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At least 1,243 records · Page 69

Exploring the capabilities of optical pump X-ray probe NEXAFS spectroscopy to track photo-induced dynamics mediated by conical intersections

X-ray spectroscopy is gaining a growing interest in the scientific community, as it represents a versatile and powerful experimental toolbox for probing the dynamics of both core and valence electronic excitations, nuclear motions and material structure, with element and site specificity. Among the various X-ray based techniques, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, which investigates the energy and probability of resonant core-to-valence transitions, has started to be applied to organic molecules: a recent UV-pump X-ray probe time-resolved NEXAFS experiment [Wolf et al., Nat. Commun., 2017, 8, 1] has shown the capability of the technique to provide information about the ultrafast internal conversion between the bright ππ* and the dark nπ* electronic states of the nucleobase thymine. In the present contribution we introduce an accurate theoretical approach for the simulation of NEXAFS spectra of organic molecules, employing azobenzene as a test case. The electronic structure calculations, which provide both energy levels and transition probabilities of core-to-valence excitations, were here performed with a high level multiconfigurational method, the restricted active space self consistent field (RASSCF/RASPT2). GS- and nπ*-NEXAFS spectra were obtained on the top of key molecular geometries (as the optimized cis, trans and conical intersection(s) structures) as well as along the fundamental isomerization coordinates (namely, symmetric and asymmetric bendings of the phenyl rings, and torsion around the central dihedral). We eventually characterize and explain the origin of the simulated signals, highlighting the specific signatures that make it possible to follow the excited state evolution from the nπ* Franck–Condon point, towards the conical intersection(s).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Budget Constrained Machine Learning for Early Prediction of Adverse Outcomes for COVID-19 Patients

Background: Machine learning (ML) based risk stratification models of Electronic Health records (EHR) data may help to optimize treatment of COVID-19 patients, but are often limited by their lack of clinical interpretability and cost of laboratory tests. We develop a ML based tool for predicting adverse outcomes based on EHR data to optimize clinical utility under a given cost structure. This cohort study was performed using deidentified EHR data from COVID-19 patients from ProMedica Healthcare in northwest Ohio and southeastern Michigan. Methods: We tested performance of various ML approaches for predicting either increasing ventilatory support or mortality and the set of model features under a budget constraint was optimized via exhaustive search across all combinations of features. Results: The optimal sets of features for predicting ventilation under any budget constraint included demographics and comorbidities (DCM), basic metabolic panel (BMP), D-dimer, lactate dehydrogenase (LDH), erythrocyte sedimentation rate (ESR), CRP, brain natriuretic peptide (BNP), and procalcitonin and for mortality included DCM, BMP, complete blood count, D-dimer, LDH, CRP, BNP, procalcitonin and ferritin. Conclusions: This study presents a quick, accurate and cost-effective method to evaluate risk of deterioration for patients with SARS-CoV-2 infection at the time of clinical evaluation.

Cadena Pico, JoseE.↗

Multidisciplinary design optimization in Architecture, Engineering, and Construction: a detailed review and call for collaboration

The design of buildings has become a complex and multidisciplinary problem involving multiple conflicting objectives as architects and designers address competing technical, economic, environmental, and societal concerns. This has been driving research in Architecture, Engineering, and Construction (AEC) toward rigorous multidisciplinary decision-making frameworks that generate and evaluate numerous design alternatives using multi-objective optimization in concert with simulation and analysis models of varying fidelity and computational expense. While such frameworks are well known and widely employed in the aerospace and systems engineering domains, efforts by design professionals and researchers in the AEC field are scattered at best. In this paper, we provide a detailed review of recent developments in optimization frameworks in the AEC field and subsequently highlight how such developments are largely compartmentalized into separate domains such as structural, energy, daylighting, and other performance factors. Herein, we further discuss the technical challenges involved in concurrent coupled multidisciplinary design optimization (MDO) in the AEC field such as interoperability issues between Building Information Modeling (BIM) environments, analysis/simulation tools, and optimization frameworks. We conclude by outlining research needed for more unified modeling and simulation-based optimization frameworks to aid in complex and multidisciplinary building design processes. We also highlight the need for the identification and development of multi-fidelity simulation tools for use across multiple design phases. As such, this paper contributes a novel roadmap to leverage aerospace and systems engineering research in MDO into the field of AEC, along with a call for researchers in the MDO community to seek collaborations in AEC field.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Manufacturing and Validation of a Novel Composite Component for Aircraft Main Landing Gear Bay

Composite materials may reduce the final weight of the aircraft structural components, in addition to improve fatigue performance and corrosion resistance. In order to achieve the optimization of air transport systems, making them increasingly sustainable, the structural design must be surely reviewed, starting to follow the “composite thinking” philosophy. The present research provides some relevant outcomes concerning the design of a composite sample for the main landing gear bay of a large commercial airplane (EASA CS25 category), within ITEMB (integrated full composite main landing gear bay concept) project, a program of Clean Sky 2 EU research framework. The most ambitious goal is to develop a new generation of lower center fuselage (LCF) with an innovative integrated landing system in the fuselage, which is considered the next frontier in the development of landing systems for medium-haul aircraft, such as the Airbus A320 aircraft family. The development of a different architecture, with the landing gear integrated within the related fuselage bay, could lead to a simplification of the whole subassembly with potential advantage in terms of construction and assembly times. Final target of the project is the manufacturing of an innovative monolithic composite structure that will replace the actual configuration (a mixed structure of metal and composite subassemblies) reducing or actually removing all the cost of assembly and increasing the production rate. This paper presents the main results of the work, introducing the main processing steps and prototype results; in the last part of the work, also some experimental tests on significant element are introduced as the first assessment of the technology readiness level that has been achieved.

36 MATERIALS SCIENCE↗

Atomic-Scale Behavior of Radiation-Resistant ZnO under High-Energy Electron Bombardment

Understanding the atomic structure and defect characteristics of ZnO thin films is crucial for optimizing their electronic properties and performance in advanced applications. Here, we investigate the atomic structure and defect characteristics of atomic layer deposition (ALD)-grown ZnO thin films by using aberration-corrected scanning transmission electron microscopy (STEM). Atomic-resolution imaging identifies prevalent stacking faults, dipole disorder, and various grain boundary types, which are believed to influence the electronic properties of ZnO. Additionally, real-time electron beam exposure experiments demonstrate structural transformations, including crystal growth and surface rearrangements. These findings provide insights into the growth mechanisms of ALD ZnO under high-energy electron irradiation conditions, an important finding for the use of polycrystalline ZnO wide bandgap semiconductors in space-like conditions. In conclusion, our results underscore the capability of STEM in directly visualizing and quantifying atomic-scale defects and beam-induced transformations in radiation-resistant ZnO.

Defects↗

Analytical ab initio hessian from a deep learning potential for transition state optimization

Identifying transition states—saddle points on the potential energy surface connecting reactant and product minima—is central to predicting kinetic barriers and understanding chemical reaction mechanisms. In this work, we train a fully differentiable equivariant neural network potential, NewtonNet, on thousands of organic reactions and derive the analytical Hessians. By reducing the computational cost by several orders of magnitude relative to the density functional theory (DFT) ab initio source, we can afford to use the learned Hessians at every step for the saddle point optimizations. We show that the full machine learned (ML) Hessian robustly finds the transition states of 240 unseen organic reactions, even when the quality of the initial guess structures are degraded, while reducing the number of optimization steps to convergence by 2–3× compared to the quasi-Newton DFT and ML methods. All data generation, NewtonNet model, and ML transition state finding methods are available in an automated workflow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Seismic Characterization of the Nevada National Security Site Using Joint Body Wave, Surface Wave, and Gravity Inversion

As a part of the series of Source Physics Experiments (SPE) conducted on the Nevada National Security Site in southern Nevada, we have developed a local–to–regional scale seismic velocity model of the site and surrounding area. Accurate earth models are critical for modeling sources like the SPE to investigate the role of earth structure on the propagation and scattering of seismic waves. We combine seismic body waves, surface waves, and gravity data in a joint inversion procedure to solve for the optimal 3D seismic compressional and shear–wave velocity structures and earthquake locations subject to model smoothness constraints. Earthquakes, which are relocated as part of the inversion, provide P – and S –body–wave absolute and differential travel times. Active source experiments in the region augment this dataset with P –body–wave absolute times and surface–wave dispersion data. Dense ground–based gravity observations and surface–wave dispersion derived from ambient noise in the region fill in many areas where body–wave data are sparse. In general, the top 1–2 km of the surface is relatively poorly sampled by the body waves alone. However, the addition of gravity and surface waves to the body–wave dataset greatly enhances structural resolvability in the near surface. Here, we discuss the methodology we developed for simultaneous inversion of these disparate data types and briefly describe results of the inversion in the context of previous work in the region.

58 GEOSCIENCES↗

Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries

Type I modular polyketide synthases (PKSs) are multi-domain enzymes functioning like assembly lines. Many engineering attempts have been made for the last three decades to replace, delete and insert new functional domains into PKSs to produce novel molecules. However, inserting heterologous domains often destabilize PKSs, causing loss of activity and protein misfolding. To address this challenge, here we develop a fluorescence-based solubility biosensor that can quickly identify engineered PKSs variants with minimal structural disruptions. Using this biosensor, we screen a library of acyltransferase (AT)-exchanged PKS hybrids with randomly assigned domain boundaries, and we identify variants that maintain wild type production levels. We then probe each position in the AT linker region to determine how domain boundaries influence structural integrity and identify a set of optimized domain boundaries. Overall, we have successfully developed an experimentally validated, high-throughput method for making hybrid PKSs that produce novel molecules.

59 BASIC BIOLOGICAL SCIENCES↗

Physics makes the difference: Bayesian optimization and active learning via augmented Gaussian process

Abstract Both experimental and computational methods for the exploration of structure, functionality, and properties of materials often necessitate the search across broad parameter spaces to discover optimal experimental conditions and regions of interest in the image space or parameter space of computational models. The direct grid search of the parameter space tends to be extremely time-consuming, leading to the development of strategies balancing exploration of unknown parameter spaces and exploitation towards required performance metrics. However, classical Bayesian optimization (BO) strategies based on the Gaussian process (GP) do not readily allow for the incorporation of the known physical behaviors or past knowledge. Here we explore a hybrid optimization/exploration algorithm created by augmenting the standard GP with a structured probabilistic model of the expected system’s behavior. This approach balances the flexibility of the non-parametric GP approach with a rigid structure of physical knowledge encoded into the parametric model. The fully Bayesian treatment of the latter allows additional control over the optimization via the selection of priors for the model parameters. The method is demonstrated for a noisy version of a standard univariate test function used to evaluate optimization algorithms and further extended to physical lattice models. This methodology is expected to be universally suitable for injecting prior knowledge in the form of physical models and past data in the BO framework.

42 ENGINEERING↗

Synthesis of superconducting freestanding infinite-layer nickelate heterostructures on the millimetre scale

The development of superconductivity in infinite-layer nickelates through hole-doping relies on the controlled synthesis of Ni in a high oxidation state, followed by topotactic reduction to a very low oxidation state. So far, superconductivity has been realized only in epitaxial thin films. Here, in this work, we integrate these techniques with heterostructures that include an epitaxial soluble buffer layer, enabling the release of freestanding (Nd,Sr)NiO 2 heterostructures. The released heterostructures exhibit comparable structural and electronic properties to those of optimized thin films, with lateral dimensions ranging from millimetres to ~100 μm, depending on the degree of strain released with respect to the initial substrate. The changes in the superconducting transition temperature upon release of the heterostructure mirror those reported for variations in substrate and pressure, suggesting a common underlying response to strain in the infinite-layer nickelate superconductivity. These freestanding structures will facilitate a range of experimental studies without the constraints of substrates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantitative Prediction of Optical Absorption in Molecular Solids from an Optimally Tuned Screened Range-Separated Hybrid Functional

In this work, we show that fundamental gaps and optical spectra of molecular solids can be predicted quantitatively and nonempirically within the framework of time-dependent density functional theory (TDDFT) using the recently developed optimally tuned screened range-separated hybrid (OT-SRSH) functional approach. In this scheme, the electronic structure of the gas-phase molecule is determined by optimal tuning of the range-separation parameter in a range-separated hybrid functional. Screening and polarization in the solid state are taken into account by adding long-range dielectric screening to the functional form, with the modified functional used to perform self-consistent periodic-boundary calculations for the crystalline solid. We provide a comprehensive benchmark for the accuracy of our approach by considering the X23 set of molecular solids and comparing results obtained from TDDFT with those obtained from many-body perturbation theory in the GW-BSE approximation. We additionally compare results obtained from dielectric screening computed within the random-phase approximation to those obtained from the computationally more efficient many-body dispersion approach and find that this influences the fundamental gap but has little effect on the optical spectra. Our approach is therefore robust and can be used for studies of molecular solids that are typically beyond the reach of computationally more intensive methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine Learning assisted optimization and parameter space exploration dataset of spin ice Hamiltonian

This repository contains both simulated and experimental structure factor data for the data challenge involving the inverse scattering problem. The simulated data were generated during a machine-learning-assisted optimization routine described in ref[1]. The experimental structure factor was measured on a rare-earth oxide, Dy2Ti2O7 using diffuse neutron scattering from time-of-flight techniques on the CORELLI instrument at the Spallation Neutron Source, Oak Ridge National Laboratory. A Metropolis Monte Carlo code implemented to run in a High-performance computing setting was used to calculated simulated structure factors for the spin-ice Hamiltonian at 680 mK, which is the same temperature as for the experimental data. The total size of all the files in this repository is 5.12 GB. A detailed description of the files is given below. ExperimentalData_630mK.dat – A linearized version of 3-dimensional experimental data of size 61×81×21. This data was processed to remove an estimation of non-magnetic background, including nuclear scattering signal and instrumentation background. Parameters.dat – 6700 samples were evaluated over the 4-dimensional parameter space (J_1, J_2, J_3 and J_(3^' )). There is an additional parameter, D in the spin Hamiltonian to mimic the dipolar interaction between magnetic ions. However, this parameter, D was fixed to a value determined by prior work. This file contains five columns for the parameters J_1, J_2, J_3, J_(3^' ) and D respectively. 3D_Simulation_Data.dat – The simulated structure factor, S(Q) data are included in this file. Each raw contains a linearized array of 3D volumes of S(Q) calculated for the parameter set given in the corresponding row of the file Parameters.dat. The size of the volume data was matched to the experimental data. Qx(h,-h,0).dat, Qy(k,k,-2k).dat, Qz(l,l,l).dat – These files contain the h, k, and l values along with the reciprocal vectors [h,-h,0], [k,k,-2k] and [l,l,l] respectively.

36 MATERIALS SCIENCE↗

Use of a segmented cell for the combinatorial development of platinum group metal-free electrodes for polymer electrolyte fuel cells

The development of novel platinum group metal (PGM)-free catalysts is a difficult task, particularly when coupled with the integration into a cathode catalyst layer (CCL). The optimization of such PGM-free electrode structures is often non-linear and iterative, making it a demanding task due to the high number of parameters that affect performance. To accelerate both materials discovery and electrode development, this work demonstrates the application of a high-resolution segmented cell (SC) with 121 segments of 0.413 cm 2 size for combinatorial high-throughput PGM-free catalyst screening and CCL optimization. The approach utilizes three flow-field strips with active areas of 4.45 cm 2 each, distributed over 11 segments. Electrodes with identical catalyst material and fabrication method result in reproducible data with typically less than 10% variation between each segment and match in performance with differential single cell data. High throughput testing of combinatorial sample sets, with varied PGM-free electrocatalyst materials or electrode composition, demonstrated the ability to rapidly discern high performing outliers, and establish or confirm trends in electrode optimization. The results indicated significant performance benefits of electrodes with ionomer content of 45 wt% over lower values, and of water rich inks with 82% water content over those with 50%.

30 DIRECT ENERGY CONVERSION↗

Opportunities and Challenges for Machine Learning-Assisted Enzyme Engineering

Enzymes can be engineered at the level of their amino acid sequences to optimize key properties such as expression, stability, substrate range, and catalytic efficiency or even to unlock new catalytic activities not found in nature. Because the search space of possible proteins is vast, enzyme engineering usually involves discovering an enzyme starting point that has some level of the desired activity followed by directed evolution to improve its “fitness” for a desired application. Recently, machine learning (ML) has emerged as a powerful tool to complement this empirical process. ML models can contribute to (1) starting point discovery by functional annotation of known protein sequences or generating novel protein sequences with desired functions and (2) navigating protein fitness landscapes for fitness optimization by learning mappings between protein sequences and their associated fitness values. In this Outlook, we explain how ML complements enzyme engineering and discuss its future potential to unlock improved engineering outcomes.

60 APPLIED LIFE SCIENCES↗

ORNL_AISD_NiNb

This dataset describes the nickel-niobium solid solution binary alloy, where the two constituent elements nickel (Ni) and niobium (Nb) are randomly placed on an underlying crystal lattice. This dataset for nickel-niobium (Ni-Nb) alloys available includes the formation energy and bulk modulus for each crystal structure. Each atomic sample has a disordered phase which is obtained starting from an initial regular crystal structure of type body-centered cubic (BCC), face-centered cubic (FCC), or hexagonal compact packed (HCP). The geometry optimization ensures that all the alloy samples reached the equilibrium with negative formation energy. We perform geometry optimizations using the LAMMPS simulation package [1], a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. We utilized the embedded atom model (EAM) potential for Ni and Nb developed in a previous study [2]. The potential could describe behaviors of the liquid and solid phases of Ni-Nb alloy. The structural factors and angular distributions of three atoms are well-matched with X-ray and ab initio-based molecular dynamics data. We prepared the three different crystals with different initial lattice parameters (3.52 Ã… for FCC, 3.32 Ã… for BCC, and 3.5 Ã… for HCP). We performed energy minimization in two steps. Firstly, we minimized the structures with an isotropic unit cell to minimize the side effects from our arbitrary lattice parameters for all other compositions. Then, we applied geometry optimization with a triclinic (non-orthogonal) unit cell to fully minimize the stress components to calculate the elastic constants. In this procedure, we chose 10,000 as the maximum number of allowable steps aimed at obtaining fully relaxed atomic geometries. The dataset consists of three sets of crystal structures. The first set contains 46,086 irregular crystal structures, each of them with 54 atoms, obtained through optimization starting from a regular BCC crystal structure. The second set contains 24,543 irregular crystal structures, each of them with 32 atoms, obtained through optimization starting from a regular FCC crystal structure. The third set contains 39,303 irregular crystal structures, each of them with 48 atoms, obtained through optimization starting from a regular HCP crystal structure. The atomic configurations within each set span the possible compositional range. The three sets have been unified in a global dataset, which is extremely heterogeneous in terms of crystal structures, lattice volumes, and atomic configurations. Organization of files inside the dataset: the dataset contains three subdirectories called • BCC_opt • FCC_opt • HCP_opt based on the type of initial regular structure used to start the geometry optimization. Inside each of these folders, every atomic structure is identified by a string “A_B_Câ€, where A denotes the number of Nb in the system, B denotes index of structure with a given Nb number, and C denotes the total number of structures generated with a given Nb number. For each optimized crystal structure identified by the unique string of characters “A_B_Câ€, three files are provided: • A_B_C_opt.xyz: The optimized geometries in xyz format • A_B_C_opt.cfg: The optimized geometries in cfg format. It includes cell information and atomic energy, and forces calculated from LAMMPS. • A_B_C.elastic: Raw data of 21 elastic constants from LAMMPS output. • A_B_C.bulk: Calculated upper and lower bounds of bulk modulus and averaged one based on Voigt-Reuss-Hill approach from *.elastic. References: [1] A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in 't Veld, A. Kohlmeyer, S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott, and S. J. Plimpton. LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Comp. Phys. Comm., 271:108171, 2022. [2] Y Zhang, R Ashcraft, MI Mendelev, CZ Wang, and KF Kelton. Experimental and molecular dynamics simulation study of structure of liquid and amorphous ni62nb38 alloy. The Journal of chemical physics, 145(20):204505, 2016.

36 MATERIALS SCIENCE↗

Budget constrained machine learning for early prediction of adverse outcomes for COVID-19 patients

Abstract The combination of machine learning (ML) and electronic health records (EHR) data may be able to improve outcomes of hospitalized COVID-19 patients through improved risk stratification and patient outcome prediction. However, in resource constrained environments the clinical utility of such data-driven predictive tools may be limited by the cost or unavailability of certain laboratory tests. We leveraged EHR data to develop an ML-based tool for predicting adverse outcomes that optimizes clinical utility under a given cost structure. We further gained insights into the decision-making process of the ML models through an explainable AI tool. This cohort study was performed using deidentified EHR data from COVID-19 patients from ProMedica Health System in northwest Ohio and southeastern Michigan. We tested the performance of various ML approaches for predicting either increasing ventilatory support or mortality. We performed post hoc analysis to obtain optimal feature sets under various budget constraints. We demonstrate that it is possible to achieve a significant reduction in cost at the expense of a small reduction in predictive performance. For example, when predicting ventilation, it is possible to achieve a 43% reduction in cost with only a 3% reduction in performance. Similarly, when predicting mortality, it is possible to achieve a 50% reduction in cost with only a 1% reduction in performance. This study presents a quick, accurate, and cost-effective method to evaluate risk of deterioration for patients with SARS-CoV-2 infection at the time of clinical evaluation.

97 MATHEMATICS AND COMPUTING↗

Grand canonically optimized grain boundary phases in hexagonal close-packed titanium

Grain boundaries (GBs) profoundly influence the properties and performance of materials, emphasizing the importance of understanding the GB structure and phase behavior. As recent computational studies have demonstrated the existence of multiple GB phases associated with varying the atomic density at the interface, we introduce a validated, open-source GRand canonical Interface Predictor (GRIP) tool that automates high-throughput, grand canonical optimization of GB structures. While previous studies of GB phases have almost exclusively focused on cubic systems, we demonstrate the utility of GRIP in an application to hexagonal close-packed titanium. We perform a systematic high-throughput exploration of tilt GBs in titanium and discover previously unreported structures and phase transitions. In low-angle boundaries, we demonstrate a coupling between point defect absorption and the change in the GB dislocation network topology due to GB phase transformations, which has important implications for the accommodation of radiation-induced defects.

36 MATERIALS SCIENCE↗

Application of differential resonant high-energy X-ray diffraction to three-dimensional structure studies of nanosized materials: A case study of Pt–Pd nanoalloy catalysts

Atoms in many of the increasingly complex nanosized materials of interest to science and technology do not necessarily occupy the vertices of Bravais lattices. The atomic scale structure of such materials is difficult to determine by traditional X-ray diffraction and so their functional properties remain difficult to optimize by rational design. Here, the three-dimensional structure of Pt x Pd 100– x nanoalloy particles is determined, where x = 0, 14, 36, 47, 64 and 100, by a non-traditional technique involving differential resonant high-energy X-ray diffraction experiments conducted at the K edge of Pt and Pd. The technique is coupled with three-dimensional modeling guided by the experimental total and element-specific atomic pair distribution functions. Furthermore, using DFT (density functional theory) calculation based on the positions of atoms in the obtained three-dimensional structure models, the catalytic performance of Pt–Pd particles is explained. Furthermore, differential resonant high-energy X-ray diffraction is shown to be an excellent tool for three-dimensional structure studies of nanosized materials. The experimental and modeling procedures are described in good detail, to facilitate their wider usage.

36 MATERIALS SCIENCE↗