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At least 433 records · Page 24

X-ray absorption spectroscopy of trivalent Eu, Gd, Tb, and Dy chlorides and oxychlorides

Growing interest in next generation molten salt nuclear reactors necessitates a fundamental understanding of the chemical and physico-chemical properties of fission products, including elements of the lanthanide series. In this study, we probed coordination environment of Eu, Gd, Tb, and Dy in their chloride salts with both laboratory and synchrotron scale X-ray absorption spectroscopy (XAS). Here the aerobic melting was carried out with LnCl 3 ·nH 2 O, where Ln is Eu, Gd, Tb, and Dy, and yielded predominant formation of oxychlorides (LnOCl), that was confirmed by extended X-ray absorption fine structure (EXAFS) analysis and X-ray diffraction (XRD). Density functional theory (DFT) and time-dependent density functional theory (TDDFT) computations were performed to obtain ground state structures, lattice parameters, and to simulate L 3 -edge XANES (X-ray absorption near edge structure) spectra of the LnCl 3 ·nH 2 O and LnOCl. A blue shift, initially predicted by our calculations, was also observed for the experimental Ln L 3 -edge XANES spectra of the hydrated trichlorides vs oxychlorides, highlighting the power of combining the predictive ability of theory with experiment to elucidate the properties of the compounds of interest. The blue shift is indicative of structural stabilization of LnCl 3 ·nH 2 O due to higher symmetry compared with LnOCl. To the best of knowledge, this is a first study providing the framework for fundamental insights into the structure of Ln trichlorides and oxychlorides in support of future characterization of lanthanides in the molten salt environment.

36 MATERIALS SCIENCE↗

Computationally efficient Bayesian estimation of graphical networks for omics data

Graphical networks are useful, widely-used modeling approaches to represent complex biological processes with biological measurements generated by platforms such as mass spectrometry. Bayesian analyses of graphical networks for omics data have several advantages over their frequentist counterparts, such as the inclusion of prior knowledge in the estimation of models. However, Bayesian approaches to date have only been feasible for data with a couple hundred biomolecules due to prohibitive computational time, but omics data often contains tens of thousands of biomolecules. Here, we present and illustrate a more computationally efficient approach named BPlane (Bayesian PseudoLikelihood-based Algorithm for Network Estimation) to extend Bayesian modeling capabilities for larger-sized datasets, such as most untargeted proteomics data. Via simulation, we demonstrate that BPlane produces substantial computational savings over a current state-of-the-art Bayesian algorithm while maintaining competitive edge detection accuracy. On a SARS-CoV2 proteomics data with 7000 proteins, the competing algorithm takes three times as long to complete the first iteration as BPlane takes to converge after over 100 iterations.

EM algorithm↗

Understanding the Impact of Data Staging for Coupled Scientific Workflows

We report the rate of data generated by cutting-edge experimental science facilities and large-scale simulations enabled by current high-performance computing (HPC) systems has continued to grow at a far greater pace than the development of the network and storage capabilities on which these systems rely. To cope with this challenge, scientist are moving toward the creation of autonomous experiments and HPC simulations using machine learning. However, efficiently moving, storing, and processing large amounts of data away from the point of origin presents an incredible challenge. In-memory computing, in situ analysis, data staging, and data streaming are recognized viable alternatives to traditional file-based methods for transferring data between coupled workflows. However, the performance trade-offs and limitations for these methods are not fully understood when used in HPC applications. This article presents a comprehensive performance assessment of the current solutions for data staging when applied to applications that are not necessary I/O intensive which makes them not ideal candidates for these methods. Our study is based on experiments running at scale on Oak Ridge National Laboratory's Summit supercomputer using applications and simulations that cover typical computational motifs and patterns. We investigated the usability and cost/benefit trade-offs of staging algorithms for HPC applications under different scenarios and highlight opportunities for optimizing the dataflow between coupled simulation workflows.

97 MATHEMATICS AND COMPUTING↗

On the Robustness of Network Community Structure Under Addition of Edges

Communities represent important functional modules in networked systems. A key goal in preserving such communities is understanding their robustness under perturbations. Previous research has studied the impact of node removals and edge removals on the community structure. However, the impact of edge additions on the robustness of the community structure is relatively unknown. Edge additions or false positive edges may simulate measurement errors or external exceptional events that threaten the functionality of networked systems. Here, we study the impact of edge additions on the community structure using Lancichinetti-Fortunato-Radicchi (LFR) benchmark networks. We show that, for a fixed network size, the impact of edge additions is greater on networks with initially weak community structure than on networks with strongly clustered structures. In addition, we find that the perception of the impact is also dependent on the community detection algorithm used to uncover communities. In particular, we found that modularity-based methods such as Leiden and Louvain are less affected than information-theoretic and message passing-based methods such as Infomap and Label Propagation. Our results demonstrate that edge addition can (a) significantly impact the community structure of networks based on their initial conditions, and (b) the perception of the impact is dependent on the community detection algorithm used. We describe limitations, open challenges, and how this methodology can inform the design of resilient networked systems under edge additions.

97 MATHEMATICS AND COMPUTING↗

Topical Group on Application and Industry Community Engagement Frontier Snowmass 2021 (Summary Report)

HEP community leads and operates cutting-edge experiments for the DOE Office of Science which have challenging sensing, data processing, and computing requirements that far surpass typical industrial applications. To make necessary progress in the energy, material, and fundamental sciences, development of novel technologies is often required to enable these advanced detector and accelerator programs. Our capabilities include efficient co-design, which is a prerequisite to enable the deployment of advanced techniques in a scientific setting where development spans from rapid prototyping to robust and reliable production scale. This applies across the design spectrum from the low level fabrication techniques to the high level software development. It underpins the requirement for a holistic approach of innovation that accelerates the cycle of technology development and deployment. The challenges set by the next generation of experiments requires a collaborative approach between academia, industry and national labs. Just a single stakeholder will be unable to deliver the technologies required for the success of the scientific goals. Tools and techniques developed for High Energy Physics (HEP) research can accelerate scientific discovery more broadly across DOE Office of Science and other federal initiatives and also benefit industry applications.

43 PARTICLE ACCELERATORS↗

Building a Computational and Experimental Rapid Response Pipeline to Counter the Coronavirus Disease 2019 Outbreak and Emerging Biothreats

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs, especially where protective candidates can be rapidly identified or developed for emerging biothreats and escape variants. Current cutting-edge technologies for this purpose still rely on pathogen-exposed convalescent volunteers and a large screening effort to find a proverbial needle in a haystack. Computational design of protective antibodies based on pre-existing templates skips those requirements and allows for greater control over the breadth and target epitope, while also co-optimizing for potency and developability or other biophysical characteristics. We approached this problem by building and expanding an in vitro experimental rapid antibody production and characterization pipeline to support development of an autonomous, closed loop, active learning software system based on structural simulation and ground truth experimental data to design and evaluate antibody antigen interactions. Starting from early in the pandemic, we targeted SARS-CoV-2, the causative agent of COVID-19, by re-purposing neutralizing antibodies against SARS-CoV-1 that had been identified in the wake of that outbreak in the early 2000’s. We successfully re-targeted three different anti-SARS-CoV-1 antibodies to neutralize SARS-CoV-2 in vitro, where the antibodies were generated externally and tested through conventional binding and neutralization assays internally or with collaborators. As antibodies were identified from the blood of humans infected with SARS-CoV-2, we shifted to collaborate with academic partners to develop improved versions of their human-derived antibodies. This work reached its most important stage in rapid response to the emergence of the Omicron variant of concern (VOC) in late 2021. In a matter of weeks, enabled by on demand innovation to our screening pipeline, we computationally designed and experimentally characterized derivative antibodies of COV2-2130, one of two antibodies from Vanderbilt that form the basis of the AstraZeneca Evusheld prophylactic drug product. This drug product suffers a serious loss of efficacy against Omicron BA.1 and BA.1.1, the first Omicron strains. Due to tight integration of computational design and experimental evaluation, we were able to identify a pair of designs with potent neutralization of the main targets Omicron BA.1 and BA.1.1; but also the earlier Delta variant, and subsequent Omicron strains including BA.2, BA.4, BA.5, and BA.2.75, demonstrating that our multi-target design process can, by its nature, produce robust antibody designs that strictly improve over the parental antibody. These results, recognized by a 2022 Director’s Science and Technology award, have enabled the follow-on GUIDE program, to commence in FY23. While earlier design campaigns were substantially outsourced, we have engineered better and faster processes internally to better compliment, calibrate, and speed computational designs. As part of the follow-on GUIDE program, we will stand up a rapid and high-throughput antibody production and characterization facility staffed with the expertise and capabilities to foster our current collaboration across PLS and ENG as well as other partnerships toward computational design of biologics.

59 BASIC BIOLOGICAL SCIENCES↗

High-throughput and data-driven search for stable optoelectronic AMSe 3 materials

The rapid advancement in emerging optoelectronic technologies demands highly efficient, affordable, and ecofriendly materials. In this context, ternary chalcogenides, especially ternary selenides, show early promise as a material class due to their stability and remarkable electronic, optical, and transport properties. In this work, we integrate first-principles-based high-throughput computations with machine learning (ML) techniques to predict the thermodynamic stability and optoelectronic properties of 920 valency-satisfied selenide compounds. Through investigating polymorphism, our study reveals the edge-sharing orthorhombic Pnma phase (NH 4 CdCl 3 -type) as the most stable structure for most ternary selenides. High-fidelity supervised ML models are trained and tested to accelerate stability and band gap predictions. These data-driven models pin down the most influential features that dominantly control key material characteristics. The multistep high-throughput computations identify the ternary selenides with optimal direct band gaps, light carrier masses, and strong optical absorption edges. The extensive materials screening considering phase stability, toxicity, and defect tolerance, finally identifies the seven most suitable candidates for photovoltaic applications. Two of these final compounds, SrZrSe 3 and SrHfSe 3 , have already been synthesized in a single-phase form, with the latter showing an optically suitable band gap, aligning well with our findings. The non-adiabatic molecular dynamics reveal sufficiently long photoexcited charge carrier lifetimes (on the order of nanoseconds) in some of these selected selenide materials, indicating their exciting characteristics. Overall, our study suggests a robust in silico framework that can be extended to screen large datasets of various material classes for identifying promising photoactive candidates.

36 MATERIALS SCIENCE↗

Evaluating the Effect of Vane Trailing Edge Flow on Turbine Rim Sealing

Abstract Modern gas turbine development continues to move toward increased overall efficiency, driven in part by higher firing temperatures that point to a need for more cooling air to prevent catastrophic component failure. However, using additional cooling flow bled from the upstream compressor causes a corresponding detriment to overall efficiency. A primary candidate for cooling flow optimization is purge flow, which contributes to sealing the stator–rotor cavity and prevents ingestion of hot main gas path (MGP) flow into the wheelspace. Previous research has identified that the external main gas path flow physics play a significant role in driving rim seal ingestion. However, the potential impact of other cooling flow features on ingestion behavior, such as vane trailing edge (VTE) flow, is absent in the open literature. This paper presents experimental measurements of rim cavity cooling effectiveness collected from a one-stage turbine operating at engine-representative Reynolds and Mach numbers. Carbon dioxide (CO2) was used as a tracer gas in both the purge flow and vane trailing edge flow to investigate flow migration into and out of the wheelspace. Results show that the vane trailing edge flow does in fact migrate into the rim seal and that there is a superposition relationship between individual cooling flow contributions. Computational fluid dynamics (CFD) simulations using unsteady Reynolds-averaged Navier–Stokes (URANS) were used to confirm VTE flow ingestion into the rim seal cavity. Radial and circumferential traverse surveys were performed to quantify cooling flow radial migration through the main gas path with and without vane trailing edge flow. The surveys confirmed that vane trailing edge flow is entrained into the wheelspace as purge flow is reduced. Local CO2 measurements also confirmed the presence of VTE flow deep in the wheelspace cavity.

Engineering↗

Transforming Energy Through Computational Excellence: Advanced Scientific Visualization Reveals Energy Insights

The National Renewable Energy Laboratory's world-class researchers and analysts, along with the Insight Center (our state-of-the-art scientific visualization facility) make data immersion a reality, allowing users to step into and explore their data. With the rise of large, diverse, and distributed data sets, scientific visualization is now critical to the process of scientific discovery and to managing and analyzing data and extracting insights. NREL provides visualization capabilities and facilities that are supported by state-of-the-art equipment, leading-edge techniques, and expert staff.

data science↗

Bigpicc: a graph-based approach to identifying carcinogenic gene combinations from mutation data

Abstract Genome data from cancer patients represents relationships between the presence of a gene mutation and cancer occurrence in a patient. Different types of cancer in human are thought to be caused by combinations of two to nine gene mutations. Identifying these combinations through traditional exhaustive search requires the amount of computation that scales exponentially with the combination size and in most cases is intractable even for cutting-edge supercomputers. We propose a parameter-free heuristic approach that leverages the intrinsic topology of gene-patient mutations to identify carcinogenic combinations. The biological relevance of the identified combinations is measured by using them to predict the presence of tumor in previously unseen samples. The resulting classifiers for 16 cancer types perform on par with exhaustive search results, and score the average of 80.1% sensitivity and 91.6% specificity for the best choice of hit range per cancer type. Our approach is able to find higher-hit carcinogenic combinations targeting which would take years of computations using exhaustive search.

Biochemistry & Molecular Biology↗

Using the Stix finite element RF code to investigate operation optimization of the ICRF antenna on Alcator C-Mod

Abstract As the Ion Cyclotron Radio Frequency range (ICRF) heating becomes more favorable in fusion devices, the urgency of predicting and mitigating impurity generation that arises from it becomes more pressing. In the ICRF regime, rectified Radio Frequency (RF) sheaths are known to form at antenna and material edges that influence negative effects like sputtering and a decrease in heating efficiency. Methods to mitigate the formation of these RF sheaths through RF image currents cancellation have been experimentally studied. A power-phasing scan done on Alcator C-Mod in which the amount of power on the two inner straps ( P in ) versus the total 4 straps ( P tot ) was varied showed a minimization of enhanced potentials between P in / P tot ∼ 0.7–0.9 while impurities were minimized for P in / P tot ∼ 0.5–0.8. New capabilities in the realm of representing the RF sheath numerically now allow for these experiments to be simulated. Given the size of the sheath relative to the scale of the device, it can be approximated as a Boundary Condition (BC). A new parallelized cold-plasma wave equation solver called Stix implements a non-linear sheath impedance model BC formulated by Myra et al (2015 Phys. Plasmas 22 062507) through the method of finite elements using the MFEM library [ http://mfem.org ]. It is seen that Stix shows qualitative agreement with the measured C-Mod enhanced potentials.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

America’s Cutting Edge CNC machining and metrology training

This paper describes the workforce development activities supported by America’s Cutting Edge (ACE), a national initiative for machine tool technology development and advancement. ACE is supported by the Department of Defense Industrial Base Analysis and Sustainment (IBAS) program from the Office of Industrial Policy. Both the online and in-person components of the computer numerically controlled (CNC) machining and metrology training programs are summarized and participation information is provided.

99 GENERAL AND MISCELLANEOUS↗

Diffraction of radio-frequency waves by plasma turbulence in the edge of a tokamak

The Mie-Lorenz-Debye theory of scattering of radio frequency waves (RF) by filamentary structures in the edge of a tokamak plasma has been established in prior publications. These results have been verified. Theory and computations show that RF can be reflected, refracted, and diffracted by turbulence. Furthermore, the filamentary structures lead to side scattering of waves and excitation of wave modes different from the launched RF. It is important to quantify the overall effect of turbulence on the propagation of RF since efficiency of heating and current drive by RF waves depends upon the wave characteristics. The commonly used RF ranges vary from the low frequency ion-cyclotron (IC) waves, to medium frequency lower-hybrid (LH) waves, to high-frequency electron cyclotron (EC) waves with wavelengths respectively, large, comparable, or smaller than the radial dimensions of the filaments. Currently, we discuss the scattering as well as the forces exerted by different RF in the edge plasma. Also, we present a code for 3D full wave scattering analysis of arbitrary tensor permittivity and plasma density profiles. The study is applicable to ITER-like plasmas, as well as to plasmas in medium sized tokamaks such as TCV, ASDEX-U and DIII-D and high field concepts like SPARC.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Using Machine Learning for Quantum Annealing Accuracy Prediction

Quantum annealers, such as the device built by D-Wave Systems, Inc., offer a way to compute solutions of NP-hard problems that can be expressed in Ising or quadratic unconstrained binary optimization (QUBO) form. Although such solutions are typically of very high quality, problem instances are usually not solved to optimality due to imperfections of the current generations quantum annealers. In this contribution, we aim to understand some of the factors contributing to the hardness of a problem instance, and to use machine learning models to predict the accuracy of the D-Wave 2000Q annealer for solving specific problems. We focus on the maximum clique problem, a classic NP-hard problem with important applications in network analysis, bioinformatics, and computational chemistry. By training a machine learning classification model on basic problem characteristics such as the number of edges in the graph, or annealing parameters, such as the D-Wave’s chain strength, we are able to rank certain features in the order of their contribution to the solution hardness, and present a simple decision tree which allows to predict whether a problem will be solvable to optimality with the D-Wave 2000Q. We extend these results by training a machine learning regression model that predicts the clique size found by D-Wave.

97 MATHEMATICS AND COMPUTING↗

Fractional chiral hinge insulator

We propose and study a wave function describing an interacting three-dimensional fractional chiral hinge insulator (FCHI) constructed by Gutzwiller projection of two noninteracting second-order topological insulators with chiral hinge modes at half filling. We use large-scale variational Monte Carlo computations to characterize the model states via the entanglement entropy and charge-spin fluctuations. We show that the FCHI possesses fractional chiral hinge modes characterized by a central charge c = 1 and Luttinger parameter K = 1/2, like the edge modes of a Laughlin 1/2 state. The bulk and surface topology is characterized by the topological entanglement entropy (TEE) correction to the area law. While our computations indicate a vanishing bulk TEE, we show that the gapped surfaces host an unconventional two-dimensional topological phase. In a clear departure from the physics of a Laughlin 1/2 state, we find a TEE per surface compatible with (ln √2 )/2, half that of a Laughlin 1/2 state. This value cannot be obtained from topological quantum field theory for purely two-dimensional systems. For the sake of completeness, we also investigate the topological degeneracy.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Multiobjective Dynamic Optimization for Optimal Load-Following of Natural Gas Combined Cycle Power Plants under Stress Constraints

With the increasing penetration of intermittent renewable energy sources into the electric grid, there is an associated need for conventional thermal power plants that are designed to operate at base-load conditions to cycle their load rapidly and frequently and operate under low-load conditions. Fast load-following operations lead to plant efficiency loss and the reduction of equipment life. A high-fidelity dynamic model of a natural gas combined cycle power plant, with rigorous equipment level submodels, is developed to capture the plant transient performance and the thermomechanical stress evolution at the high-pressure drum is computed to assess the drum life consumption. Stress evolution is modeled for the location of the edge at the drum/downcomer junction that experiences high circumferential stress amplitude during the fast load-following operation, leading to higher fatigue damage than locations considered under existing design standards. A dynamic optimization problem is solved for optimal load-following operation. Depending on the value of the stress constraint and the desired ramp rate, satisfying the desired stress constraint may be infeasible without relaxing the ramp rate. A multiobjective dynamic optimization problem is solved using a lexicographic approach that minimizes ramp rate relaxation and maximizes efficiency while satisfying stress constraints, avoiding spraying to saturation, and maintaining main steam and reheat steam temperature within bounds. It was observed that the optimal ramp rate can be highly nonlinear as opposed to the industry-standard linear ramp rate. Nonlinear optimal ramp-rate profiles not only help to avoid stress constraints that may be unavoidable by using the linear profile but also result in higher efficiency than the linear profile. Furthermore, the study shows that there is a strong tradeoff between the relaxation in the plant ramp rate and the time-average thermal efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effect of aspect ratio on plasma response to resonant magnetic perturbations in tokamak devices

A systematic numerical study is carried out, computing and comparing the plasma response to the resonant magnetic perturbation (RMP) field, applied for controlling edge localized modes (ELMs), in a series of tokamak plasmas with varying aspect ratio and utilizing the MARS-F code. The aspect ratio is scanned either by varying the plasma major radius at a fixed minor radius or by varying the latter while fixing the former. Both approaches yield similar results when compared in terms of quantities with proper normalizations. In general, a non-monotonic dependence of the resonant response field (normalized by the vacuum counterpart) near the plasma edge is found with varying aspect ratio, indicating that a given ELM control coil current configuration strongly favors plasmas with a certain aspect ratio. This optimal aspect ratio, on the other hand, depends on the toroidal as well as poloidal (i.e., coil phasing) spectra of the applied RMP field. The equilibrium (edge) safety factor, the plasma shape, and the plasma toroidal flow are all fixed to ensure that the effects identified here are predominantly due to the plasma aspect ratio.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗