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At least 1,387 records · Page 77

Hydrogen Localization and Cluster Formation in α-Zr from First-Principles Investigations

We report alpha-zirconium (α-Zr) is a hydrogen atom host material used in nuclear energy and semiconducting applications due to Zr's excellent properties such as corrosion resistance, low thermal neutrons cross-section, and thermodynamically favorable interstitial sequestering of H atoms. Herein we use density functional theory simulations to systematically analyze the initial stages of H insertion in the Zr matrix, and determine optimal hydrogen localization, distribution, and clustering tendencies from a thermodynamics and kinetics perspective. Our results suggest that H occupation of tetrahedral sites is strongly favored, consistent with previous experimental and theoretical studies. Further, a cooperative effect in H localization is shown where H atoms favor clustering. The H pair is found to be the most stable by occupying tetrahedral sites with pairs at second nearest-neighbor positions (TTn2). Among the four H atom clusters, the most favorable configuration has two TTn2 pairs forming "box " or "zig-zag" shaped-cluster with the pairs separated by 3.03 or 3.25 Å, respectively. Nudged elastic band simulations suggest that the formation of TTn2 is facile and is limited by the small diffusion barrier of the monomer of less than 0.1 eV. Further, the formation routes for the 4H atom clusters are also presented. The current study can serve as a foundation to systematically model H atom clustering in metals and alloys.

36 MATERIALS SCIENCE↗

Prediction of Structures and Atomization Energies of Coinage Metals, (M)n, n < 20: Extrapolation of Normalized Clustering Energies to Predict the Cohesive Energy

The geometries of the group 11 coinage metals (n = 2-20) were optimized to determine the lowest energy isomers for each cluster size, singlets for even numbers and doublets for odd numbers. For copper and silver, 2-D (planar) geometries were favored up to n = 6. For gold, 2D (planar) geometries were favored up to n = 13. Normalized clustering energies were plotted as a function of cluster size (n-1/3, for n = 4-20) with various DFT functionals and the CCSD(T)-F12b method and were extrapolated to predict the bulk cohesive energy. In the case of copper and silver, there is excellent agreement between the cohesive energies predicted at the CCSD(T)-F12b level of theory and the experimental values. For gold, the CCSD(T)-F12b values needed to be corrected for spin-orbit relativistic effects to obtain good agreement with experiment. Electronic properties including the HOMO-LUMO gaps for the even clusters and the spin densities for the odd clusters were calculated. The lowest gap is predicted to occur for n = 16 where the HOMO and LUMO are very similar in shape.

Persuad, Rudradatt R.↗

Tensile behavior of diffusion bonded AA6061 - AA6061 with variation in cooling method

Hot isostatically pressed AA6061 cladding is an important structural component of the high performance, Zr-laminated U-10Mo monolithic fuel system for the application in research and test reactors. In this study, the mechanical behavior of two diffusion bonded aluminum alloy, AA6061, was examined using tensile testing. Solid-to-solid diffusion bonding between two pieces of AA6061 was performed by isothermal annealing at 560 °C for 1.5 h, and diffusion couples were subsequently cooled via three different cooling methods: furnace cooling, air cooling, and water quenching. Dog-bone shaped tensile specimens, with 10 mm in gauge length (with diffusion bonded interface in the middle), and 1.5 × 1.5 mm 2 gauge cross-sections, were fabricated from the diffusion bonded AA6061 by electro-discharge machining. Yield strength (% EL at failure) of furnace cooled, air cooled and water quenched tensile specimens determined was 82 ~ 89 MPa (10 ~ 30%), 112 ~ 116 MPa (10 ~ 14%), and 149 ~ 164 MPa (10 ~ 17%), respectively. This variation in mechanical behavior was examined with cooling-rate dependent, concentrated precipitation of Mg 2 Si at the diffusion bonded interface, with due respect for mechanical properties of the AA6061 alloy that inherently vary as a function of cooling rate from 560 °C. Finite element analysis using ABAQUS was employed to augment experimental findings with the appropriate microstructural constituents and alloy properties. Results suggest that the strength is dominated by matrix/bulk properties of AA6061, while ductility is strongly influenced by the cooling method dependent presence of Mg 2 Si precipitates at the interface.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Direct strain correlations at the single-atom level in three-dimensional core-shell interface structures

Abstract Nanomaterials with core-shell architectures are prominent examples of strain-engineered materials. The lattice mismatch between the core and shell materials can cause strong interface strain, which affects the surface structures. Therefore, surface functional properties such as catalytic activities can be designed by fine-tuning the misfit strain at the interface. To precisely control the core-shell effect, it is essential to understand how the surface and interface strains are related at the atomic scale. Here, we elucidate the surface-interface strain relations by determining the full 3D atomic structure of Pd@Pt core-shell nanoparticles at the single-atom level via atomic electron tomography. Full 3D displacement fields and strain profiles of core-shell nanoparticles were obtained, which revealed a direct correlation between the surface and interface strain. The strain distributions show a strong shape-dependent anisotropy, whose nature was further corroborated by molecular statics simulations. From the observed surface strains, the surface oxygen reduction reaction activities were predicted. These findings give a deep understanding of structure-property relationships in strain-engineerable core-shell systems, which can lead to direct control over the resulting catalytic properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A mathematical analysis of carbon fixing materials that grow, reinforce, and self-heal from atmospheric carbon dioxide

Carbon fixing materials are a new class of self-healing, self-reinforcing materials we have introduced that utilize ambient CO 2 to chemically add to an ever extending carbon backbone. This class of materials can utilize biological or non-biological photocatalysts and support a wide range of potential backbone chemistries. However, there is no analysis to date that describes their fundamental limits in terms of chemical kinetics and mass transfer. In this computational study, we employ a reaction engineering, and materials science analysis to answer basic questions about the maximum growth rate, photocatalytic requirements and limits of applicable materials. Our proposed mathematical framework envelops three main functions required for carbon fixing materials: (1) adsorption of CO 2 from air, (2) photocatalytic reduction of CO 2 into selected monomers, and (3) polymerization of CO 2 -derived monomers. First, by performing a Damköhler number analysis, we derive criteria for the cross over from kinetic control to mass transfer limited growth, setting upper limits on performance of a potential photocatalyst. Next, we analyze photocatalytic reduction of CO 2 to single carbon products, using known catalytic pathways and kinetic data. We identify formaldehyde as a C1 intermediate having unique potential for incorporation into the material backbone of carbon fixing materials. As an example, we find that a diamond-shaped reaction network graph for CO 2 reduction, passing through CO and HCOOH intermediates, accurately describes kinetic data for cobalt-promoted TiO 2 nanoparticles at room temperature and 1 atm CO 2 . Finally, as an applied case study, we consider and analyze the example of a carbon fixing poly(oxymethylene) system with embedded catalyst promoting the photocatalytic reduction of CO 2 to formaldehyde. The latter then trimerizes to a trioxane monomer which subsequently polymerizes to polyoxymethylene. This reaction engineering analysis introduces benchmarks for carbon fixing materials with respect to achievable rates of photocatalysis, adsorption, and polymerization. These results should prove valuable for the design, evaluation, and benchmarking of this emergent and new class of environmentally sustainable materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Monte Carlo control loops for cosmic shear cosmology with DES Year 1 data

Weak lensing by large-scale structure is a powerful probe of cosmology and of the dark universe. This cosmic shear technique relies on the accurate measurement of the shapes and redshifts of background galaxies and requires precise control of systematic errors. Monte Carlo control loops (MCCL) is a forward modeling method designed to tackle this problem. It relies on the ultra fast image generator (UFig) to produce simulated images tuned to match the target data statistically, followed by calibrations and tolerance loops. Here, we present the first end-to-end application of this method, on the Dark Energy Survey (DES) Year 1 wide field imaging data. We simultaneously measure the shear power spectrum $C_ℓ$ and the redshift distribution $n(z)$ of the background galaxy sample. The method includes maps of the systematic sources, point spread function (PSF), an approximate Bayesian computation (ABC) inference of the simulation model parameters, a shear calibration scheme, and a fast method to estimate the covariance matrix. We find a close statistical agreement between the simulations and the DES Y1 data using an array of diagnostics. In a nontomographic setting, we derive a set of $C_ℓ$ and $n(z)$ curves that encode the cosmic shear measurement, as well as the systematic uncertainty. Following a blinding scheme, we measure the combination of $Ω_m$, $σ_8$, and intrinsic alignment amplitude $A_{IA}$, defined as $S_8D_{IA}=σ_8(Ω_m/0.3)^{0.5}D_{IA}$, where $D_{IA}=1-0.11(A_{IA}-1)$. We find $S_8D_{IA}=0.8954_{-0.039}^{+0.054}$, where systematics are at the level of roughly 60% of the statistical errors. We discuss these results in the context of earlier cosmic shear analyses of the DES Y1 data. Our findings indicate that this method and its fast runtime offer good prospects for cosmic shear measurements with future wide-field surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

Cryptate binding energies towards high throughput chelator design: metadynamics ensembles with cluster–continuum solvation

A tiered forcefield/semiempirical/meta-GGA pipeline together with a thermodynamic scheme designed with error cancellation in mind was developed to calculate binding energies of [2.2.2] cryptate complexes of mono- and divalent cations. Stable complexes of Na, K, Rb, Ca, Zn and Pb were generated, revealing consistent cation–N lengths but highly variable cation–O lengths and an amine stacking mechanism potentially augmenting the cation size selectivity. Metadynamics, used for searching the high-dimensional potential energy surface, together with a cluster–continuum model for affordable – yet accurate – solvation modeling, enabled the discovery of more stable geometries than those previously reported. Similar solvation energy curve shapes for lone vs. coordinated ions enabled rapid solvation convergence via the cancellation of errors stemming from finite cluster sizes. In conclusion, an R 2 of 0.850 vs. experimental aqueous binding energies was obtained, validating this scheme as the backbone of a high-throughput workflow for chelator design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nonlinear spectroscopy in the condensed phase: The role of Duschinsky rotations and third order cumulant contributions

First-principles modeling of nonlinear optical spectra in the condensed phase is highly challenging because both environment and vibronic interactions can play a large role in determining spectral shapes and excited state dynamics. In this work, we compute two dimensional electronic spectroscopy (2DES) signals based on a cumulant expansion of the energy gap fluctuation operator, with specific focus on analyzing mode mixing effects introduced by the Duschinsky rotation and the role of the third order term in the cumulant expansion for both model and realistic condensed phase systems. We show that for a harmonic model system, the third order cumulant correction captures effects introduced by a mismatch in curvatures of ground and excited state potential energy surfaces, as well as effects of mode mixing. We also demonstrate that 2DES signals can be accurately reconstructed from purely classical correlation functions using quantum correction factors. We then compute nonlinear optical spectra for the Nile red and methylene blue chromophores in solution, assessing the third order cumulant contribution for realistic systems. We show that the third order cumulant correction is strongly dependent on the treatment of the solvent environment, revealing the interplay between environmental polarization and the electronic-vibrational coupling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A chemical kinetics theory for interpreting the non-monotonic temperature dependence of enzymatic reactions

Abstract. One notable observation of enzymatic chemical reactions is that, for a given abundance of enzymes and substrates, temperature increases cause reaction rates to first increase consistent with the Arrhenius relationship, then plateau, and finally fall off quickly to zero at high temperatures. While many mathematical functions have been used to describe this pattern, we here propose a chemical kinetics theory which successfully replicates this observation and provides insights into the processes responsible for these dynamics. The chemical kinetics theory combines the law of mass action, von Smoluchowski's diffusion-limited chemical reaction theory, and Eyring's transition state theory. This new theory reveals that the thermally reversible enzyme denaturation ensured by the ceaseless thermal motion of molecules and ions in an enzyme solution explains the plateau and subsequent decrease in chemical reaction rates with increasing temperature. The temperature-dependent affinity parameter (K) that relates enzymes and substrates through their binding also affects the shape of the emergent temperature response. We demonstrate that with an increase in substrate availability, K shifts the optimal temperature, where reaction rates plateau, towards higher values. Further, we show that the chemical kinetics theory accurately represents 12 sets of published enzyme assay data and includes the popular mechanistic model by Ratkowsky et al. (2005) as a special case. Given its good performance and solid theoretical underpinning, we believe this new theory will facilitate the construction of more mechanistic-based environmental biogeochemical models.

Tang, Jinyun↗

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

Abstract Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli , AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

Smooth trends in fermium charge radii and the impact of shell effects

The quantum-mechanical nuclear-shell structure determines the stability and limits of the existence of the heaviest nuclides with large proton numbers Z ≳ 100. Shell effects also affect the sizes and shapes of atomic nuclei, as shown by laser spectroscopy studies in lighter nuclides. However, experimental information on the charge radii and the nuclear moments of the heavy actinide elements, which link the heaviest naturally abundant nuclides with artificially produced superheavy elements, is sparse. Here we present laser spectroscopy measurements along the fermium (Z = 100) isotopic chain and an extension of data in the nobelium isotopic chain (Z = 102) across a key region. Multiple production schemes and different advanced techniques were applied to determine the isotope shifts in atomic transitions, from which changes in the nuclear mean-square charge radii were extracted. A range of nuclear models based on energy density functionals reproduce well the observed smooth evolution of the nuclear size. Both the remarkable consistency of model prediction and the similarity of predictions for different isotopes suggest a transition to a regime in which shell effects have a diminished effect on the size compared with lighter nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Outsourced hearing in an orb-weaving spider that uses its web as an auditory sensor

Hearing is a fundamental sense of many animals, including all mammals, birds, some reptiles, amphibians, fish, and arthropods. The auditory organs of these animals are extremely diverse in anatomy after hundreds of millions of years of evolution, yet all are made up of cellular tissue and are morphologically part of the bodies of animals. Here, we show that hearing in the orb-weaving spider Larinioides sclopetarius is not constrained by the organism’s body but is extended through outsourcing hearing to its extended phenotype, the proteinaceous, self-manufactured orb web. We find that the wispy, wheel-shaped orb web acts as a hyperacute acoustic antenna to capture the sound-induced air particle movements that approach the maximum physical efficiency better than the acoustic responsivity of all previously known eardrums. By sensing the motion of web threads, the spider remotely detects and localizes the source of an incoming airborne acoustic wave, such as those emitted by approaching prey or predators. By outsourcing its acoustic sensors to its web, the spider is released from body size constraints and permits the araneid spider to increase its sound-sensitive surface area enormously, up to 10,000 times greater than the spider itself. The spider also enables the flexibility to functionally adjust and regularly regenerate its external "eardrum" according to its needs. The outsourcing and supersizing of auditory function in spiders provides unique features for studying extended and regenerative sensing and designing novel acoustic flow detectors for precise fluid dynamic measurement and manipulation.

60 APPLIED LIFE SCIENCES↗

TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii

Abstract Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt‐loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme‐coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum , TrmB‐dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii . The ∆ trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name t rm B s u p pressor, or TbsP (a.k.a. “tablespoon”). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild‐type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose‐dependent transcription of gapII , which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii .

Biochemistry & Molecular Biology↗

BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data

Bacterial microcompartments (BMCs) are protein-based organelles found across the bacterial tree of life. They consist of a shell, made of proteins that oligomerize into hexagonally and pentagonally shaped building blocks, that surrounds enzymes constituting a segment of a metabolic pathway. The proteins of the shell are unique to BMCs. They also provide selective permeability; this selectivity is dictated by the requirements of their cargo enzymes. We have recently surveyed the wealth of different BMC types and their occurrence in all available genome sequence data by analyzing and categorizing their components found in chromosomal loci using HMM (Hidden Markov Model) protein profiles. To make this a “do-it yourself” analysis for the public we have devised a webserver, BMC Caller (https://bmc-caller.prl.msu.edu), that compares user input sequences to our HMM profiles, creates a BMC locus visualization, and defines the functional type of BMC, if known. Shell proteins in the input sequence data are also classified according to our function-agnostic naming system and there are links to similar proteins in our database as well as an external link to a structure prediction website to easily generate structural models of the shell proteins, which facilitates understanding permeability properties of the shell. Additionally, the BMC Caller website contains a wealth of information on previously analyzed BMC loci with links to detailed data for each BMC protein and phylogenetic information on the BMC shell proteins. Our tools greatly facilitate BMC type identification to provide the user information about the associated organism’s metabolism and enable discovery of new BMC types by providing a reference database of all currently known examples.

59 BASIC BIOLOGICAL SCIENCES↗

Dual-Responsive Macromolecular Surfaces with Binary Patterns

The development of nanopatterned interfaces incorporating multiple stimuli-responsive polymers has great potential for advancing smart sensors and molecular capture devices, yet it remains challenging due to limitations in patterning techniques and “grafting from” methods. Here, we present a binary-patterned surface featuring honeycomb-shaped photothermal polypyrrole (PPy) and thermally responsive poly(ethylene glycol methyl ether acrylate-co-poly(ethylene glycol) methyl ether acrylate) [poly(EGMEA-co-PEGMEA)] brushes within the cavities, fabricated using colloidal lithography and surface-initiated photoinduced electron transfer-reversible addition–fragmentation chain transfer (SI-PET-RAFT) polymerization. The morphology of the surface can be precisely tuned by adjusting the height of each domain. This design integrates unique topographical features with the stimuli-responsiveness of the polymer, enabling the collapse of the copolymer brushes through direct heating or photothermal conversion of PPy under near-IR light. In conclusion, this innovative system offers potential capture-release functionality, providing versatility for diverse applications and enhancing adaptability across different functional scenarios.

Copolymers↗

Charge Transfer Plasmonics in Bespoke Graphene/α-RuCl 3 Cavities

Surface plasmon polaritons (SPPs) provide a window into the nano-optical, electrodynamic response of their host material and its dielectric environment. Graphene/α-RuCl 3 serves as an ideal model system for imaging SPPs since the large work function difference between these two layers facilitates charge transfer that hole dopes graphene with n ~ 10 13 cm –2 free carriers. In this work, we study the emergent THz response of graphene/α-RuCl 3 heterostructures using our home-built cryogenic scanning near-field optical microscope. Using phase-resolved imaging, we clearly observe long wavelength, heavily damped THz SPPs in a series of variable-size graphene cavities. From this, we extract the plasmonic wavelength and scattering rate in the graphene/α-RuCl 3 heterostructures. We determine that the measured plasmon wavelength and electronic scattering rate match our heterostructures’ theoretically predicted values. Here, our results demonstrate that shaping graphene into bespoke cavity structures enables observation and quantification of SPPs in heavily doped graphene that are largely not addressable with other experimental techniques. Moreover, the manifest lack of metallicity observed in the adjacent doped α-RuCl 3 layer provides significant constraints on the nature of the interfacial charge transfer in this 2D heterostructure.

36 MATERIALS SCIENCE↗

A multi-sheath model for highly nonlinear plasma wakefields

An improved description for nonlinear plasma wakefields with phase velocities near the speed of light is presented and compared against fully kinetic particle-in-cell simulations. These wakefields are excited by intense particle beams or lasers pushing plasma electrons radially outward, creating an ion bubble surrounded by a sheath of electrons characterized by the source term S≡−1enp(ρ−Jz/c), where ρ and Jz are the charge and axial current densities, respectively. Previously, the sheath source term was described phenomenologically with a positive-definite function, resulting in a positive definite wake potential. In reality, the wake potential is negative at the rear of the ion column which is important for self-injection and accurate beam loading models. To account for this, we introduce a multi-sheath model in which the source term, S, of the plasma wake can be negative in regions outside the ion bubble. Using this model, we obtain a new expression for the wake potential and a modified differential equation for the bubble radius. Numerical results obtained from these equations are validated against particle-in-cell simulations for unloaded and loaded wakes. The new model provides accurate predictions of the shape and duration of trailing bunch current profiles that flatten plasma wakefields. It is also used to design a trailing bunch for a desired longitudinally varying loaded wakefield. We present beam loading results for laser wakefields and discuss how the model can be improved for laser drivers in future work. Finally, we discuss differences between the predictions of the multi- and single-sheath models for beam loading.

Dalichaouch, T. N. (ORCID:0000000247350150)↗

Effect of surface defects on damage and failure of dynamically driven cylindrical shells

Here, in this work, expanding cylinder experiments are performed using a gas gun on the aluminum 6061 alloy to understand the dynamic deformation and failure behavior of this material in the presence of surface defects in the form of scratches. The experiments are then modeled with the modified Tepla (for tensile plasticity) model, which is equipped with the damage yield function of Gurson [“Continuum theory of ductile rupture by void nucleation and growth: Part I—Yield criteria and flow rules for porous ductile media,” (1977)] and Tvergaard and Needleman [Acta Metall. 32(1), 157–169 (1984)], over-stress viscosity [F. Addessio and J. Johnson, J. Appl. Phys. 74(3), 1640–1648 (1993)], and the underlying viscoplastic model of Preston et al. [J. Appl. Phys. 93(1), 211–220 (2003)] (Preston–Tonks–Wallace model) for the dense material. The Tepla model parameters were calibrated using the Bayesian approach against experimentally measured free-surface velocity data obtained from plate impact experiments on the aluminum 6061 alloy. The evolution of radial expansion and shapes of the deformed cylinder from the simulations on a pristine cylinder wall and a cylinder wall with a longitudinal surface defect shows excellent agreement with the corresponding experimental results. Finally, the role of surface defect size and cylinder wall geometry on the dynamic strength of the cylinder wall was also investigated through a series of simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗