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At least 1,387 records · Page 77

Uranium (VI) Adsorbate Structures on Portlandite [Ca(OH)2] Type Surfaces Determined by Computational Modelling and X-ray Absorption Spectroscopy

Portlandite [Ca(OH) 2 ] is a potentially dominant solid phase in the high pH fluids expected within the cementitious engineered barriers of Geological Disposal Facilities (GDF). This study combined X-ray Absorption Spectroscopy with computational modelling in order to provide atomic-scale data which improves our understanding of how a critically important radionuclide (U) will be adsorbed onto this phase under conditions relevant to a GDF environment. Such data are fundamental for predicting radionuclide mass transfer. Surface coordination chemistry and speciation of uranium with portlandite [Ca(OH) 2 ] under alkaline groundwater conditions (ca. pH 12) were determined by both in situ and ex situ grazing incidence extended X-ray absorption fine structure analysis (EXAFS) and by computational modelling at the atomic level. Free energies of sorption of aqueous uranyl hydroxides, [UO 2 (OH) n ] 2–n (n = 0–5) with the (001), (100) and (203) or (101) surfaces of portlandite are predicted from the potential of mean force using classical molecular umbrella sampling simulation methods and the structural interactions are further explored using fully periodic density functional theory computations. Although uranyl is predicted to only weakly adsorb to the (001) and (100) clean surfaces, there should be significantly stronger interactions with the (203/101) surface or at hydroxyl vacancies, both prevalent under groundwater conditions. The uranyl surface complex is typically found to include four equatorially coordinated hydroxyl ligands, forming an inner-sphere sorbate by direct interaction of a uranyl oxygen with surface calcium ions in both the (001) and (203/101) cases. In contrast, on the (100) surface, uranyl is sorbed with its axis more parallel to the surface plane. The EXAFS data are largely consistent with a surface structural layer or film similar to calcium uranate, but also show distinct uranyl characteristics, with the uranyl ion exhibiting the classic dioxygenyl oxygens at 1.8 Å and between four and five equatorial oxygen atoms at distances between 2.28 and 2.35 Å from the central U absorber. These experimental data are wholly consistent with the adsorbate configuration predicted by the computational models. These findings suggest that, under the strongly alkaline conditions of a cementitious backfill engineered barrier, there would be significant uptake of uranyl by portlandite to inhibit the mobility of U(VI) from the near field of a geological disposal facility.

36 MATERIALS SCIENCE↗

WinPSSP : a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

The direct-space methods software Powder Structure Solution Program ( PSSP ) [Pagola & Stephens (2010). J. Appl. Cryst. 43 , 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs. WinPSSP is a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinates into the Rietveld analysis software GSAS. WinPSSP performance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.

60 APPLIED LIFE SCIENCES↗

How Aqueous Solvation Impacts the Frequencies and Intensities of Infrared Absorption Bands in Flavin: The Quest for a Suitable Solvent Model

FTIR spectroscopy accompanied by quantum chemical simulations can reveal important information about molecular structure and intermolecular interactions in the condensed phase. Simulations typically account for the solvent either through cluster quantum mechanical (QM) models, polarizable continuum models (PCM), or hybrid quantum mechanical/molecular mechanical (QM/MM) models. Recently, we studied the effect of aqueous solvent interactions on the vibrational frequencies of lumiflavin, a minimal flavin model, using cluster QM and PCM models. Those models successfully reproduced the relative frequencies of four prominent stretching modes of flavin’s isoalloxazine ring in the diagnostic 1450–1750 cm−1 range but poorly reproduced the relative band intensities. Here, we extend our studies on this system and account for solvation through a series of increasingly sophisticated models. Only by combining elements of QM clusters, QM/MM, and PCM approaches do we obtain an improved agreement with the experiment. The study sheds light more generally on factors that can impact the computed frequencies and intensities of IR bands in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SU-F-T-29: The Important of Each Fraction Image-Guided Planning for Postoperative HDR-Brachytherapy in Endometrial Carcinoma

Purpose: Cylindrical applicators are often used for postoperative HDRbrachytherapy in endometrial carcinoma. It has been considered that dosimetric variation between fractions for this treatment is minimal and might not be necessary to perform treatment planning for every fractions. At our institute, it is traditional to perform treatment planning with CT simulation on the first fraction and uses this plan for the rest of treatment. This study was aim to evaluate the errors of critical structure doses between the fractions when simulation and planning were done for first fraction only. Methods: Treatment plans of 10 endometrial carcinoma patients who received postoperative HDR-brachytherapy and underwent CT-simulation for every HDR-fractions at our department were retrospectively reviewed. All of these patients were treated with cylindrical applicator and prescribed dose 15Gy in 3 fractions to 0.5cm from vaginal surface. The treatment plan from the first fraction was used to simulate in second and third CT-simulation. Radiation dose for critical structures in term of Dose-to-2cc (D2cc) were evaluated and compared between planning CT. Results: The D2cc for bladder and rectum were evaluated. For bladder, the mean error of D2cc estimation for second and third fractions was 7.6% (0.1–20.1%, SD=5.7). And the mean error for D2cc of rectum was 8.5% (0.1–29.4%, SD=8.5). Conclusion: The critical structure doses could be significant difference between fractions which may affects treatment outcomes or toxicities. From our data, image-guided brachytherapy at least with CT-Simulation should be done for every treatment fractions.

60 APPLIED LIFE SCIENCES↗

Valence shell electronically excited states of norbornadiene and quadricyclane

The absolute photoabsorption cross sections of norbornadiene (NBD) and quadricyclane (QC), two isomers with chemical formula C 7 H 8 that are attracting much interest for solar energy storage applications, have been measured from threshold up to 10.8 eV using the Fourier transform spectrometer at the SOLEIL synchrotron radiation facility. The absorption spectrum of NBD exhibits some sharp structure associated with transitions into Rydberg states, superimposed on several broad bands attributable to valence excitations. Sharp structure, although less pronounced, also appears in the absorption spectrum of QC. Assignments have been proposed for some of the absorption bands using calculated vertical transition energies and oscillator strengths for the electronically excited states of NBD and QC. Natural transition orbitals indicate that some of the electronically excited states in NBD have a mixed Rydberg/valence character, whereas the first ten excited singlet states in QC are all predominantly Rydberg in the vertical region. In NBD, a comparison between the vibrational structure observed in the experimental 1 1 B 1 –1 1 A 1 (3sa 1 ← 5b 1 ) band and that predicted by Franck–Condon and Herzberg–Teller modeling has necessitated a revision of the band origin and of the vibrational assignments proposed previously. Similar comparisons have encouraged a revision of the adiabatic first ionization energy of NBD. Simulations of the vibrational structure due to excitation from the 5b 2 orbital in QC into 3p and 3d Rydberg states have allowed tentative assignments to be proposed for the complex structure observed in the absorption bands between ~5.4 and 7.0 eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of disordered TiO 2 phases from ab initio based deep neural network simulations

Amorphous TiO 2 (a-TiO 2 ) is widely used in many fields, ranging from photo-electrochemistry to bio-engineering, hence detailed knowledge of its atomic structure is of scientific and technological interest. Here we use an ab initio-based deep neural network potential (DP) to simulate large scale atomic models of crystalline and disordered TiO 2 with molecular dynamics. Our DP reproduces the structural properties of all (11) TiO 2 crystalline phases, predicts the densities and structure factors of molten and amorphous TiO 2 with only a few percent deviation from experiments, and describes the pressure dependence of the amorphous structure in agreement with recent observations. Furthermore, it can be extended to model additional structures and compositions and can be thus of great value in the study of TiO 2 -based (nano-)materials.

36 MATERIALS SCIENCE↗

Pulsed Thermal Tomography Nondestructive Examination of Additively Manufactured Reactor Materials and Components (Final Technical Report)

Metal Additive Manufacturing (AM) is a promising method for cost-efficient fabrication of complex shape structures for applications in harsh environment, such as in a nuclear reactor. However, internal defects (pores) occur in high-strength AM alloys, which are manufactured with Laser Powder Bed Fusion (LPBF) AM method. Pulsed Infrared Thermography (PIT) is an efficient nondestructive evaluation (NDE) method to examine actual structures, because this method offers one-sided non-contact measurements, and fast processing of large sample areas. However, imaging of material defects, particularly defects with sizes at microscopic level, is challenging. In this report, we benchmark the performance of several Unsupervised Learning (UL) algorithms designed to enhance imaging of microscopic defects in metals with PIT. UL aims to learn the latent principal patterns (dictionaries) in PIT data to detect defects with minimal human supervision. Performance of Independent Component Analysis (ICA), Sparse Coding (SC), Principal Component Analysis (PCA) and Exploratory Factor Analysis (EFA) was compared using F-score, UL model training time and defects reconstruction time. We obtained the average F-score of 0.75, and a highest F-score of 0.89 for the EFA algorithm. Overall, EFA outperforms other UL algorithms considered in this study. In another approach, we investigate Thermal Tomography (TT), which is a computational method for reconstruction of depth profile of internal material defects from PIT nondestructive evaluation (NDE). TT algorithm obtains depth reconstructions of thermal effusivity, which has been shown to provide visualization of subsurface internals defects in metals. In many applications, one needs to determine the defect shape and orientation from reconstructed effusivity images. Interpretation of TT images is non-trivial because of blurring, which increases with depth due to heat diffusion-based nature of image formation. We have developed a deep learning convolutional neural network (CNN) to classify size and orientation of subsurface material defects in TT images. CNN was trained with TT images produced with computer simulations of 2D metallic structures (thin plates) containing elliptical subsurface voids. Performance of CNN was investigated using test TT images developed with computer simulations of plates containing elliptical defects, and defects with shape imported from scanning electron microscopy (SEM) images. CNN demonstrated the ability to classify radii and angular orientation of elliptical defects in previously unseen test TT images. We have also demonstrated that CNN trained on TT images of elliptical defects is capable of classifying shape and orientation of irregular defects. Training the CNN on irregular defect shapes instead of on elliptical shapes would make the resulting classifications more descriptive of actual defect shapes. However, this requires a much higher volume of SEM images of material defects, which are difficult to obtain because of random occurrence of defects in LPBF. To address this challenge, we developed a generative adversarial network (GAN) to augment the existing dataset of SEM defect images. The GAN model is demonstrated to create novel yet realistic defect shapes that can be used as input for simulated PTT images to train CNN. We also investigate several approaches based on Gaussian Random Circle and Bezier Curves for constructing parametric models of irregular-shape defects.

36 MATERIALS SCIENCE↗

2.8-Å crystal structure of Escherichia coli YidC revealing all core regions, including flexible C2 loop

YidC/Alb3/Oxa1 family proteins are involved in the insertion and assembly of membrane proteins. The core five transmembrane regions of YidC, which are conserved in the protein family, form a positively charged cavity open to the cytoplasmic side. The cavity plays an important role in membrane protein insertion. In all reported structural studies of YidC, the second cytoplasmic loop (C2 loop) was disordered, limiting the understanding of its role. Here, we determined the crystal structure of YidC including the C2 loop at 2.8 Å resolution with R/R{sub free} = 21.8/27.5. This structure and subsequent molecular dynamics simulation indicated that the intrinsic flexible C2 loop covered the positively charged cavity. This crystal structure provides the coordinates of the complete core region including the C2 loop, which is valuable for further analyses of YidC.

60 APPLIED LIFE SCIENCES↗

Myna: Connecting powder bed fusion build data to simulation tools for digital twin applications

Additive manufacturing (AM), as a digital process, can generate a detailed digital thread linking a part’s design and manufacturing to its operational performance. As AM systems advance, an increasing amount of process data is stored in manufacturing databases. In principle, this data can be utilized by simulation-based digital twin approaches, such as real-time process control and asynchronous post-processing guidance. However, few tools currently exist for systematically integrating digital thread data with computational tools. Here, in this study, we propose a software package, called Myna, for connecting data from powder bed fusion processes to simulation tools. The utility of such a platform is demonstrated using build data from the Oak Ridge National Laboratory Manufacturing Demonstration Facility “Peregrine v2023-10” public dataset to automatically configure and run 54 semi-analytical 3DThesis melt pool simulations, 78 numerical Additive FOAM melt pool simulations, and 3 ExaCA microstructure simulations. The simulated, spatially registered microstructures are then compared directly with electron backscatter diffraction characterization of the corresponding as-built part locations. The resulting simulated microstructure showed variation as a function of process parameters, particularly stripe width; however, the experimental data had little variation between the microstructure texture and grain size resulting from different processing conditions. Analysis of the discrepancies suggest that it is possible a two-phase ferritic-austenitic solidification model is needed to accurately predict grain size and texture for certain stainless steel 316L feedstock compositions under powder bed fusion conditions, providing direction for future research. As illustrated here, due to the number and complexity of the simulations involved in AM process-structure–property predictions, automated methods to connect process data and simulations will remain necessary tools for testing hypotheses and implementing digital twin applications.

Knapp, Gerald L. [Oak Ridge National Laboratory (O↗

Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering

Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light–absorbing (Pr)–to–far-red light–absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa. Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an “II”-framed close form of the Pfr state to an “O”-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.

59 BASIC BIOLOGICAL SCIENCES↗

Optimization of Ca14MgSb11 through Chemical Substitutions on Sb Sites: Optimizing Seebeck Coefficient and Resistivity Simultaneously

In thermoelectric materials, chemical substitutions are widely used to optimize thermoelectric properties. The Zintl phase compound, Yb14MgSb11, has been demonstrated as a promising thermoelectric material at high temperatures. It is iso-structural with Ca14AlSb11 with space group I41/acd. Its iso-structural analog, Ca14MgSb11, was discovered to be a semiconductor and have vacancies on the Sb(3) sites, although in its nominal composition it can be described as consisting of fourteen Ca2+ cations with one [MgSb4]9− tetrahedron, one Sb37− linear anion and four isolated Sb3− anions (Sb(3) site) in one formula unit. When Sn substitutes Sb in Ca14MgSb11, optimized Seebeck coefficient and resistivity were achieved simultaneously although the Sn amount is small (<2%). This is difficult to achieve in thermoelectric materials as the Seebeck coefficient and resistivity are inversely related with respect to carrier concentration. Thermal conductivity of Ca14MgSb11-xSnx remains almost the same as Ca14MgSb11. The calculated zT value of Ca14MgSb10.80Sn0.20 reaches 0.49 at 1075 K, which is 53% higher than that of Ca14MgSb11 at the same temperature. The band structure of Ca14MgSb7Sn4 is calculated to simulate the effect of Sn substitutions. Compared to the band structure of Ca14MgSb11, the band gap of Ca14MgSb7Sn4 is smaller (0.2 eV) and the Fermi-level shifts into the valence band. The absolute values for density of states (DOS) of Ca14MgSb7Sn4 are smaller near the Fermi-level at the top of valence band and 5p-orbitals of Sn contribute most to the valence bands near the Fermi-level.

Hu, Yufei (ORCID:0000000308898786)↗

Diversity in the Common Fold: Structural Insights into Class D β-Lactamases from Gram-Negative Pathogens

Class D β-lactamases (DBLs) represent a major threat to antibiotic efficacy by hydrolyzing β-lactam drugs, including last-resort carbapenems, thereby driving antimicrobial resistance in Gram-negative bacteria. The enzymes share a structurally conserved two-domain α/β architecture with seven active-site motifs and three flexible extended loops (the P-loop, Ω-loop, and newly designated B-loop) that surround the active site. While each of these loops is known to influence enzyme function, their coordinated roles have not been fully elucidated. To investigate the significance of their interplay, we compared the sequences and crystal structures of 40 DBLs from clinically relevant Gram-negative pathogens and performed molecular dynamics simulations on selected representatives. Combined structural and dynamical analyses revealed a strong correlation between B-loop architecture and carbapenemase activity in the pathogens Klebsiella and Acinetobacter, particularly regarding loop length and spatial organization. These findings emphasize the B-loop’s critical contribution, in concert with the P- and Ω-loops, in tuning active site versatility, substrate recognition, catalytic activity, and structural stability. A deeper understanding of how these motifs and loops govern DBL function may inform the development of novel antibiotics and inhibitors targeting this class of enzymes.

antibiotic resistance↗

Photoluminescence properties of modulation-doped In{sub x}Al{sub 1–x}As/In{sub y}Ga{sub 1–y}As/In{sub x}Al{sub 1–x}As structures with strained inas and gaas nanoinserts in the quantum well

The photoluminescence spectra of modulation-doped InAlAs/InGaAs/InAlAs heterostructures with quantum wells containing thin strained InAs and GaAs inserts are investigated. It is established that the insertion of pair InAs layers and/ or a GaAs transition barriers with a thickness of 1 nm into a quantum well leads to a change in the form and energy position of the photoluminescence spectra as compared with a uniform In{sub 0.53}Ga{sub 0.47}As quantum well. Simulation of the band structure shows that this change is caused by a variation in the energy and wave functions of holes. It is demonstrated that the use of InAs inserts leads to the localization of heavy holes near the InAs layers and reduces the energy of optical transitions, while the use of GaAs transition barriers can lead to inversion of the positions of the light- and heavy-hole subbands in the quantum well. A technique for separately controlling the light- and heavy-hole states by varying the thickness and position of the GaAs and InAs inserts in the quantum well is suggested.

36 MATERIALS SCIENCE↗

Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase

Enzymes in the prolyl oligopeptidase family possess unique structures and substrate specificities that are important for their biological activity and for potential biocatalytic applications. In this work, the crystal structures of Pyrococcus furiosus (Pfu) prolyl oligopeptidase (POP) and the corresponding S477C mutant were determined to 1.9 and 2.2 Å resolution, respectively. The wild type enzyme crystallized in an open conformation, indicating that this state is readily accessible, and it contained bound chloride ions and a prolylproline ligand. These structures were used as starting points for molecular dynamics simulations of Pfu POP conformational dynamics. The simulations showed that large-scale domain opening and closing occurred spontaneously, providing facile substrate access to the active site. Movement of the loop containing the catalytically essential histidine into a conformation similar to those found in structures with fully formed catalytic triads also occurred. This movement was modulated by chloride binding, providing a rationale for experimentally observed activation of POP peptidase catalysis by chloride. Thus, the structures and simulations reported in this study, combined with existing biochemical data, provide a number of insights into POP catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomistic tensile deformation mechanisms of Fe with gradient nano-grained structure

Large-scale molecular dynamics (MD) simulations have been performed to investigate the tensile properties and the related atomistic deformation mechanisms of the gradient nano-grained (GNG) structure of bcc Fe (gradient grains with d from 25 nm to 105 nm), and comparisons were made with the uniform nano-grained (NG) structure of bcc Fe (grains with d = 25 nm). The grain size gradient in the nano-scale converts the applied uniaxial stress to multi-axial stresses and promotes the dislocation behaviors in the GNG structure, which results in extra hardening and flow strength. Thus, the GNG structure shows slightly higher flow stress at the early plastic deformation stage when compared to the uniform NG structure (even with smaller grain size). In the GNG structure, the dominant deformation mechanisms are closely related to the grain sizes. For grains with d = 25 nm, the deformation mechanisms are dominated by GB migration, grain rotation and grain coalescence although a few dislocations are observed. For grains with d = 54 nm, dislocation nucleation, propagation and formation of dislocation wall near GBs are observed. Moreover, formation of dislocation wall and dislocation pile-up near GBs are observed for grains with d = 105 nm, which is the first observation by MD simulations to our best knowledge. The strain compatibility among different layers with various grain sizes in the GNG structure should promote the dislocation behaviors and the flow stress of the whole structure, and the present results should provide insights to design the microstructures for developing strong-and-ductile metals.

36 MATERIALS SCIENCE↗

DFT investigation on structure, electronic and magnetic properties of Cr{sub n} (n=2-8) clusters

A density functional investigation on the series of chromium clusters, i.e., Cr{sub n} (n=2-8) is performed for finding their lowest energy structures and various electronic and magnetic properties. For electronic properties, we have predicted binding energy, HOMO-LUMO (HLG), chemical hardness (η) etc., and also for magnetic behavior, we have predicted the magnetic moments of the lowest energy cluster isomers. A systematic search imposing all possible initial magnetic configurations of the clusters is considered for finding lowest energy structures. All the calculations is carried out using a very popular GGA functional Perdew, Burke and Ernzerhof (PBE), as implemented in the VASP code.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Intermittency, coherent structures and dissipation in plasma turbulence

Collisionless dissipation in turbulent plasmas such as the solar wind and the solar corona has been an intensively studied subject recently, with new insights often emerging from numerical simulation. Here we report results from high resolution, fully kinetic simulations of plasma turbulence in both two (2D) and three (3D) dimensions, studying the relationship between intermittency and dissipation. The simulations show development of turbulent coherent structures, characterized by sheet-like current density structures spanning a range of scales. An approximate dissipation measure is employed, based on work done by the electromagnetic field in the local electron fluid frame. This surrogate dissipation measure is highly concentrated in small subvolumes in both 2D and 3D simulations. Fully kinetic simulations are also compared with magnetohydrodynamics (MHD) simulations in terms of coherent structures and dissipation. The interesting result emerges that the conditional averages of dissipation measure scale very similarly with normalized current density J in 2D and 3D particle-in-cell and in MHD. To the extent that the surrogate dissipation measure is accurate, this result implies that on average dissipation scales as ∼J{sup 2} in turbulent kinetic plasma. Multifractal intermittency is seen in the inertial range in both 2D and 3D, but at scales ∼ion inertial length, the scaling is closer to monofractal.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Systematic comparison of crystalline and amorphous phases: Charting the landscape of water structures and transformations

Systematically resolving different crystalline phases starting from the atomic positions, a mandatory step in algorithms for the prediction of structures or for the simulation of phase transitions, can be a non-trivial task. Extending to amorphous phases and liquids which lack the discrete symmetries, the problem becomes even more difficult, involving subtle topological differences at medium range that, however, are crucial to the physico-chemical and spectroscopic properties of the corresponding materials. Typically, system-tailored order parameters are devised, like global or local symmetry indicators, ring populations, etc. We show that a recently introduced metric provides a simple and general solution to this intricate problem. In particular, we demonstrate that a map can be traced displaying distances among water phases, including crystalline as well as amorphous states and the liquid, consistently with experimental knowledge in terms of phase diagram, structural features, and preparation routes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗