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At least 1,171 records · Page 65

Nonenzymatic RNA copying with a potentially primordial genetic alphabet

Nonenzymatic RNA copying is thought to have been responsible for the replication of genetic information during the origin of life. However, chemical copying with the canonical nucleotides (A, U, G, and C) strongly favors the incorporation of G and C and disfavors the incorporation of A and especially U because of the stronger G:C vs. A:U base pair and the weaker stacking interactions of U. Recent advances in prebiotic chemistry suggest that the 2-thiopyrimidines were precursors to the canonical pyrimidines, raising the possibility that they may have played an important early role in RNA copying chemistry. Furthermore, 2-thiouridine (s 2 U) and inosine (I) form by deamination of 2-thiocytidine (s 2 C) and A, respectively. We used thermodynamic and crystallographic analyses to compare the I:s 2 C and A:s 2 U base pairs. We find that the I:s 2 C base pair is isomorphic and isoenergetic with the A:s 2 U base pair. The I:s 2 C base pair is weaker than a canonical G:C base pair, while the A:s 2 U base pair is stronger than the canonical A:U base pair, so that a genetic alphabet consisting of s 2 U, s 2 C, I, and A generates RNA duplexes with uniform base pairing energies. Consistent with these results, kinetic analysis of nonenzymatic template-directed primer extension reactions reveals that s 2 C and s 2 U substrates bind similarly to I and A in the template, and vice versa. Our work supports the plausibility of a potentially primordial genetic alphabet consisting of s 2 U, s 2 C, I, and A and offers a potential solution to the long-standing problem of biased nucleotide incorporation during nonenzymatic template copying.

Science & Technology - Other Topics↗

Hund’s flat band in a frustrated spinel oxide

Electronic flat bands associated with quenched kinetic energy and heavy electron mass have attracted great interest for promoting strong electronic correlations and emergent phenomena such as high-temperature charge fractionalization and superconductivity. Intense experimental and theoretical research has been devoted to establishing the rich nontrivial metallic and heavy fermion phases intertwined with such localized electronic states. Here, in this study, we investigate the transition metal oxide spinel LiV 2 O 4 , an enigmatic heavy fermion compound lacking localized f orbital states. We use angle-resolved photoemission spectroscopy and dynamical mean-field theory to reveal a kind of correlation-induced flat band with suppressed interatomic electron hopping arising from intra-atomic Hund’s coupling. The appearance of heavy quasiparticles is ascribed to a proximate orbital-selective Mott state characterized by fluctuating local moments as evidenced by complementary magnetotransport measurements. The spectroscopic fingerprints of long-lived quasiparticles and their disappearance with increasing temperature further support the emergence of a high-temperature “bad” metal state observed in transport data. This work resolves a long-standing puzzle on the origin of heavy fermion behavior and unconventional transport in LiV 2 O 4 . Simultaneously, it opens a path to achieving flat bands through electronic interactions in d-orbital systems with geometrical frustration, potentially enabling the realization of exotic phases of matter such as the fractionalized Fermi liquids.

36 MATERIALS SCIENCE↗

Zymogen and activated protein C have similar structural architecture

Activated protein C is a trypsin-like protease with anticoagulant and cytoprotective properties that is generated by thrombin from the zymogen precursor protein C in a reaction greatly accelerated by the cofactor thrombomodulin. The molecular details of this activation remain elusive due to the lack of structural information. We now fill this gap by providing information on the overall structural organization of these proteins using single molecule Förster resonance energy transfer and small angle X-ray scattering. Under physiological conditions, both zymogen and protease adopt a conformation with all domains vertically aligned along an axis 76 Å long and maximal particle size of 120 Å. This conformation is stabilized by binding of Ca 2+ to the Gla domain and is affected minimally by interaction with thrombin. Hence, the zymogen protein C likely interacts with the thrombin-thrombomodulin complex through a rigid body association that produces a protease with essentially the same structural architecture. This scenario stands in contrast to an analogous reaction in the coagulation cascade where conversion of the zymogen prothrombin to the protease meizothrombin by the prothrombinase complex is linked to a large conformational transition of the entire protein. The presence of rigid EGF domains in protein C as opposed to kringles in prothrombin likely accounts for the different conformational plasticity of the two zymogens. The new structural features reported here for protein C have general relevance to vitamin K-dependent clotting factors containing EGF domains, such as factors VII, IX, and X.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interferometric measurements of graphene-based membranes for micromechanical applications

Recent studies on piezoelectricity in 2D materials, such as graphene, have revealed their potential in multiple applications including microelectromechanical systems. Herein, we reveal piezoelectricity in few-layer graphene sheets deposited on amorphous Si 3 N 4 membranes. The response in the center of square membrane of 6.7 × 6.7 mm 2 size reaches about 14 nm at resonance and could be further enhanced by adjusting the composite structure. Resonance piezoelectric phenomena are fully consistent with the earlier piezoresponse force microscopy observations on free-standing piezoelectric graphene and open up a possibility of using 2D materials in micromechanical applications.

36 MATERIALS SCIENCE↗

An efficient random-sampling method for calculating double occupancy of Gutzwiller wave function in single-band 1D and 2D lattices

In this paper, we report a random sampling method for computing the expectation value of physical quantities based on the Gutzwiler variational wave function. As the first application, we calculated the double occupancy, which is a critical quantity for under- standing the correlation effects in many-body systems, for single-band 1D and 2D lattices. We demonstrated that the random sampling scheme is more efficient than an existing Metropolis Monte-Carlo algorithm. For the 1D Hubbard model with only nearest-neighbor hopping, our results are almost identical to the exact analytic solution. We have also studied systems to which analytic solutions are not available, including the 1D lattices with next-nearest-neighbor hopping and 2D lattices. In addition, constraints on real-space con gurations can be easily implemented in the current scheme to further improve the Gutzwiller wave function. As an example, we calculated the double occupancy for 1D Hubbard model by applying the constraint that all double-occupied sites are paired with an empty site. With enhanced correlation between double-occupied and empty sites, the constraint results in much improved ground-state energy for 1D Hubbard model with strong on-site repulsion.

74 ATOMIC AND MOLECULAR PHYSICS↗

Separate-Effects Tests for Studying Temperature-Gradient-Driven Cracking in UO 2 Pellets

We report a variety of normal operation and accident scenarios can generate thermal stresses large enough to cause cracking in light-water reactor (LWR) fuel pellets. Cracking of fuel pellets can lead to reduced heat removal, higher centerline temperatures, and localized stress in cladding, all of which impact fuel performance. It is important to experimentally characterize the thermal and mechanical behavior in the pellet before and after cracking to improve cracking models in fuel performance codes. However, in-reactor observation and measurement of cracking is very challenging due to the harsh environment and logistics. Recently, an experimental pellet cracking test stand was developed for separate effects testing of normal operations and accident temperature conditions, using thermal imaging to capture the pellet surface temperature for evaluation of thermal stresses and optical imaging to capture the evolution of cracking in real time. Experiments were performed using depleted uranium dioxide (UO 2 ) pellets, which are useful for collecting data valuable for development and validation of cracking models. A combination of induction and resistance heating was used to create an average temperature gradient of 236°C/cm and 193°C/cm before and after cracking respectively. Characterization of the pellets were done before as well as after cracking. The cracking patterns are somewhat different than those expected in a typical reactor because of the differences in thermal conditions and pellet microstructure. However, if the actual conditions of these experiments are reproduced in computational models, these out-of-pile tests on UO 2 pellets provide relevant data for modeling purposes.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Photonuclear Production of 67 Cu From Gallium

Copper-67 is a radioisotope of interest for medical imaging and therapy as well as for under- standing stellar and interstellar evolution pertaining to the formation of proton-rich nuclei. Since 67 Cu decays 100% to 67 Zinc, understanding this reaction can shed light on the abundance of this and other p-nuclei elements in the universe. Here, the photonuclear production of 67 Cu from 71 Ga and natural gallium is examined as an alternative to its photoproduction from zinc. Two research and development production runs were performed at Thomas Jefferson National Accelerator Facility using an electron linac. During the first run, an 805-W, 30.9-MeV beam was used to irradiate a 1-mm tungsten radiator to create a bremsstrahlung flux. The resulting gamma photons irradiated 50.9 g of natural gallium encased in a graphite crucible for 24.2 h; 7.02 Bq/W∙s∙kg of 67 Cu activity was produced. During the second run, a 4380-W, 31.5-MeV beam was used for 12.0 h on the same target containing 60 g of natural gallium; 6.41 Bq/W∙s∙kg of 67 Cu activity was produced. Because of the difficulties in spectroscopically differentiating 67 Cu from 67 Ga, prior to each run, an isotopically pure 71 Ga disk was irradiated using a 100-W beam for 1 h, at the same respective energies. Finally, these baseline irradiations allowed for separation of 67 Cu from 67 Ga in the spectroscopic measurements of the natural gallium targets.

07 ISOTOPE AND RADIATION SOURCES↗

Contribution of Lobe Power to Experiment Heating in the Advanced Test Reactor

In order to ease the computational burden associated with designing irradiation experiments in the Advanced Test Reactor (ATR), scaling factors are often used to estimate design parameters at different lobe powers. Here, this paper examines the validity of long-standing assumptions about the contribution of lobe power to total experiment heating in the ATR. For each of the ATR’s 77 different experiment positions, the fractional contribution of each of the ATR’s five lobes to the total heating in that position is calculated and compared to traditional assumptions. The updated fractional contributions are then used to scale heating rates in a sample problem, and the results are compared to traditional scaling methods as well as explicit MC21 heating calculations. It is concluded that for experiment locations in close proximity to the ATR driver fuel (i.e. flux traps and the A, H, and B positions), heating rates scaled with the updated fractional contributions generally agree better with explicit MC21 calculations than do heating rates scaled using the traditionally assumed contributions. For the I positions, which are located on the very periphery of the ATR core, both scaling methods led to poor results when compared against explicit calculations due to the effect that movement of the outer shim control cylinders has on the experiment heating in those positions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A modified many-body dissipative particle dynamics model for mesoscopic fluid simulation: methodology, calibration, and application for hydrocarbon and water

The many-body dissipative particle dynamics (mDPD) is a prominent mesoscopic multiphase model for fluid transport in mesoconfinement. However, it has been a long-standing challenge for mDPD (and other multiphase-enabled DPD models) to accurately predict real-fluid static and dynamic properties simultaneously. We have developed a modified mDPD model to overcome the issue and a rigorous calibration approach that uses reference data, including experimental and/or molecular dynamics (MD) simulations to parameterise the modified mDPD for real fluids. We choose heptane as a representative example of hydrocarbon in source rocks to demonstrate the model's capability to accurately predict the equation of state (EOS), free surface tension, diffusivity, and viscosity. Our timing test shows that the modified mDPD is 400–500 times faster than its MD counterpart for simulating bulk heptane in equivalent volumes. To further demonstrate the robustness of the model, we revisited the benchmark problem of mesoscopic modelling of water, in which all the previous works on DPD reported only a limited portion of the water properties. Here, we show that the modified mDPD can provide accurate modelling of water static and dynamic properties and an EOS that matches the experimental data to a large range of confinement pressure.

42 ENGINEERING↗

LAMP Diagnostics at the Point-of-Care: Emerging Trends and Perspectives for the Developer Community

Over the past decade, loop-mediated isothermal amplification (LAMP) technology has played an important role in molecular diagnostics. Amongst numerous nucleic acid amplification assays, LAMP stands out in terms of sample-to-answer time, sensitivity, specificity, cost, robustness, and accessibility, making it ideal for field-deployable diagnostics in resource-limited regions. In this review, we outline the front-end LAMP design practices for point-of-care (POC) applications, including sample handling and various signal readout methodologies. Next, we explore existing LAMP technologies that have been validated with clinical samples in the field. We summarize recent work that utilizes reverse transcription (RT) LAMP to rapidly detect SARS-CoV-2 as an alternative to standard PCR protocols. Finally, we describe challenges in translating LAMP from the benchtop to the field and opportunities for future LAMP assay development and performance reporting. Despite the popularity of LAMP in the academic research community and a recent surge in interest in LAMP due to the COVID-19 pandemic, there are numerous areas for improvement in the fundamental understanding of LAMP, which are needed to elevate the field of LAMP assay development and characterization.

60 APPLIED LIFE SCIENCES↗

Role of uncertainties in protecting ecological resources during remediation and restoration

Cleanup of contaminated waste sites is a National priority to protect human health and the environment, while restoring land to productive uses. While there are uncertainties with under standing risk to individuals from exposure, the aim of this study was to focus on uncertainties and complexities for ecological systems, complicated by hundreds of species occupying any remediation site which participate in multiple-interacting food webs. The ability to better predict the effectiveness of remediation in fostering future ecosystems might facilitate remedy selection and improve strategic environmental management. This investigation examined (1) uncertainties in ecosystem processes, (2) uncertainties in exposure from contamination before remediation, and (3) uncertainties during remediation. Two Department of Energy sites Hanford Site and Savannah River Site were used as case studies to illustrate how the uncertainties affect eco-receptors. Several types of ecological, physical, and human dimension uncertainties are defined. Ecological uncertainties include temporal, spatial, individual, developmental, and exogenous types. Physical uncertainties are weather-related, watershed variations, slope/aspect, soil/sediment structure and form, unforeseen events, and temporal patterns. Human dimension uncertainties include current land use, future land use, extractive and non-extractive recreation. The effects of remedial strategies varied between the two sites because Hanford is a primarily arid shrub-steppe ecotype, while Savannah River is a wet forest ecotype. Defining the associated ecological sensitivities and uncertainties and providing examples might help policy-makers, managers, planners, and contractors to be aware of issues to consider throughout planning, remediation, and restoration. Adding ecological uncertainty analysis to risk evaluations and remediation planning is analogous to using safety factors in human health risk assessment.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Machine Learning Algorithms for Automated NIF Capsule Mandrel Selection

Small shells, approximately 2 mm in diameter, made from Poly(α-methylstyrene) (PAMS) are used as mandrels in the production of glow discharge polymer capsules located at the center of inertial confinement fusion experiments. The visual inspection process of microscope images of these shell mandrels, including detection of micron-sized defects on the shell surface as well as the handling and sorting, is a very labor-intensive, repetitive, and highly subjective process that stands to benefit greatly from automation. As part of an effort to decrease the number of labor hours spent in capsule handling, inspection, and metrology, the development of robotic systems was presented in a paper by Carlson et al., “Automation in Target Fabrication” [Fusion Sci. Technol., Vol. 70, p. 274 (2016)]. The current work expands the automated image acquisition systems developed previously and adds the use of convolutional neural networks to select capsules best suited for use in the downstream production process. Through the use of these machine learning algorithms, the selection process becomes robust, repeatable, and operator independent. Finally, as an added benefit the system developed as part of this work is able to provide defect statistics on entire shell batches and feed this information upstream to the production team.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

In-Field Testing of Components for Feedback and Control of the ITER Disruption Mitigation System

Here, the shattered pellet injection (SPI) method has been chosen as the disruption mitigation system (DMS) for ITER. To protect the device from plasma disruptions that cause damaging heat and electromagnetic loads, SPI is used to inject high-Z material into the plasma. The process of SPI utilizes cryogenic cooling to form solid pellets. Pellets are accelerated down a barrel and into an angled surface, causing the pellet to shatter prior to entering the tokamak chamber. For the DMS to function reliably, the 27 separate shattered pellet injectors planned for ITER must rely on many components to provide accurate feedback data and for control functions. Each component in the DMS is exposed to an elevated background magnetic field depending on its placement and proximity to the plasma chamber. A Helmholtz coil test stand that is operated at Oak Ridge National Laboratory was utilized to test the components in relevant background field levels to assess component performance. This paper details the test design and results for in-field component operation for a variety of components. This list includes the following components: two different network switches for camera connectivity, a VAT fast shutter valve intended to reduce the flow of SPI propellant gas into the torus, a solenoid control valve intended for use in the pellet formation process, pressure/vacuum switches to be used for feedback and control, a printed circuit board piezo pressure sensor to be used to measure breech pressure, and various relays for the high-voltage pulsed power supply used to drive the SPI propellant valve.

Disruption mitigation↗

CityLearn v2: energy-flexible, resilient, occupant-centric, and carbon-aware management of grid-interactive communities

As more distributed energy resources become part of the demand-side infrastructure, quantifying their energy flexibility on a community scale is crucial. CityLearn v1 provided an environment for benchmarking control algorithms. However, there is no standardized environment utilizing realistic building-stock datasets for distributed energy resource control benchmarking without co-simulation or third-party frameworks. CityLearn v2 extends CityLearn v1 by providing a stand-alone simulation environment that leverages the End-Use Load Profiles for the U.S. Building Stock dataset to create grid-interactive communities for resilient, multi-agent, and objective control of distributed energy resources with dynamic occupant feedback. While the v1 environment used pre-simulated building thermal loads, the v2 environment uses data-driven thermal dynamics and eliminates the need for co-simulation with building energy performance software. This work details the v2 environment and provides application examples that use reinforcement learning control to manage battery energy storage system, vehicle-to-grid control, and thermal comfort during heat pump power modulation.

Nweye, Kingsley↗

Parabacteroides distasonis : intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health

Parabacteroides distasonis is the type strain for the genus Parabacteroides, a group of gram-negative anaerobic bacteria that commonly colonize the gastrointestinal tract of numerous species. First isolated in the 1930s from a clinical specimen as Bacteroides distasonis, the strain was re-classified to form the new genus Parabacteroides in 2006. Currently, the genus consists of 15 species, 10 of which are listed as 'validly named' (P. acidifaciens, P. chartae, P. chinchillae, P. chongii, P. distasonis, P. faecis, P. goldsteinii, P. gordonii, P. johnsonii, and P. merdae) and 5 'not validly named' (P. bouchesdurhonensis, P. massiliensis, P. pacaensis, P. provencensis, and P. timonensis) by the List of Prokaryotic names with Standing in Nomenclature. The Parabacteroides genus has been associated with reports of both beneficial and pathogenic effects in human health. Herein, we review the literature on the history, ecology, diseases, antimicrobial resistance, and genetics of this bacterium, illustrating the effects of P. distasonis on human and animal health.

59 BASIC BIOLOGICAL SCIENCES↗

The 2022 magneto-optics roadmap

Abstract Magneto-optical (MO) effects, viz. magnetically induced changes in light intensity or polarization upon reflection from or transmission through a magnetic sample, were discovered over a century and a half ago. Initially they played a crucially relevant role in unveiling the fundamentals of electromagnetism and quantum mechanics. A more broad-based relevance and wide-spread use of MO methods, however, remained quite limited until the 1960s due to a lack of suitable, reliable and easy-to-operate light sources. The advent of Laser technology and the availability of other novel light sources led to an enormous expansion of MO measurement techniques and applications that continues to this day (see section 1). The here-assembled roadmap article is intended to provide a meaningful survey over many of the most relevant recent developments, advances, and emerging research directions in a rather condensed form, so that readers can easily access a significant overview about this very dynamic research field. While light source technology and other experimental developments were crucial in the establishment of today’s magneto-optics, progress also relies on an ever-increasing theoretical understanding of MO effects from a quantum mechanical perspective (see section 2), as well as using electromagnetic theory and modelling approaches (see section 3) to enable quantitatively reliable predictions for ever more complex materials, metamaterials, and device geometries. The latest advances in established MO methodologies and especially the utilization of the MO Kerr effect (MOKE) are presented in sections 4 (MOKE spectroscopy), 5 (higher order MOKE effects), 6 (MOKE microscopy), 8 (high sensitivity MOKE), 9 (generalized MO ellipsometry), and 20 (Cotton–Mouton effect in two-dimensional materials). In addition, MO effects are now being investigated and utilized in spectral ranges, to which they originally seemed completely foreign, as those of synchrotron radiation x-rays (see section 14 on three-dimensional magnetic characterization and section 16 on light beams carrying orbital angular momentum) and, very recently, the terahertz (THz) regime (see section 18 on THz MOKE and section 19 on THz ellipsometry for electron paramagnetic resonance detection). Magneto-optics also demonstrates its strength in a unique way when combined with femtosecond laser pulses (see section 10 on ultrafast MOKE and section 15 on magneto-optics using x-ray free electron lasers), facilitating the very active field of time-resolved MO spectroscopy that enables investigations of phenomena like spin relaxation of non-equilibrium photoexcited carriers, transient modifications of ferromagnetic order, and photo-induced dynamic phase transitions, to name a few. Recent progress in nanoscience and nanotechnology, which is intimately linked to the achieved impressive ability to reliably fabricate materials and functional structures at the nanoscale, now enables the exploitation of strongly enhanced MO effects induced by light–matter interaction at the nanoscale (see section 12 on magnetoplasmonics and section 13 on MO metasurfaces). MO effects are also at the very heart of powerful magnetic characterization techniques like Brillouin light scattering and time-resolved pump-probe measurements for the study of spin waves (see section 7), their interactions with acoustic waves (see section 11), and ultra-sensitive magnetic field sensing applications based on nitrogen-vacancy centres in diamond (see section 17). Despite our best attempt to represent the field of magneto-optics accurately and do justice to all its novel developments and its diversity, the research area is so extensive and active that there remains great latitude in deciding what to include in an article of this sort, which in turn means that some areas might not be adequately represented here. However, we feel that the 20 sections that form this 2022 magneto-optics roadmap article, each written by experts in the field and addressing a specific subject on only two pages, provide an accurate snapshot of where this research field stands today. Correspondingly, it should act as a valuable reference point and guideline for emerging research directions in modern magneto-optics, as well as illustrate the directions this research field might take in the foreseeable future.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Kaon physics: a cornerstone for future discoveries

The kaon physics programme, long heralded as a cutting-edge frontier by the European Strategy for Particle Physics, continues to stand at the intersection of discovery and innovation in high-energy physics (HEP). With its unparalleled capacity to explore new physics at the multi-TeV scale, kaon research is poised to unveil phenomena that could reshape our understanding of the Universe. This document highlights the compelling physics case, with emphasis on exciting new opportunities for advancing kaon physics not only in Europe but also on a global stage. As an important player in the future of HEP, the kaon programme promises to drive transformative breakthroughs, inviting exploration at the forefront of scientific discovery.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Local structural investigation of non-crystalline materials at high pressure: the case of GeO 2 glass

Abstract Local structures play a crucial role in the structural polyamorphism and novel electronic properties of amorphous materials, but their accurate measurement at high pressure remains a formidable challenge. In this article, we use the local structure of network-forming GeO 2 glass as an example, to present our recent approaches and advances in high-energy x-ray diffraction, high-pressure x-ray absorption fine structure, and ab initio first-principles density functional theory calculations and simulations. Although GeO 2 glass is one of the best studied materials in the field of high pressure research due to its importance in glass theory and geophysical significance, there are still some long-standing puzzles, such as the existence of appreciable distinct fivefold [5] Ge coordination at low pressure and the sixfold-plus [6+] Ge coordination at ultrahigh pressure. Our work sheds light on the origin of pressure-induced polyamorphism of GeO 2 glass, and the [5] Ge polyhedral units may be the dominant species in the densification mechanism of network-forming glasses from tetrahedral to octahedral amorphous structures.

Physics↗