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At least 919 records · Page 51

Evaluation system and web infrastructure for the second cryo-EM model challenge

An evaluation system and a web infrastructure were developed for the second cryo-EM model challenge. The evaluation system includes tools to validate stereo-chemical plausibility of submitted models, check their fit to the corresponding density maps, estimate their overall and per-residue accuracy, and assess their similarity to reference cryo-EM or X-ray structures as well as other models submitted in this challenge. The web infrastructure provides a convenient interface for analyzing models at different levels of detail. As a result, it includes interactively sortable tables of evaluation scores for different subsets of models and different sublevels of structure organization, and a suite of visualization tools facilitating model analysis.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal structures and second-order NLO properties of borogermanates

Borogermanates are a class of very important compounds in materials chemistry. In this paper, the syntheses, structures, and properties of metal borogermanates are reviewed. Organically templated borogermanates with zeolite-like open-frameworks show potential applications as microporous materials. Many compounds in alkali or alkaline-earth borogermanate systems are structurally acentric or polar, some of which exhibit excellent Second Harmonic Generation (SHG) coefficients, wide transparency regions, and high optical-damage thresholds as well as excellent thermal stability. Most of the lanthanide borogermanates are structurally centrosymmetric and not SHG active; however, they are able to emit strong luminescence in visible or near-IR region. In the B-rich compounds, BO{sub 3} and BO{sub 4} groups can be polymerized into a variety of discrete polynuclear anionic cluster units or extended architectures via B-O-B bridges; whereas in the Ge-rich compounds, GeO{sub 4} and GeO{sub 6} polyhedra can also be polymerized. The combinations of borate and germinate afforded rich structural and topological types. - Graphical abstract: Borogermanates are a class of very important compounds in materials chemistry. Both BO{sub x} (x=3, 4) and GeO{sub y} (y=4, 6) polyhedra can be polymerized into a variety of discrete polynuclear anionic cluster units or extended architectures. The combinations of borate and germanate groups in the same oxide framework not only give rise to a rich structural chemistry, but also afford many polar compounds with good SHG properties. Highlights: Black-Right-Pointing-Pointer Borogermanates are a class of new materials. Black-Right-Pointing-Pointer They feature to be the combination of B and Ge atoms into the same oxide framework. Black-Right-Pointing-Pointer They can form a large number of novel 2D and 3D framework structures. Black-Right-Pointing-Pointer Some of them are acentric or polar with moderate strong SHG responses.

36 MATERIALS SCIENCE↗

Second harmonic generation response of the cubic chalcogenides Ba( 6-x )Sr x [Ag( 4-y )Sn( y/4 )](SnS 4 ) 4

We synthesized the barium/strontium solid solution sequence Ba 6-x Sr x [Ag( 4-y )Sn( y/4 )](SnS 4 ) 4 for nonlinear optical (NLO) applications in the infrared (IR) via a flux synthesis route. All title compounds are isotypic, crystallizing in the cubic space group I$\bar{_4}$ 3d and are composed of a three-dimensional (3D) anionic framework of alternating corner-sharing SnS 4 and AgS 4 tetrahedra charge balanced by Ba and Sr. The shrinkage of Ba/Sr-S bond lengths causes the tetrahedra in the anionic framework to become more distorted, which results in a tunable band gap from 1.58 to 1.38 eV with increasing x values. The performance of the barium limit (x=0) is also superior to that of Sr (x=6), but surprisingly second harmonic generation (SHG) of the solid solution remains strong and is insensitive to the value of x over the range 0-3.8. Results show that the non-type-I phase-matched SHG produced by these cubic chalcogenides display intensities higher than the benchmark AgGaSe 2 from 600 to 1000 nm.

Haynes, Alyssa S.↗

Effects of cold predeformation on dissolution of second-phase Al2Cu particles during solution treatment of 2219 Al-Cu alloy forgings

Highlights: • Cold predeformation (CPD) was performed on 2219 Al-Cu alloy forgings. • CPD promoted the dissolution of coarse Al{sub 2}Cu particles during solution treatment. • CPD increased the driving force to precipitate θ′ phases during aging treatment. • Increasing CPD improved the tensile properties of the forgings. - Abstract: Cold predeformation (CPD, before solution treatment) at different pre-compressing deformations of 0, 5, and 10% was performed on 2219 Al-Cu alloy forgings, and its effect on the dissolution of second-phase Al{sub 2}Cu particles during solution treatment was investigated. The results indicated that a higher number of coarse Al{sub 2}Cu particles dissolved in the Al matrix during solution treatment in samples processed with CPD. Upon increasing CPD from 0 to 10%, the area fraction of the coarse particles decreased from 2.57 to 0.57%, while their mean size decreased from 12.5 to 8.7 μm. The corresponding driving force for precipitation during the subsequent aging treatment process increased, the main precipitates in the material transitioned from the θ″ phase to the θ′ phase, and the area fraction of the precipitates increased from 6.1 to 18.1%. As a result, a significant increase in ultimate tensile strength (by 61.2 MPa), yield strength (by 63.2 MPa), and tensile elongation (by 2.2%) was obtained.

36 MATERIALS SCIENCE↗

A realistic guide misalignment model for the Second Target Station instruments at the Spallation Neutron Source

The Second Target Station (STS) at the Spallation Neutron Source, including a suite of initial instrument concepts, are being designed in Oak Ridge. The moderator size at STS is significantly smaller than that of the First Target Station, making the guide misalignment a more prominent concern. Here a realistic misalignment model based on Monte Carlo neutron ray tracing simulation was developed to evaluate the impacts of both the random misalignment and floor settlement on the performance of a toy model of 150 m straight guide system, and MENUS, an STS instrument concept with a typical guide design of two opposing Montel mirrors. The study shows that longer instruments, and instruments with complex curved mirrors/guides are sensitive to significant performance penalties due to misalignments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Optimization of the Second Target Station cold source moderators using an automated workflow

The Second Target Station (STS) at the US Department of Energy’s Oak Ridge National Laboratory is designed to become the world’s highest peak-brightness spallation source of cold neutrons. Successful completion of the STS, which is currently in the preliminary design phase, will provide transformative new capabilities to examine novel materials for future technologies. At STS, neutrons will be generated by spallation reactions in a solid tungsten target. They will be moderated and thermalized in two cold (20 K) para-hydrogen moderators. Careful optimization of these moderators is essential to the project’s success. To find optimal moderator designs, an advanced optimization workflow integrates high-fidelity neutronics calculations using the Monte Carlo N-Particle (MCNP) transport code MCNP6.2 with state-of-the-art optimization algorithms in the Dakota optimization toolkit. For each design iteration, a parametrized solid CAD geometry is generated in Creo and automatically converted into an unstructured mesh geometry by Attila 4MC for the neutronics calculation with MCNP. Iterations repeat until optimal designs are found. Herein this paper presents the results of a sensitivity and optimization study for the cylindrical and tube moderators. Both moderators can be optimized for maximum peak brightness, maximum time-integrated brightness, or any combination between these extremes. Maximum peak brightness is achieved by using smaller optimal dimensions of the moderators, whereas maximum time-integrated brightness is achieved by using larger dimensions. A Pareto front details the designs that optimally balance both brightness metrics. The Pareto front can be found in only 40–110 iterations with 4–5 design parameters when using the efficient global and Pareto-set optimization algorithms in Dakota. Additionally, important engineering constraints can be taken into account, such as the coupling between the cylindrical moderator radius and aluminum vessel wall thicknesses required to ensure structural integrity of the vessels. This interaction has a significant impact on the resulting optimal designs. Our new, highly efficient, fully automated optimization workflow will be used to optimize additional STS components in the future and can be adopted for design and optimization studies at other experimental neutron and accelerator facilities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Optimization of neutron chopper and optics for CENTAUR, the SANS/WANS diffractometer at the spallation neutron source second target station

Herein this report presents the physics design and optimization of the neutron chopper and optics systems for the CENTAUR instrument, a multifunctional small-angle and wide-angle neutron scattering diffractometer for the Spallation Neutron Source Second Target Station. This instrument will offer a wide range of capabilities, including small-angle neutron scattering with wide Q coverage (e.g., 0.001–20 Å –1 ), providing a tool to investigate structures from atomic to mesoscopic scales simultaneously. To efficiently transport desired neutrons from the compact high-brightness cold source, several innovative designs are utilized: a time-zero chopper with a straight guide system for short-wavelength neutrons, octagonal guides for higher flux, and a correlation chopper to reduce inelastic scattering. The optimization process considers factors such as useable time-integrated flux, instrument resolution, brilliance transfer, divergence, and acceptance diagram uniformity. The overall design prioritizes flexibility to accommodate diverse user requirements.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Second gadolinium loading to Super-Kamiokande

The first loading of gadolinium (Gd) into Super-Kamiokande in 2020 was successful, and the neutron capture efficiency on Gd reached 50%. To further increase the Gd neutron capture efficiency to 75%, 26.1 tons of Gd 2 (SO 4 ) 3 ∙ 8H 2 O was additionally loaded into Super-Kamiokande (SK) from May 31 to July 4, 2022. As the amount of loaded Gd 2 (SO 4 ) 3 ∙ 8H 2 O was doubled compared to the first loading, the capacity of the powder dissolving system was doubled. We also developed new batches of gadolinium sulfate with even further reduced radioactive impurities. In addition, a more efficient screening method was devised and implemented to evaluate these new batches of Gd 2 (SO 4 ) 3 ∙ 8H 2 O. Following the second loading, the Gd concentration in SK was measured to be 333.5 ± 2.5 ppm via an Atomic Absorption Spectrometer (AAS). From the mean neutron capture time constant of neutrons from an Am/Be calibration source, the Gd concentration was independently measured to be 332.7 ± 6.8(sys.) ± 1.1(stat.) ppm, consistent with the AAS result. Furthermore, during the loading the Gd concentration was monitored continually using the capture time constant of each spallation neutron produced by cosmic-ray muons, and the final neutron capture efficiency was shown to become 1.5 times higher than that of the first loaded phase, as expected.

Gadolinium↗

Coupled beam-target-moderator optimization for the Second Target Station

To support the design of the Second Target Station, that aims to provide the world’s highest peak brightness of cold neutrons, studies that optimize the dimensions of the target and moderators are invaluable. In this work, we investigate the influence of the target dimensions and beam profile on the performance and optimal size of the moderators. We perform optimization runs with detailed MCNP6.2 simulations using high-fidelity unstructured mesh geometries generated from parametrized CAD models. We demonstrate that small changes in target height do not influence the moderator performance if the beam dimensions are chosen adequately. We quantify the effect of beam footprint and target width on the moderator performance and show that the optimal moderator dimensions are insensitive to limited changes in target and beam profile.

Dakota↗

Micro Fourier Transform Profilometry (μFTP): 3D shape measurement at 10,000 frames per second

We report that fringe projection profilometry is a well-established technique for optical 3D shape measurement. However, in many applications, it is desirable to make 3D measurements at very high speed, especially with fast moving or shape changing objects. In this work, we demonstrate a new 3D dynamic imaging technique, Micro Fourier Transform Profilometry (μFTP), which can realize an acquisition rate up to 10,000 3D frame per second (fps). The high measurement speed is achieved by the number of patterns reduction as well as high-speed fringe projection hardware. In order to capture 3D information in such a short period of time, we focus on the improvement of the phase recovery, phase unwrapping, and error compensation algorithms, allowing to reconstruct an accurate, unambiguous, and distortion-free 3D point cloud with every two projected patterns. We also develop a high-frame-rate fringe projection hardware by pairing a high-speed camera and a DLP projector, enabling binary pattern switching and precisely synchronized image capture at a frame rate up to 20,000 fps. Lastly, based on this system, we demonstrate high-quality textured 3D imaging of 4 transient scenes: vibrating cantilevers, rotating fan blades, flying bullet, and bursting balloon, which were previously difficult or even unable to be captured with conventional approaches.

3D shape measurement↗

Oil price states and drivers: An analysis of the second-month spot-futures price differential

Oil remains a dominant component of global energy use, and its price, characterized by frequent changes and an ever-present potential for large swings, continues to be a focus of industry participants, policymakers and analysts attention. Here, this study examines the behavior of future spot oil prices using a continuous-time hidden Markov model (HMM) and daily price data spanning years 2007 to 2024. We identify six states in the second-month WTI spot-futures price differential and assess the roles of eleven futures price, quantity, financial market, and geopolitical/volatility variables in each state. The model yields several insights into the workings of the oil market and the relative roles of these drivers. We find support for several theoretical and empirical findings in the oil market literature, including the role of inventory, volatility/risk, and market responses to contango/backwardation in futures markets. A novel finding is that “normal contango” conditions represent a significant portion of next-day states in our in-sample data. Under the most volatile normal contango state, many of the oil market drivers differ markedly in coefficient signs and magnitudes from those in other states. The resulting model also performed well out-of-sample and would, in addition to understanding the impact of market drivers, be useful for short-term forecasting. Overall, the findings highlight the highly non-linear, regime-dependent interactions of the oil price and its drivers, emphasizing the importance of detailed information to market stakeholders.

Oladosu, Gbadebo A. [Oak Ridge National Laboratory↗

Prenatal caffeine ingestion induces transgenerational neuroendocrine metabolic programming alteration in second generation rats

Our previous studies have demonstrated that prenatal caffeine ingestion induces an increased susceptibility to metabolic syndrome with alterations of glucose and lipid metabolic phenotypes in adult first generation (F1) of intrauterine growth retardation (IUGR) rats, and the underlying mechanism is originated from a hypothalamic–pituitary–adrenal (HPA) axis-associated neuroendocrine metabolic programming alteration in utero. This study aims to investigate the transgenerational effects of this programming alteration in adult second generation (F2). Pregnant Wistar rats were administered with caffeine (120 mg/kg·d) from gestational day 11 until delivery. Four groups in F2 were set according to the cross-mating between control and caffeine-induced IUGR rats. F2 were subjected to a fortnight ice water swimming stimulus on postnatal month 4, and blood samples were collected before and after stress. Results showed that the majority of the activities of HPA axis and phenotypes of glucose and lipid metabolism were altered in F2. Particularly, comparing with the control group, caffeine groups had an enhanced corticosterone levels after chronic stress. Compared with before stress, the serum glucose levels were increased in some groups whereas the triglyceride levels were decreased. Furthermore, total cholesterol gain rates were enhanced but the high-density lipoprotein-cholesterol gain rates were decreased in most caffeine groups after stress. These transgenerational effects were characterized partially with gender and parental differences. Taken together, these results indicate that the reproductive and developmental toxicities and the neuroendocrine metabolic programming mechanism by prenatal caffeine ingestion have transgenerational effects in rats, which may help to explain the susceptibility to metabolic syndrome and associated diseases in F2. - Highlights: • Caffeine-induced neuroendocrine metabolic programming of HPA has hereditary effect. • Caffeine-induced reproductive and developmental toxicities in F1 have hereditary effect. • Caffeine-induced programming of HPA axis in F2 has gender and parental differences.

60 APPLIED LIFE SCIENCES↗

Bacteriophage SP6 encodes a second tailspike protein that recognizes Salmonella enterica serogroups C{sub 2} and C{sub 3}

SP6 is a salmonella phage closely related to coliphage K1-5. K1-5 is notable in that it encodes two polysaccharide-degrading tailspike proteins, an endosialidase that allows it to infect E. coli K1, and a lyase that enables it to infect K5 strains. SP6 is similar to K1-5 except that it encodes a P22-like endorhamnosidase tailspike, gp46, allowing it to infect group B Salmonella. We show here that SP6 can also infect Salmonella serogroups C{sub 2} and C{sub 3} and that a mutation in a putative second tailspike, gp47, eliminates this specificity. Gene 47 was fused to the coding region of the N-terminal portion of the Pseudomonas aeruginosa R2 pyocin tail fiber and expressed in trans such that the fusion protein becomes incorporated into pyocin particles. These pyocins, termed AvR2-SP47, killed serogroups C{sub 2} and C{sub 3}Salmonella. We conclude that SP6 encodes two tail proteins providing it a broad host range among Salmonella enterica. - Highlights: • SP6 is a “dual specificity” bacteriophage that encodes two different receptor binding proteins giving it a broad host range. • These receptor binding proteins can be used to re-target the spectrum of R-type bacteriocins to Salmonella enterica. • Both SP6 and the engineered R-type bacteriocins can kill the Salmonella serovars most associated with human disease making them attractive for development as antimicrobial agents.

60 APPLIED LIFE SCIENCES↗

Optimization of greenhouse gas emissions in second-hand consumer product recovery through reuse platforms

Highlights: • Effects of waste diversion on flow of products to reuse processes. • Framework for solid waste management that focuses on reuse processes for waste diversion. • Application of framework on the material flow and GHG emissions from clothing reuse. - Abstract: Product reuse in the solid waste management sector is promoted as one of the key strategies for waste prevention. This practice is considered to have favorable impact on the environment, but its benefits have yet to be established. Existing research describes the perspective of “avoided production” only, but has failed to examine the interdependent nature of reuse practices within an entire solid waste management system. This study proposes a new framework that uses optimization to minimize the greenhouse gas emissions of an integrated solid waste management system that includes reuse strategies and practices such as reuse enterprises, online platforms, and materials exchanges along with traditional solid waste management practices such as recycling, landfilling, and incineration. The proposed framework uses material flow analysis in combination with an optimization model to provide the best outcome in terms of GHG emissions by redistributing product flows in the integrated solid waste management system to the least impacting routes and processes. The optimization results provide a basis for understanding the contributions of reuse to the environmental benefits of the integrated solid waste management system and the exploration of the effects of reuse activities on waste prevention. A case study involving second-hand clothing is presented to illustrate the implementation of the proposed framework as applied to the material flow. Results of the case study showed the considerable impact of reuse on GHG emissions even for small replacement rates, and helped illustrate the interdependency of the reuse sector with other waste management practices. One major contribution of this study is the development of a framework centered on product reuse that can be applied to identify the best management strategies to reduce the environmental impact of product disposal and to increase recovery of reusable products.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Engineering a Cysteine-Free Form of Human Fibroblast Growth Factor-1 for “Second Generation” Therapeutic Application

Human fibroblast growth factor-1 (FGF-1) has broad therapeutic potential in regenerative medicine but has undesirable biophysical properties of low thermostability and 3 buried cysteine (Cys) residues (at positions 16, 83, and 117) that interact to promote irreversible protein unfolding under oxidizing conditions. Mutational substitution of such Cys residues eliminates reactive buried thiols but cannot be accomplished simultaneously at all 3 positions without also introducing further substantial instability. The mutational introduction of a novel Cys residue (Ala66Cys) that forms a stabilizing disulfide bond (i.e., cystine) with one of the extant Cys residues (Cys83) effectively eliminates one Cys while increasing overall stability. This increase in stability offsets the associated instability of remaining Cys substitution mutations and permits production of a Cys-free form of FGF-1 (Cys16Ser/Ala66Cys/Cys117Ala) with only minor overall instability. The addition of a further stabilizing mutation (Pro134Ala) creates a Cys-free FGF-1 mutant with essentially wild-type biophysical properties. The elimination of buried free thiols in FGF-1 can substantially increase the protein half-life in cell culture. In this work, we show that the effective cell survival/mitogenic functional activity of a fully Cys-free form is also substantially increased and is equivalent to wild-type FGF-1 formulated in the presence of heparin sulfate as a stabilizing agent. The results identify this Cys-free FGF-1 mutant as an advantageous “second generation” form of FGF-1 for therapeutic application.

59 BASIC BIOLOGICAL SCIENCES↗

Influence of heterogeneity on second-kind self-similar solutions for viscous gravity currents

We report experimental, theoretical and numerical results on the effects of horizontal heterogeneities on the propagation of viscous gravity currents. We use two geometries to highlight these effects: (a) a horizontal channel (or crack) whose gap thickness varies as a power-law function of the streamwise coordinate; (b) a heterogeneous porous medium whose permeability and porosity have power-law variations. We demonstrate that two types of self-similar behaviours emerge as a result of horizontal heterogeneity: (a) a first-kind self-similar solution is found using dimensional analysis (scaling) for viscous gravity currents that propagate away from the origin (a point of zero permeability); (b) a second-kind self-similar solution is found using a phase-plane analysis for viscous gravity currents that propagate toward the origin. These theoretical predictions, obtained using the ideas of self-similar intermediate asymptotics, are compared with experimental results and numerical solutions of the governing partial differential equation developed under the lubrication approximation. All three results are found to be in good agreement.

42 ENGINEERING↗

A Second Amorphous Layer Underneath Surface Oxide

Abstract Formation of a nanometer-scale oxide surface layer is common when a material is exposed to oxygen-containing environment. Employing aberration-corrected analytical transmission electron microscopy and using single crystal SnSe as an example, we show that for an alloy, a second thin amorphous layer can appear underneath the outmost oxide layer. This inner amorphous layer is not oxide based, but instead originates from solid-state amorphization of the base alloy when its free energy rises to above that of the metastable amorphous state; which is a result of the composition shift due to the preferential depletion of the oxidizing species, in our case, the outgoing Sn reacting with the oxygen atmosphere.

Materials Science↗

Phase-Change Behavior and Nonlinear Optical Second and Third Harmonic Generation of the One-Dimensional K (1– x ) Cs x PSe 6 and Metastable β-CsPSe 6

The APSe(6) (A = K, K(1-x)Csx, Cs) family of one-dimensional (1D) materials was studied to examine the effects of the cation size on the nonlinear optical (NLO) response. The family has high-performing NLO properties with the noncentrosymmetric parent material, KPSe6, having infinite 1D chains of 1/(infinity)[PSe6-]. This structure has been successfully substituted with cesium up to K0.6Cs0.4PSe6 while retaining the polar character. All compounds crystallize in the space group Pca2(1) and have band gaps of 2.1 eV. In situ powder X-ray diffraction experiments using synchrotron radiation were used to determine the specifics of the amorphous to crystalline behavior and the crystallization and melting kinetics of the APSe(6) system. These measurements revealed a new phase, beta-CsPSe6, which is metastable and crystallizes in the noncentrosymmetric tetragonal space group P (4) over bar2(1)c with a = 12.526(2) angstrom, c = 12.781(3) angstrom, V = 2005.3(6) angstrom(3), and Z = 8. The structure is composed of 2 sets of mutually perpendicular 1/8[PSe6-] chains charge-balanced by Cs cations, and the band gap of beta-CsPSe6 is 1.9 eV. Second harmonic generation (SHG) measurements demonstrate that substitution of Cs into KPSe6 maintains the strong NLO signal with a very high SHG coefficient (chi((2))) of similar to 150 pm/V for K(1-x)CsxPSe6 and 30 pm/V for beta-CsPSe6. Laser-induced damage threshold analysis reveals APSe(6) exhibits two-photon absorption (2PA) at 1064 nm with input laser intensity greater than 1 GW/cm(2) and optical damage from 2PA at similar to 2 GW/cm(2). The materials also exhibit strong third harmonic generation (THG) with THG coefficients (chi((3)) x 10(5)) for KPSe6, K0.6Cs0.4PSe6, alpha-CsPSe6, and beta-CsPSe6 to be 2.6, 3.1, 1.8, and 1.1 pm(2)/V-2, respectively.

Haynes, Alyssa S.↗