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At least 325 records · Page 18

Hazma meets HERWIG4DM: precision gamma-ray, neutrino, and positron spectra for light dark matter

Herein we present a new open-source package, Hazma 2, that computes accurate spectra relevant for indirect dark matter searches for photon, neutrino, and positron production from vector-mediated dark matter annihilation and for spin-one dark matter decay. The tool bridges across the regimes of validity of two state of the art codes: Hazma 1, which provides an accurate description below hadronic resonances up to center-of-mass energies around 250 MeV, and Herwig4DM, which is based on vector meson dominance and measured form factors, and accurate well into the few GeV range. The applicability of the combined code extends to approximately 1.5 GeV, above which the number of final state hadrons off of which we individually compute the photon, neutrino, and positron yield grows exceedingly rapidly. We provide example branching ratios, particle spectra and conservative observational constraints from existing gamma-ray data for the well-motivated cases of decaying dark photon dark matter and vector-mediated fermionic dark matter annihilation. Finally, we compare our results to other existing codes at the boundaries of their respective ranges of applicability. Hazma 2 is freely available on GitHub athttps://github.com/LoganAMorrison/Hazma.

79 ASTRONOMY AND ASTROPHYSICS↗

Multifunctional Optical Outcouplers for Efficient and Stable White OLEDs (Final Technical Report)

Replacing fluorescence by phosphorescence in OLED-based solid-state lighting can realize the Department of Energy’s efficiency target of 83% Internal Quantum Efficiency (IQE). The principal challenge, however, is to fix the poor stability of phosphorescent blue OLEDs. To address this, we have fabricated novel plasmonic architectures that improve device stability by decreasing the exciton lifetime of the emitters without drastically decreasing the light extraction efficiency. We describe the impact on stability of these structures in high efficiency blue phosphorescent OLEDs. Although the benefit is appreciable, we find that targeting ‘bright’ triplets on phosphorescent emitter molecules is an incomplete solution, and that it is also necessary to stabilize ‘dark’ triplets formed in the host and blocking layers. We demonstrate substantial improvements in stability using the latter approach, and conclude with a discussion of potential approaches to managing dark triplets in OLEDs.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Characterizing Reactive Transport Behavior in a Three-Dimensional Discrete Fracture Network

While several studies have linked network and in-fracture scale properties to conservative transport behavior in subsurface fractured media, studies on reactive transport cases remain relatively underdeveloped. In this study, we explore the behavior of an irreversible kinetic reaction during the interaction of two solute plumes, one consisting of species A and the other species B. When the plumes converge, these species react kinetically to form a new species C via A+B→kC. This reactive system is studied using a three-dimensional discrete fracture network (DFN) model coupled with reactive Lagrangian particle tracking. We find that the interplay of network topology and chemical properties of the reactive solutes controls reactive transport processes. The network topology drives species A and B together, and the chemical properties dictate whether and how quickly a reaction occurs. Results demonstrate that reactions are most likely to occur in high-velocity fractures that make up the network backbone. The interplay between species’ chemical properties and transport is characterized by a non-dimensional Damköhler (Da) number. We show that the spatial distribution of reactions is sensitive to Da, which subsequently influences late-time tailing behavior in outlet breakthrough time distributions. The results of this study provide initial insights into how an irreversible reaction occurs during transport in a fracture network, using a methodology that can be applied to study reactive transport in a wide range of fractured media environments and contexts.

58 GEOSCIENCES↗

Discovery and molecular basis of subtype-selective cyclophilin inhibitors

Abstract Although cyclophilins are attractive targets for probing biology and therapeutic intervention, no subtype-selective cyclophilin inhibitors have been described. We discovered novel cyclophilin inhibitors from the in vitro selection of a DNA-templated library of 256,000 drug-like macrocycles for cyclophilin D (CypD) affinity. Iterated macrocycle engineering guided by ten X-ray co-crystal structures yielded potent and selective inhibitors (half maximal inhibitory concentration (IC 50 ) = 10 nM) that bind the active site of CypD and also make novel interactions with non-conserved residues in the S2 pocket, an adjacent exo-site. The resulting macrocycles inhibit CypD activity with 21- to >10,000-fold selectivity over other cyclophilins and inhibit mitochondrial permeability transition pore opening in isolated mitochondria. We further exploited S2 pocket interactions to develop the first cyclophilin E (CypE)-selective inhibitor, which forms a reversible covalent bond with a CypE S2 pocket lysine, and exhibits 30- to >4,000-fold selectivity over other cyclophilins. These findings reveal a strategy to generate isoform-selective small-molecule cyclophilin modulators, advancing their suitability as targets for biological investigation and therapeutic development.

Biochemistry & Molecular Biology↗

Improving PCM Waste Management Through New Approaches to Screening for LLW Treatment and Disposal - 20145

A major step forward in the management of Plutonium Contaminated Material (PCM) Waste has been taken at the Sellafield site with the introduction of new capabilities to enable wastes previously conservatively designated as PCM Intermediate Level Waste (ILW) to be re-classified for treatment as Low Level Waste (LLW). The Sellafield site, located in the North West of England, within the United Kingdom (UK), has operated plutonium processing plants and waste facilities for almost 70 years. During this time management of the raw PCM waste produced has presented a variety of challenges. The waste is currently processed by high force waste compaction in the Waste Treatment Complex (WTC). The WTC converts 200 litre drums of raw PCM waste into a compacted, grout encapsulated monolith form within stainless steel containment, ready for emplacement within the UK's Geological Disposal Facility (GDF) when it becomes available. To help progress some of the wastes waiting for treatment, recent improvements have been made with the introduction of new waste assay instrumentation which enables the identification of a 'candidate' waste potentially suitable for disposal via the LLW treatment route. Opening a new LLW route for previously designated PCM has been a major advance in PCM waste management policy. It has required a range of technical assessment arrangements to be developed, tested and commissioned and involved the engagement of a wide range of stakeholders. In particular, very detailed technical analysis methods have been developed to ensure that there is a robust and conservative approach to the final sentencing of waste. Following completion of commissioning tests, the first 86 m{sup 3} of previously designated PCM waste was successfully treated through the LLW route and consigned to LLW disposal in June 2019. The direct benefit of sentencing waste to the correct waste route (LLW) is the significant cost savings across the complete range of waste management activities. This work is also strategically important for demonstrating to a range of stakeholders including workforce and regulators, that waste previously designated as PCM can be re-classified in a systematic and justifiable way without increasing risk to personnel or the wider environment. By ensuring that waste is being managed appropriately it will be possible to carry out more remediation work safely, in less time, and at a lower cost. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Transforming an ATP-dependent enzyme into a dissipative, self-assembling system

Nucleoside triphosphate (NTP)-dependent protein assemblies such as microtubules and actin filaments have inspired the development of diverse chemically fueled molecular machines and active materials but their functional sophistication has yet to be matched by design. Given this challenge, we asked whether it is possible to transform a natural adenosine 5'-triphosphate (ATP)-dependent enzyme into a dissipative self-assembling system, thereby altering the structural and functional mode in which chemical energy is used. Furthermore we report that FtsH (filamentous temperature-sensitive protease H), a hexameric ATPase involved in membrane protein degradation, can be readily engineered to form one-dimensional helical nanotubes. FtsH nanotubes require constant energy input to maintain their integrity and degrade over time with the concomitant hydrolysis of ATP, analogous to natural NTP-dependent cytoskeletal assemblies. Yet, in contrast to natural dissipative systems, ATP hydrolysis is catalyzed by free FtsH protomers and FtsH nanotubes serve to conserve ATP, leading to transient assemblies whose lifetimes can be tuned from days to minutes through the inclusion of external ATPases in solution.

59 BASIC BIOLOGICAL SCIENCES↗

The interplay between chromophore and protein determines the extended excited state dynamics in a single-domain phytochrome

Phytochromes are a diverse family of bilin-binding photoreceptors that regulate a wide range of physiological processes. Their photochemical properties make them attractive for applications in optogenetics and superresolution microscopy. Phytochromes undergo reversible photoconversion triggered by the Z ⇌ E photoisomerization about the double bond in the bilin chromophore. However, it is not fully understood at the molecular level how the protein framework facilitates the complex photoisomerization dynamics. In this work, we have studied a single-domain bilin-binding photoreceptor All2699g1 ( Nostoc sp. PCC 7120) that exhibits photoconversion between the red light-absorbing (P r ) and far red-absorbing (P fr ) states just like canonical phytochromes. We present the crystal structure and examine the photoisomerization mechanism of the P r form as well as the formation of the primary photoproduct Lumi-R using time-resolved spectroscopy and hybrid quantum mechanics/molecular mechanics simulations. We show that the unusually long excited state lifetime (broad lifetime distribution centered at ~300 picoseconds) is due to the interactions between the isomerizing pyrrole ring D and an adjacent conserved Tyr142. The decay kinetics shows a strongly distributed character which is imposed by the nonexponential protein dynamics. Our findings offer a mechanistic insight into how the quantum efficiency of the bilin photoisomerization is tuned by the protein environment, thereby providing a structural framework for engineering bilin-based optical agents for imaging and optogenetics applications.

59 BASIC BIOLOGICAL SCIENCES↗

Drift orbit islands of energetic particles due to 3D fields in ITER

In this study, we report a comparative study of the orbit islands formed by the guiding center drift motion of test energetic particles (EPs), including both high-energy deuterium ions and fusion-born α-particles, with respect to the magnetic islands formed by tracing the field lines, for an ITER plasma representing the 15 MA baseline scenario. The particle drift orbit is modified by the presence of static resonant magnetic perturbations (RMPs) of different toroidal mode numbers n (n = 1 and 3 in this study), forming orbit islands in the Poincaré plane by passing EPs. The key findings are as follows. (i) With an n = 1 RMP field, the size of the orbit islands combined with the total RMP field, including the plasma response, is about three times smaller than that obtained by assuming the corresponding vacuum field. (ii) The orbit island size is not sensitive to the EP energy, and is comparable to those of the magnetic islands. (iii) Passing EPs with outward radial orbital drift form orbit islands that shift inward with respect to the corresponding magnetic islands, and vice versa. This radial shift, ΔΨ, measured in the normalized equilibrium poloidal flux, is quantified as ΔΨ ≃ 0.03X for the ITER baseline plasma and assuming n = 1 RMPs, with $X\equiv {(M/{M}_{\mathrm{p}})}^{1/2}{(E[\mathrm{M}\mathrm{e}\mathrm{V}])}^{1/2}{Z}^{-1}$, where M is the particle mass, Mp is the proton mass, E is the particle energy, and Z is the particle charge number. (iv) Trapped EPs do not form drift orbit islands, even in the presence of the 3D fields produced by the 90 kAt ELM control coil current in ITER, and thus possess good confinement properties. Nevertheless, the deformation of the trapped particle drift orbits in the Poincaré plane shows that the canonical toroidal angular momentum of EPs is no longer conserved in the presence of the RMP fields.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Systems with multi-circuited, phase-change composite heat exchangers

A system comprising a first plurality of microchannels, a second plurality of microchannels in thermal communication with the first plurality of microchannels such that the first plurality of microchannels and second plurality of microchannels form a heat exchanger, and a phase change composite in thermal communication with the heat exchanger and methods of operating are disclosed herein.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Modelling and simulation of brinicle formation

Below the Arctic sea ice, under the right conditions, a flux of icy brine flows down into the sea. The icy brine has a much lower fusion point and is denser than normal seawater. As a result, it sinks while freezing everything around it, forming an ice channel called a brinicle (also known as ice stalactite). In this paper, we develop a mathematical model for this phenomenon, assuming cylindrical symmetry. The fluid is considered to be viscous and quasi-stationary. The heat and salt transport are weakly coupled to the fluid motion and are modelled with the corresponding conservation equations, accounting for diffusive and convective effects. Finite-element discretization is employed to solve the coupled system of partial differential equations. We find that the model can capture the general behaviour of the physical system and generate brinicle-like structures while also recovering dendrite composition, which is a physically expected feature aligned with previous experimental results. This represents, to our knowledge, the first complete model proposed that captures the global structure of the physical phenomenon even though it has some discrepancies, such as brine accumulation.

97 MATHEMATICS AND COMPUTING↗

Analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets?

Fungal infections cause >1 million deaths annually and the emergence of antifungal resistance has prompted the exploration for novel antifungal targets. Quadruplexes are four-stranded nucleic acid secondary structures, which can regulate processes such as transcription, translation, replication and recombination. They are also found in genes linked to virulence in microbes, and ligands that bind to quadruplexes can eliminate drug-resistant pathogens. Using a computational approach, we quantified putative quadruplex-forming sequences (PQS) in 1359 genomes across the fungal kingdom and explored their presence in genes related to virulence, drug resistance and biological processes associated with pathogenicity in Aspergillus fumigatus. Here we present the largest analysis of PQS in fungi and identify significant heterogeneity of these sequences throughout phyla, genera and species. PQS were genetically conserved in Aspergillus spp. and frequently pathogenic species appeared to contain fewer PQS than their lesser/non-pathogenic counterparts. GO-term analysis identified that PQS-containing genes were involved in processes linked with virulence such as zinc ion binding, the biosynthesis of secondary metabolites and regulation of transcription in A. fumigatus. Although the genome frequency of PQS was lower in A. fumigatus, PQS could be found enriched in genes involved in virulence, and genes upregulated during germination and hypoxia. Moreover, PQS were found in genes involved in drug resistance. Quadruplexes could have important roles within fungal biology and virulence, but their roles require further elucidation.

59 BASIC BIOLOGICAL SCIENCES↗

The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis

Streptococcus mutans, found in the human oral cavity, is a significant contributor to the pathogenesis of dental caries. This bacterium expresses three genetically distinct types of glucosyltransferases named GtfB (GTF-I), GtfC (GTF-SI) and GtfD (GTF-S) that play critical roles in the development of dental plaque. The catalytic domains of GtfB, GtfC and GtfD contain conserved active-site residues for the overall enzymatic activity that relate to hydrolytic glycosidic cleavage of sucrose to glucose and fructose, release of fructose and generation of a glycosyl-enzyme intermediate in the reducing end. In a subsequent transglycosylation step, the glucosyl moiety is transferred to the nonreducing end of an acceptor to form a growing glucan polymer chain made up of glucose molecules. It has been proposed that both sucrose breakdown and glucan synthesis occur in the same active site of the catalytic domain, although the active site does not appear to be large enough to accommodate both functions. These three enzymes belong to glycoside hydrolase family 70 (GH70), which shows homology to glycoside hydrolase family 13 (GH13). GtfC synthesizes both soluble and insoluble glucans (α-1,3 and α-1,6 glycosidic linkages), while GtfB and GtfD synthesize only insoluble or soluble glucans, respectively. Here, crystal structures of the catalytic domains of GtfB and GtfD are reported. These structures are compared with previously determined structures of the catalytic domain of GtfC. With this work, apo structures and inhibitor-complex structures with acarbose are now available for the catalytic domains of GtfC and GtfB. The structure of GtfC with maltose allows further identification and comparison of active-site residues. A model of sucrose binding to GtfB is also included. The new structure of the catalytic domain of GtfD affords a structural comparison of the three S. mutans glycosyltransferases. Unfortunately, the catalytic domain of GtfD is not complete since crystallization resulted in the structure of a truncated protein lacking approximately 200 N-terminal residues of domain IV.

59 BASIC BIOLOGICAL SCIENCES↗

Influence of Photovoltaic Shading on Rooftop Heat Transfer, Building Energy Loads, and Photovoltaic Power Output

Photovoltaic (PV) modules on building rooftops provide shade from summer heating, leading to a reduction in cooling load during hot seasons. However, PV shading also reduces passive solar heating during winter months, leading to an increase in the building heating load during cold seasons. In this study, the heat transfer performance of an enclosure formed by adjacent PV modules is analyzed for three locations in the United States, comparing the daily heat flux through rooftops for the case of a PV-shaded rooftop as well as an unshaded roof. Several result metrics are developed as part of this work, including the saved energy load (SEL), or the energy conserved by adding PV-shading to the rooftop, and the additional energy load (AEL), or the supplemental building energy required to replace shaded solar heating. Lastly, this work calculates the utility factor, being the ratio of SEL and PV power output to AEL as a metric of PV effectiveness. SELs are 5.2, 6.2, and 11.7 kWh/m 2 · year for Dayton, Boise, and Phoenix, respectively, while the AELs for the same locations are 1.6, 1.5, and 2.1 kWh/m 2 · year. The utility factors for the same three locations are 61, 71, and 79. In general, locations with hot, non-cloudy summers and clear skies in winter see the largest utility factor. Further, it is shown that PV shading can conserve building energy during the winter months by preventing radiative losses to cold winter skies.

13 HYDRO ENERGY↗

A weighted shifted boundary method for immersed moving boundary simulations of Stokes' flow

The Shifted Boundary Method (SBM) belongs to the class of unfitted (or immersed, or embedded) finite element methods, and relies on reformulating the original boundary value problem over a surrogate (approximate) computational domain. The surrogate domain is constructed so as to avoid cut cells and the associated problematic implementation and numerical integration issues. Accuracy is maintained by modifying the original boundary conditions using Taylor expansions: hence the name of the method, that shifts the location and values of the boundary conditions. Here, in this article, we extend the SBM to the simulation of incompressible Stokes flow, by appropriately weighting its variational form with the elemental volume fraction of active fluid. This approach allows to drastically reduce spurious pressure oscillations in time, which are produced if the total volume of active fluid were to change abruptly over a time step. The proposed Weighted SBM (W-SBM) exactly preserves states of hydrostatic equilibrium, and induces small mass and momentum conservation errors, which converge as the grid is refined. This is in analogy to cutFEMs and related unfitted approaches, which rely on an affine representation of cut boundaries. We demonstrate the robustness and accuracy of the proposed method with an extensive suite of two-dimensional tests.

97 MATHEMATICS AND COMPUTING↗

Sequence-defined structural transitions by calcium-responsive proteins

Biopolymer sequences dictate their functions, and protein-based polymers are a promising platform to establish sequence–function relationships for novel biopolymers. To efficiently explore vast sequence spaces of natural proteins, sequence repetition is a common strategy to tune and amplify specific functions. This strategy is applied to repeats-in-toxin (RTX) proteins with calcium-responsive folding behavior, which stems from tandem repeats of the nonapeptide GGXGXDXUX in which X can be any amino acid and U is a hydrophobic amino acid. To determine the functional range of this nonapeptide, we modified a naturally occurring RTX protein that forms β-roll structures in the presence of calcium. Sequence modifications focused on calcium-binding turns within the repetitive region, including either global substitution of nonconserved residues or complete replacement with tandem repeats of a consensus nonapeptide GGAGXDTLY. Some sequence modifications disrupted the typical transition from intrinsically disordered random coils to folded β rolls, despite conservation of the underlying nonapeptide sequence. Proteins enriched with smaller, hydrophobic amino acids adopted secondary structures in the absence of calcium and underwent structural rearrangements in calcium-rich environments. In contrast, proteins with bulkier, hydrophilic amino acids maintained intrinsic disorder in the absence of calcium. In conclusion, these results indicate a significant role of nonconserved amino acids in calcium-responsive folding, thereby revealing a strategy to leverage sequences in the design of tunable, calcium-responsive biopolymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SaltStone Wastewater Cement Study Using Isothermal Calorimetry, Standard Concrete Characterization Techniques, and CemGEMS - 25169

Cementitious reagents are used to solidify/stabilize aqueous radioactive, hazardous, and mixed salt solutions, and sludges to meet low-level radioactive waste (LLW) and Resource Conservation and Recovery Act (RCRA) requirements for disposal at Department of Energy (DOE). It is flexible enough to solidify radioactive wastewater saturated in complex species that include but are not limited to radioactive isotopes from the bombardment of neutrons in reactor operation, corrosion products from metallic components, and a variety of soluble organic compounds. [1,2]. Waste form testing typically includes processing or fresh properties, cured properties, compressive strength and hydraulic properties, porosity, density, saturated and unsaturated moisture transport, and leachability of contaminants in the waste form pore solution. Properties are collected over a relatively limited time, typically 28 to 365 days [3]. In addition, changes in the waste form as the result of time and changing conditions are important for concrete engineers to predict overall performance of the forms and potential release of contaminants in the disposal process via unintended filtration into the environment [4]. These predictions are determined/calculated characterizing young waste forms (relative to the standard age of concrete) and are based on transport through soluble ions in pore solutions. Characterization methods include X-ray, SEM, and isothermal calorimetry among other methods used to define the composition, amorphous vs. crystalline nature of the components, and the energetic formation mechanisms for multi-phase mineral systems. [5–7] Isothermal calorimetry is a well standardized technique for cements and concretes and can be used to predict the timing and nature of the hydration reactions.[8] The technique can measure long term energetic

Bustamante, Michael E. [Savannah River National La↗

Unique structural solution from a V H 3-30 antibody targeting the hemagglutinin stem of influenza A viruses

Broadly neutralizing antibodies (bnAbs) targeting conserved influenza A virus (IAV) hemagglutinin (HA) epitopes can provide valuable information for accelerating universal vaccine designs. Here, we report structural details for heterosubtypic recognition of HA from circulating and emerging IAVs by the human antibody 3I14. Somatic hypermutations play a critical role in shaping the HCDR3, which alone and uniquely among V H 3-30 derived antibodies, forms contacts with five sub-pockets within the HA-stem hydrophobic groove. 3I14 light-chain interactions are also key for binding HA and contribute a large buried surface area spanning two HA protomers. Comparison of 3I14 to bnAbs from several defined classes provide insights to the bias selection of V H 3-30 antibodies and reveals that 3I14 represents a novel structural solution within the V H 3-30 repertoire. The structures reported here improve our understanding of cross-group heterosubtypic binding activity, providing the basis for advancing immunogen designs aimed at eliciting a broadly protective response to IAV.

59 BASIC BIOLOGICAL SCIENCES↗

pop-cosmos : redshifts and physical properties of KiDS-1000 galaxies

ABSTRACT Principled Bayesian inference of galaxy properties has not previously been performed for wide-area weak-lensing surveys with millions of sources. We address this gap by applying the pop-cosmos generative model to perform spectral energy distribution (SED) fitting for 4 million KiDS (Kilo-Degree Survey)-1000 galaxies. Calibrated on deep COSMOS2020 photometric data, pop-cosmos specifies a physically motivated prior over the galaxy population up to $z \simeq 6$ in stellar population synthesis (SPS) parameter space. Using the Speculator SPS emulator with GPU (graphics processing unit)-accelerated Markov Chain Monte Carlo sampling, we perform full posterior inference at 8.2 GPU seconds per galaxy, obtaining joint constraints on galaxy redshifts and physical properties. We validate photometric redshifts against $\sim \!185\,\!000$ KiDS galaxies cross-matched to Dark Energy Spectroscopic Instrument Data Release 1 spectroscopic samples, achieving low bias ($2\times 10^{-3}$), scatter ($\sigma _{\mathrm{MAD}}=0.03$), and outlier fraction (3.2 per cent) for the Bright Galaxy Survey, with comparable performance (bias $3\times 10^{-2}$, $\sigma _{\mathrm{MAD}}=0.05$, 1.0 per cent outliers) for luminous red galaxies (LRGs). Within the LRG sample, we identify massive, dusty, star-forming contaminants at $z \simeq 0.4$ satisfying standard colour selections for quenched populations. We infer trends in stellar mass, star formation, metallicity, and dust across five tomographic redshift bins consistent with established scaling relations. Using specific star formation rate constraints, we identify $\sim$7 per cent of KiDS-1000 galaxies as quenched, versus 37 per cent implied by conservative colour cuts. This enables the construction of weak-lensing samples defined by physical properties while mitigating intrinsic alignment systematics and preserving statistical power. Our analysis validates pop-cosmos out of sample, establishing it as a scalable approach for galaxy evolution and cosmological analyses with photometric surveys.

Halder, Anik [Institute of Astronomy and Kavli Ins↗