γ-ray data from the Fermi Large Area Telescope (LAT) observatory. Using the empirical approach of Prandini et al. (2010) and the Fermi LAT and MAGIC spectra for this object, we estimate the redshift of this source to be 0.34 ± 0.08 ± 0.05. Also, this is a relevant result because this source is possibly one of the 10 most distant VHE blazars known to date, and with further (simultaneous) observations could play an important role in blazar population studies, as well as future constraints on the EBL and IGMF.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Application of mesh refinement to relativistic magnetic reconnection

During relativistic magnetic reconnection, antiparallel magnetic fields undergo a rapid change in topology, releasing a large amount of energy in the form of non-thermal particle acceleration. This work explores the application of mesh refinement to 2D reconnection simulations to efficiently model the inherent disparity in length-scales. We have systematically investigated the effects of mesh refinement and determined necessary modifications to the algorithm required to mitigate non-physical artifacts at the coarse–fine interface. We have used the ultrahigh-order pseudo-spectral analytical time-domain Maxwell solver to analyze how its use can mitigate the numerical dispersion that occurs with the finite-difference time-domain (or “Yee”) method. Absorbing layers are introduced at the coarse–fine interface to eliminate spurious effects that occur with mesh refinement. We also study how damping the electromagnetic fields and current density in the absorbing layer can help prevent the non-physical accumulation of charge and current density at the coarse–fine interface. Using a mesh refinement ratio of 8 for two-dimensional magnetic reconnection simulations, we obtained good agreement with the high-resolution baseline simulation, using only 36% of the macroparticles and 71% of the node-hours needed for the baseline. The methods presented here are especially applicable to 3D systems where higher memory savings are expected than in 2D, enabling comprehensive, computationally efficient 3D reconnection studies in the future.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2015

Radiation comb generation with extended Josephson junctions

We propose the implementation of a Josephson radiation comb generator based on an extended Josephson junction subject to a time dependent magnetic field. The junction critical current shows known diffraction patterns and determines the position of the critical nodes when it vanishes. When the magnetic flux passes through one of such critical nodes, the superconducting phase must undergo a π-jump to minimize the Josephson energy. Correspondingly, a voltage pulse is generated at the extremes of the junction. Under periodic driving, this allows us to produce a comb-like voltage pulses sequence. In the frequency domain, it is possible to generate up to hundreds of harmonics of the fundamental driving frequency, thus mimicking the frequency comb used in optics and metrology. We discuss several implementations through a rectangular, cylindrical, and annular junction geometries, allowing us to generate different radiation spectra and to produce an output power up to 10 pW at 50 GHz for a driving frequency of 100 MHz.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗