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At least 217 records · Page 12

Structural insights into RNase H catalytic mechanism from room-temperature X-ray and neutron crystallography of apo- and RNA/DNA hybrid-bound enzyme

RNase H enzymes are sequence-nonspecific endonucleases that cleave RNA strands in RNA/DNA hybrid duplexes, an enzymatic process essential in DNA replication and repair in both prokaryotes and eukaryotes. Also, RNase H activity of the reverse transcriptase in human immunodeficiency viruses (HIV-1 and HIV-2) is indispensable for the viral replication cycle. RNase H enzymes play an central role in the development of gene therapies and are targets for novel antivirals. It is therefore of great importance to gain a detailed understanding of the RNase H catalytic mechanism to improve drug design. We utilized Bacillus halodurans RNase H1 (BhRNase H1) to shed light on its function and catalytic mechanism. Room-temperature neutron crystallography of the wild-type and inactive D132N mutant enzymes revealed that E109, belonging to the catalytic DEDD motif, can change its protonation state, allowing us to propose its role in the protonation of the leaving O3′ hydroxyl group of RNA. X-ray crystallography has demonstrated the ability of the RNA/DNA duplex to slide along the protein surface upon metal ion binding at site M A , transforming a product mimic into a Michaelis-like complex, which confirms an essential role of the M A metal ion in catalysis.

Enzyme mechanisms↗

Stochastic room temperature creep of 316 L stainless steel

The creep behavior of 316 L stainless steel at room temperature was evaluated as a function of time and applied stress using a new high-throughput approach. Several common creep models were evaluated against the observations, leading to deeper analysis of a stress-dependent modified logarithmic creep model. Within this model, multiple sources of uncertainty were compared. Aleatoric stochastic variation between samples under nominally identical conditions was identified as the primary contributor to uncertainty in creep response. Under any particular set of conditions, the sample-to-sample variability in creep strain was as high as a factor of two, highlighting the engineering importance of characterizing large statistical datasets. The model's extrapolation capabilities were assessed by comparing predictions derived from calibration on partial, shorter-duration subsets of the data. In conclusion, these findings underscore the importance of accounting for stochastic effects in predictive modeling of aging phenomena.

High-throughput↗

DFT-based investigation of solvation of Nd(III)/Yb(III) cations in room-temperature ionic-liquid

We report a DFT study on the solvation of bare rare-earth (RE) cations [Nd(III) and Yb(III)] in the room-temperature ionic-liquid (RTIL) based on 1,3-dimethyl-imidazolium + , PF 6 - , [MMI][PF 6 ]. In the present article, we aim to investigate whether the chosen RTIL can preferentially solvate any of the RE cations under study. First, the RTIL binding to the RE cation is studied in the gas phase, and then explored with continuum solvation model employing RTIL parameters. First, we considered the formation of the first solvation shell, where the PF 6 - anions directly bond with the Ln(III) cation. We then further surrounded the first solvation shell with [MMI]+ cations to form the second solvation shell. The stability of PF 6 - coordinated complexes is studied by calculating the binding energy values. The number of PF 6 - anions for both Ln(III) cations starts with three ligands and goes until the maximum binding energy in the RTIL medium is reached. The coordination number and binding modes of PF 6 - depend on the size of the RE cation. Comparing the binding energy values between the RE cations for the first solvation shell complexes, it is noticed that Yb-complexes have relatively greater binding energy than Nd-complexes. We have further performed a Boltzmann population analysis to find out the most dominant conformer among each category of PF 6 - coordinated complexes. A study using Natural Population Analysis shows that after complexation with PF 6 - the charge on the Yb-centers lower to a greater extent than Nd-centers, implying stronger bonding between Yb and PF 6 - , which is in harmony with the binding energy analysis. Overall, the computational investigation provides an in-depth understanding of the complexation phenomena of RE cations in RTIL, which can be useful for the practical separation of RE cations using RTIL.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molten salt electrolysis and room temperature ionic liquid electrochemical processes for refining rare earth metals: Environmental and economic performance comparison

Circularizing end of life products such as electronic waste can open a new source for rare earth elements (REEs) that will decrease the demand pressure on conventional virgin production. The last step to produce REEs consists of a refining process to convert rare earth oxide (REO) to REE metal. One promising technology is processing REO via a room temperature ionic liquid, which is characterized by low energy requirements in contrast to existing REEs extraction processes. In this work, life cycle and techno-economic assessments are performed and compared against molten salt electrolysis. Here, the results show that both processes have advantages and disadvantages in terms of environmental performance, and that they are similarly competitive in terms of economic performance. A breakeven analysis suggests that future research should focus on coupling the production of REOs with the refining processes to attempt to lower REO cost and make them economically feasible in the U.S.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Benefits and challenges in deployment of low global warming potential R290 refrigerant for room air conditioning equipment in California

High global warming potential gases (“high GWP”) are the fastest growing sector of greenhouse gas emissions in the world and in California and are primarily used as refrigerant gases in refrigeration and cooling equipment. Hydrofluorocarbons (HFCs) refrigerants are the dominant type of high GWP gases with GWP values thousands of times larger than CO 2 on a 100-year timescale. Refrigerant-grade propane (“R290”) has a very low GWP (GWP = 3.3) with good thermodynamic properties and good cooling equipment performance but the flammability of any leaked refrigerant makes equipment design, handling, and maintenance critical factors to manage. This paper focuses on the potential climate benefits and costs of transitioning to R290 refrigerant in small room air conditioning (AC) units, specifically window AC, packaged terminal AC/heat pumps (PTAC/PTHP), and mini-split heat pumps. Overall climate impact for a transition to all three types of air conditioning units in the 2022–2051 timeframe is found to be from 15 to 64 million metric tons of greenhouse gas (GHG) savings in California with a cost of saved CO 2 eq that ranges from $14.50 per ton of CO 2 eq saved to -$50.30 per ton of CO 2 eq saved (net savings) depending on whether the baseline refrigerant is R32 or R410A and depending on the relative energy efficiency for R290 units compared to baseline units.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Possible Topological Hall Effect above Room Temperature in Layered Cr 1.2 Te 2 Ferromagnet

Topological Hall effect (THE) has been used as a powerful tool to unlock spin chirality in novel magnetic materials. Recent focus has been widely paid to THE and possible chiral spin textures in two-dimensional (2D) layered magnetic materials. However, the room-temperature THE has been barely reported in 2D materials, which hinders its practical applications in 2D spintronics. In this paper, we report a possible THE signal featuring antisymmetric peaks in a wide temperature window up to 320 K in Cr 1.2 Te 2 , a new quasi-2D ferromagnetic material. The temperature, thickness, and magnetic field dependences of the THE lead to potential spin chirality origin that is associated with the spin canting under external magnetic fields. Furthermore, our work holds promise for practical applications in future chiral spin-based vdW spintronic devices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Electronic Structure of Above-Room-Temperature van der Waals Ferromagnet Fe 3 GaTe 2

Fe 3 GaTe 2 , a recently discovered van der Waals ferromagnet, demonstrates intrinsic ferromagnetism above room temperature, necessitating a comprehensive investigation of the microscopic origins of its high Curie temperature ($T$ C ). In this study, we reveal the electronic structure of Fe 3 GaTe 2 in its ferromagnetic ground state using angle-resolved photoemission spectroscopy and density functional theory calculations. Our results establish a consistent correspondence between the measured band structure and theoretical calculations, underscoring the significant contributions of the Heisenberg exchange interaction ($J$ ex ) and magnetic anisotropy energy to the development of the high-$T$ C ferromagnetic ordering in Fe 3 GaTe 2 . Intriguingly, we observe substantial modifications to these crucial driving factors through doping, which we attribute to alterations in multiple spin-splitting bands near the Fermi level. In conclusion, these findings provide valuable insights into the underlying electronic structure and its correlation with the emergence of high-$T$ C ferromagnetic ordering in Fe 3 GaTe 2 .

36 MATERIALS SCIENCE↗

High-Purity Quantum Emission from an Au 24 (S-CH 2 Ph- t Bu) 20 Nanocluster at Room Temperature

Atomically precise gold nanoclusters have garnered significant attention for their diverse applications, ranging from biological labeling to optoelectronics. Their potential in optical quantum computing, which calls for ideal single-photon sources, has recently become a key area of interest. In the current work, we use photon antibunching experiments to explore the single-photon emission efficiency of atomically precise Au 24 nanoclusters protected by 4-tert-butylbenzyl mercaptan ligands (Au 24 (TBBM) 20 ). This cluster exhibits quantum emission with good photostability and without any observable blinking or spectral drift at room temperature under an inert gas atmosphere, with antibunching dips (g 2 (0)) as low as 0.07 in the solid state or, equivalently, a single-photon purity of 93% under time-gated conditions. Transient absorption and time-gated antibunching studies reveal that the short emission lifetime of this cluster and its high photoluminescence quantum yield in the solid state play critical roles in enhancing the emitted single-photon purity. This research advances the understanding of single-emitter behavior in atomically precise gold nanoclusters, contributing to the development of stable quantum emitters that are essential for quantum computing and cryptography.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Room-temperature superconductivity in a carbonaceous sulfur hydride

One of the long-standing challenges in experimental physics is the observation of room-temperature superconductivity (RTSC). Recently, high temperature conventional superconductivity in hydrogen-rich materials has been reported in several systems under high pressure. The most significant discovery in reaching RTSC is the pressure-driven disproportionation of hydrogen sulfide (H 2 S) to H 3 S with a confirmed Tc of 203 kelvin at 155 gigapascals. As H 2 S readily mixes with hydrogen to form guest-host structures at lower pressures, the comparable size of methane to H 2 S should allow molecular exchange within a large assemblage of van der Waals solids that are (highly) hydrogen-rich with H 2 inclusions that are then the building blocks for novel superconducting compounds at extreme conditions. Here, we report superconductivity in a photochemically transformed carbonaceous sulfur hydride system with a maximum superconducting transition temperature of 287.7 ± 1.2 kelvin (~15° celsius) achieved at 267 ± 10 gigapascals. The superconducting state is observed over a broad pressure range from 140 to 275 gigapascals, with a dramatic upturn in Tc above 220 gigapascals. Superconductivity is established by the observation of zero resistance, magnetic susceptibility up to 190 gigapascals, and reduction of Tc under an external magnetic field up to 9 tesla, with an upper critical magnetic field of ~62 tesla based on Ginzburg–Landau (GL) model at zero temperature. The light, quantum nature of hydrogen limits structural and stoichiometric determination using x-ray scattering techniques. Raman spectroscopy is used to probe the chemical and structural transformations pre-metallization. In conclusion, the introduction of chemical tuning within our reported ternary system could be the path forward to lowering the pressure while preserving the RTSC properties.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures

Radiation damage limits the accuracy of macromolecular structures in X-ray crystallography. Cryogenic (cryo-) cooling reduces the global radiation damage rate and, therefore, became the method of choice over the past decades. The recent advent of serial crystallography, which spreads the absorbed energy over many crystals, thereby reducing damage, has rendered room temperature (RT) data collection more practical and also extendable to microcrystals, both enabling and requiring the study of specific and global radiation damage at RT. Here, we performed sequential serial raster-scanning crystallography using a microfocused synchrotron beam that allowed for the collection of two series of 40 and 90 full datasets at 2- and 1.9-Å resolution at a dose rate of 40.3 MGy/s on hen egg white lysozyme (HEWL) crystals at RT and cryotemperature, respectively. The diffraction intensity halved its initial value at average doses ( D 1/2 ) of 0.57 and 15.3 MGy at RT and 100 K, respectively. Specific radiation damage at RT was observed at disulfide bonds but not at acidic residues, increasing and then apparently reversing, a peculiar behavior that can be modeled by accounting for differential diffraction intensity decay due to the nonuniform illumination by the X-ray beam. Specific damage to disulfide bonds is evident early on at RT and proceeds at a fivefold higher rate than global damage. The decay modeling suggests it is advisable not to exceed a dose of 0.38 MGy per dataset in static and time-resolved synchrotron crystallography experiments at RT. This rough yardstick might change for proteins other than HEWL and at resolutions other than 2 Å.

36 MATERIALS SCIENCE↗

Utility and Industry Perceptions of Control Room Modernization Over the Last 10 Years

Within the current United States (U.S.) nuclear power fleet, main control room modernization (CRM) is an important step towards cost savings. In recent decades, plants have been engaged in upgrades to varying degrees. This process requires a nuanced, balanced, and timely approach that ensures continued safety and long-term sustainability. In 2012 a survey was issued to individuals from the nuclear industry to learn their perspectives on a range of CRM issues. The survey targeted the benefits and challenges for utilities undertaking this process, including the main drivers and barriers to technology upgrades, regulatory compliance, and the effects these factors have on concepts of operations, strategic approaches, and staffing. In 2022, the survey was issued again to understand whether CRM perceptions had changed in the last 10 years. Our findings identify changes in industry thinking from a decade ago. Here we reveal perspective shifts that represent increased optimism and, in some instances, increased doubt regarding the opportunities and challenges inherent in CRM and implementation. We also report nuanced differences in CRM perspectives between utility and surrounding nuclear industry respondents.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL Mpro: insights into enzyme mechanism and drug design

The emergence of the novel coronavirus SARS-CoV-2 has resulted in a worldwide pandemic not seen in generations. Creating treatments and vaccines to battle COVID-19, the disease caused by the virus, is of paramount importance in order to stop its spread and save lives. The viral main protease, 3CL M pro , is indispensable for the replication of SARS-CoV-2 and is therefore an important target for the design of specific protease inhibitors. Detailed knowledge of the structure and function of 3CL M pro is crucial to guide structure-aided and computational drug-design efforts. Here, the oxidation and reactivity of the cysteine residues of the protease are reported using room-temperature X-ray crystallography, revealing that the catalytic Cys145 can be trapped in the peroxysulfenic acid oxidation state at physiological pH, while the other surface cysteines remain reduced. Only Cys145 and Cys156 react with the alkylating agent N -ethylmaleimide. It is suggested that the zwitterionic Cys145–His45 catalytic dyad is the reactive species that initiates catalysis, rather than Cys145-to-His41 proton transfer via the general acid–base mechanism upon substrate binding. The structures also provide insight into the design of improved 3CL M pro inhibitors.

3CL Mpro↗

Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography

SARS-CoV-2 emerged at the end of 2019 to cause an unprecedented pandemic of the deadly respiratory disease COVID-19 that continues to date. The viral main protease (M pro ) is essential for SARS-CoV-2 replication and is therefore an important drug target. Understanding the catalytic mechanism of M pro , a cysteine protease with a catalytic site comprising the noncanonical Cys145–His41 dyad, can help in guiding drug design. Here, a 2.0 Å resolution room-temperature X-ray crystal structure is reported of a Michaelis-like complex of M pro harboring a single inactivating mutation C145A bound to the octapeptide Ac-SAVLQSGF-CONH 2 corresponding to the nsp4/nsp5 autocleavage site. The peptide substrate is unambiguously defined in subsites S5 to S3′ by strong electron density. Superposition of the Michaelis-like complex with the neutron structure of substrate-free M pro demonstrates that the catalytic site is inherently pre-organized for catalysis prior to substrate binding. Induced fit to the substrate is driven by P1 Gln binding in the predetermined subsite S1 and rearrangement of subsite S2 to accommodate P2 Leu. The Michaelis-like complex structure is ideal for in silico modeling of the SARS-CoV-2 M pro catalytic mechanism.

3CL protease↗

Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive

Serial crystallography at conventional synchrotron light sources (SSX) offers the possibility to routinely collect data at room temperature using micrometre-sized crystals of biological macromolecules. However, SSX data collection is not yet as routine and currently takes significantly longer than the standard rotation series cryo-crystallography. Thus, its use for high-throughput approaches, such as fragment-based drug screening, where the possibility to measure at physiological temperatures would be a great benefit, is impaired. On the way to highthroughput SSX using a conveyor belt based sample delivery system – the CFEL TapeDrive – with three different proteins of biological relevance (Klebsiella pneumoniae CTX-M-14 β-lactamase, Nectria haematococca xylanase GH11 and Aspergillus flavus urate oxidase), it is shown here that complete datasets can be collected in less than a minute and only minimal amounts of sample are required.

36 MATERIALS SCIENCE↗

A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography

Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and structure determination. A crucial need to continue advancement is the efficient delivery of fragile and micrometre-sized crystals to the X-ray beam intersection. This paper presents an improved design of an all-polymer microfluidic `chip' for room-temperature fixed-target serial crystallography that can be tailored to broadly meet the needs of users at either synchrotron or XFEL light sources. The chips are designed to be customized around different types of crystals and offer users a friendly, quick, convenient, ultra-low-cost and robust sample-delivery platform. Compared with the previous iteration of the chip [Gilbile et al. (2021), Lab Chip , 21 , 4831–4845], the new design eliminates cleanroom fabrication. It has a larger imaging area to volume, while maintaining crystal hydration stability for both in situ crystallization or direct crystal slurry loading. Crystals of two model proteins, lysozyme and thaumatin, were used to validate the effectiveness of the design at both synchrotron (lysozyme and thaumatin) and XFEL (lysozyme only) facilities, yielding complete data sets with resolutions of 1.42, 1.48 and 1.70 Å, respectively. Overall, the improved chip design, ease of fabrication and high modifiability create a powerful, all-around sample-delivery tool that structural biologists can quickly adopt, especially in cases of limited sample volume and small, fragile crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Room Temperature Electrorefining of Rare Earth Metals from End-of-use Nd-Fe-B Magnets

Recovering rare earth elements (REE) from used permanent magnets, which contains about 30 wt.% of rare earth elements, has been persistent technological challenge. Current recycling methods relies on pyrometallurgical or hydrometallurgical processes which are energy- and chemical- intensive and not economically and environmentally viable for rare earth containing magnets. Enabling efficient and simplistic recovery and refining of REEs contained in End-of-Use (EoU) products, such as Neodymium-Iron-Boron (Nd-Fe-B) based magnets will play an important and complementary role in the total supply of REEs in the future. We designed a new electrochemical method and demonstrated a room temperature one-pot process that concurrently separates and electroplates REE from commercial Nd-Fe-B magnets. By establishing selective oxidation and reductive potential as electrochemical control parameter along with electrochemically compatible non-aqueous electrolyte system, we demonstrated selective electroleaching of lanthanides (Nd and Preseodymium (Pr)) from anode and concurrent plating as alloy at Pt cathode. The morphological and chemical evolution of the Nd-Fe-B magnets during electroleaching reveals the electrochemical stimuli and rate of dissolution depends on microstructural complexities of the Nd-Fe-B magnet. The concomitant electroplating process leads to Nd-Pr based alloy which can be used as raw metallic alloy for manufacturing new permanent magnet and other devices. Our study demonstrates a scalable separation and refining methodology, based on widely available organic electrolyte system and without any consumptive chemical use, for selective lanthanide recovery from waste magnets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electronic Public Reading Room (EPRR) Guide (V.4)

The Electronic Public Reading Room (EPRR) contains Los Alamos National Laboratory (LANL) documents required for compliance with environmental regulations and permits. Other documents that deal with environmental issues are included in EPRR.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Design Philosophy for Accelerator Control Rooms

This report describes the foundational human factors principles needed to design user interfaces for accelerator control rooms. These principles are presented as recommendations for accelerator control system interface design and are illustrated with examples drawn from accelerator operations at Fermi National Accelerator Laboratory (Fermilab). These high-level principles are intended to serve as design objectives that apply generally across all control system interfaces developed for the accelerator complex. This design philosophy document is a high-level roadmap to approach the general interface design for the accelerator complex. This philosophy applies state-of-the-art human factors principles and evidence-based design standards to an accelerator environment, which will transform the next era of accelerator interfaces as outlined by the Accelerator Controls Operations Research Network (ACORN) Project. Further work will include mapping the general design principles included in this report to more specific guidance in the form of a user interface style guide.

43 PARTICLE ACCELERATORS↗