speckle-tracking: a software suite for ptychographic X-ray speckle tracking
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99 GENERAL AND MISCELLANEOUS↗
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Computational Nanophotonics: modeling optical interactions and transport in tailored nanosystem architectures
This report describes research by George Schatz and Mark Ratner that was done over the period 10/03-5/09 at Northwestern University. This research project was part of a larger research project with the same title led by Stephen Gray at Argonne. A significant amount of our work involved collaborations with Gray, and there were many joint publications as summarized later. In addition, a lot of this work involved collaborations with experimental groups at Northwestern, Argonne, and elsewhere. The research was primarily concerned with developing theory and computational methods that can be used to describe the interaction of light with noble metal nanoparticles (especially silver) that are capable of plasmon excitation. Classical electrodynamics provides a powerful approach for performing these studies, so much of this research project involved the development of methods for solving Maxwell’s equations, including both linear and nonlinear effects, and examining a wide range of nanostructures, including particles, particle arrays, metal films, films with holes, and combinations of metal nanostructures with polymers and other dielectrics. In addition, our work broke new ground in the development of quantum mechanical methods to describe plasmonic effects based on the use of time dependent density functional theory, and we developed new theory concerned with the coupling of plasmons to electrical transport in molecular wire structures. Applications of our technology were aimed at the development of plasmonic devices as components of optoelectronic circuits, plasmons for spectroscopy applications, and plasmons for energy-related applications.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
A Simulator for Neyer Tests of Explosives
Explosives and explosive devices such as detonators are typically tested by applying a range of stimuli such as voltage or mechanical shock, and recording binary “detonated/did not detonate” responses. These are analyzed using maximum likelihood or generalized linear models to provide estimates of quantities such as the all-fire and no-fire points. Given that the true threshold for detonation is unknown a priori , sequential design methods are typically used to optimize the set of test points. One popular method, implemented in commercial software, is Neyer’s algorithm. To support simulation and experimental design, we have developed code in the R programming language to duplicate the functions of the Neyer software. We provide code for the simulator along with a description and examples of usage.
42 ENGINEERING↗
Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples
Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties of molecules in complex mixtures and, in concert, are sensitive enough to resolve even stereoisomers. Despite these experimental advances, small molecule identification is inhibited by (i) chemical reference libraries (e.g. mass spectra, collision cross section, and other measurable property libraries) representing <1% of known molecules, limiting the number of possible identifications, and (ii) the lack of a method to generate candidate matches directly from experimental features (i.e. without a library). To this end, we developed a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. We extended the VAE to include a chemical property decoder, trained as a multitask network, in order to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, with its focus on properties that can be obtained from experimental measurements (m/z, CCS) paired with its training paradigm, which involved a cascade of transfer learning iterations. First, molecular representation is learned from a large dataset of structures with m/z labels. Next, in silico property values are used to continue training, as experimental property data is limited. Finally, the network is further refined by being trained with the experimental data. This allows the network to learn as much as possible at each stage, enabling success with progressively smaller datasets without overfitting. Once trained, the network can be used to predict chemical properties directly from structure, as well as generate candidate structures with desired chemical properties. Our approach is orders of magnitude faster than first-principles simulation for CCS property prediction. Additionally, the ability to generate novel molecules along manifolds, defined by chemical property analogues, positions DarkChem as highly useful in a number of application areas, including metabolomics and small molecule identification, drug discovery and design, chemical forensics, and beyond.
Colby, Sean M↗
Thermal Hydraulics Validation Activities in the ART-GCR Campaign
The Advanced Reactor Technologies - Gas Cooled Reactor Campaign (ART-GCR) is part of the United States Department of Energy - Office of Nuclear Energy's Advanced Reactor Technologies program aimed at developing a High Temperature Gas-cooled Reactor (HTGR) which will offer enhancements in safety and efficiency. The Design, Methods, and Validation arm of the ART-GCR program provides experience and advanced tools for HTGR design and analysis. The Methods and Validation arm is developing data to validate predictions of decay heat removal through an extensive experimental campaign the Natural Convection Shutdown Heat Removal Test Facility at Argonne National Laboratory. In-core thermal hydraulics validation is being facilitated through the OECD/NEA's Thermal Hydraulic Code Validation Benchmark for High Temperature Gas-Cooled Reactors using HTTF Data. That benchmark contains code-to-code and code-to-data comparisons for 3 sets of HTGR thermal hydraulics phenomena. This ongoing benchmark activity has 16 participants from 9 countries developing leading insights into HTGR thermal hydraulics code validation. The ART-GCR campaign is also working on the development of state-of-the-art MOOSE-based models of the High Temperature Engineering Test Reactor (HTTR). Through the OECD/NEA's HTTR Loss of Forced Cooling (LOFC) program, the ART-GCR campaign is developing a multiphysics transient code validation benchmark based on 3 HTTR experiments that will provide an opportunity for international collaboration on multiphysics code validation.
22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
Structure-Aware Unsupervised, Transformational Machine Learning for Drug Discovery (DTRA Basic Research Final Report)
The major goal of this project is to develop machine learning (ML) methods to enable improved predictive power on real drug discovery for novel targets. More specifically, we planned to demonstrate the capability and effectiveness of ML tools utilizing unlabeled large-volume protein-ligand datasets. We investigated multiple pre-training approaches for 3D protein-ligand structure-based foundation models, without relying on experimental binding data. We also addressed scenarios in which crystal structures are unavailable or binding data are limited. We also planned to develop a complete pipeline to screen novel compounds as well as to demonstrate the capability and effectiveness of the developed methods by testing on a realistic drug discovery task such as SARS-CoV-2. While the major goals and milestones remain consistent with the original proposal, certain technical details have been adjusted, based on the experimental results and related outcomes.
97 MATHEMATICS AND COMPUTING↗
Use of Direct Optical Heterodyning for Measuring Hardness by the Leeb Method
In this paper, we describe a portable system for measuring the indenter velocity in hardness meters implemented according to the Leeb method. The developed system is a fiber interferometer, in which a radiation source is a semiconductor laser with a wavelength of 1550 nm. The presented experimental results confirm the ability of the system to measure indenter velocities with an uncertainty of 0.001 m/s, which satisfies the requirements of the standards for this method of measuring hardness.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Designing a mixture experiment when the components are subject to a nonlinear multiple-component constraint
This article presents a case study of developing an experimental design for a constrained mixture experiment when the experimental region is defined by single-component constraints (SCCs), linear multiple-component constraints (MCCs), and a nonlinear MCC. Traditional methods and software for designing constrained mixture experiments with SCCs and linear MCCs are not directly applicable because of the nonlinear MCC. A modification of existing methodology to account for the nonlinear MCC was developed and is described in this article. The case study involves a 15-component nuclear waste glass example in which SO3 is one of the components. SO3 has a solubility limit in glass that depends on the composition of the balance of the glass. A goal was to design the experiment so that SO3 would not exceed its predicted solubility limit for any of the experimental glasses. The SO3 solubility limit had previously been modeled by a partial quadratic mixture (PQM) model expressed in the relative proportions of the 14 other components. The PQM model was used to construct a nonlinear MCC in terms of all 15 components. In addition, there were SCCs and linear MCCs. This article discusses the waste glass example and how a layered design was generated to (i) account for the SCCs, linear MCCs, and nonlinear MCC and (ii) meet the goals of the study.
Low-activity waste↗
Uncertainty Quantification and Comparison of Weld Residual Stress Measurements and Predictions.
In pressurized water reactors, the prevention, detection, and repair of cracks within dissimilar metal welds is essential to ensure proper plant functionality and safety. Weld residual stresses, which are difficult to model and cannot be directly measured, contribute to the formation and growth of cracks due to primary water stress corrosion cracking. Additionally, the uncertainty in weld residual stress measurements and modeling predictions is not well understood, further complicating the prediction of crack evolution. The purpose of this document is to develop methodology to quantify the uncertainty associated with weld residual stress that can be applied to modeling predictions and experimental measurements. Ultimately, the results can be used to assess the current state of uncertainty and to build confidence in both modeling and experimental procedures. The methodology consists of statistically modeling the variation in the weld residual stress profiles using functional data analysis techniques. Uncertainty is quantified using statistical bounds (e.g. confidence and tolerance bounds) constructed with a semi-parametric bootstrap procedure. Such bounds describe the range in which quantities of interest, such as means, are expected to lie as evidenced by the data. The methodology is extended to provide direct comparisons between experimental measurements and modeling predictions by constructing statistical confidence bounds for the average difference between the two quantities. The statistical bounds on the average difference can be used to assess the level of agreement between measurements and predictions. The methodology is applied to experimental measurements of residual stress obtained using two strain relief measurement methods and predictions from seven finite element models developed by different organizations during a round robin study.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
The XtalOpt Evolutionary Algorithm for Crystal Structure Prediction
Significant progress has been made in the field of a priori crystal structure prediction, with a number of recent remarkable success stories. Herein, we briefly outline the methods that have been developed for finding the global minimum structure and interesting local minima without the need for experimental information. Focus is placed on describing the XTALOPT evolutionary algorithm (EA) developed in our group towards this end. XTALOPT is published under well-known open-source licenses, and the EA searches can be analyzed via the AVOGADRO chemical editor and visualizer. We describe new algorithmic developments that have made it possible to predict the structures of ever-more complex crystalline lattices. Benchmark tests, which clearly illustrate how the new developments improve the success rate and accelerate the discovery of the global minimum structure, are carried out. Lastly, we describe how XTALOPT has been employed to predict novel ternary hydrides that have the propensity for high-temperature superconductivity under pressure.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
New Mechanistic Models of Long Term Evolution of Microstructure and Mechanical Properties of Nickel Based Alloys
The report describes the development of a discrete element method (DEM) based modeling approach to quantitatively predict deformation and failure of typical nickel based superalloys. A series of experimental data, including microstructure and mechanical property characterization at 600°C, was collected for a relatively simple, model solid solution Ni-20Cr alloy (Nimonic 75) to determine inputs for the model and provide data for model validation. Nimonic 75 was considered ideal for this study because it is a certified tensile and creep reference material. A series of new DEM modeling approaches were developed to capture the complexity of metal deformation, including cubic elastic anisotropy and plastic deformation both with and without strain hardening. Our model approaches were implemented into a commercially available DEM code, PFC3D, that is commonly used by engineers. It is envisioned that once further developed, this new DEM modeling approach can be adapted to a wide range of engineering applications.
36 MATERIALS SCIENCE↗
Discovery and Synthesis of a Family of Boride Altermagnets
Borides are a rich material family. To push the boundaries of borides’ properties and applications into broader fields, we have conducted systematic theoretical and experimental searches for synthesizable phases in ternary borides TM 2 B 2 (T = 3d, M = 4d/5d transition metals). We find that TM 2 B 2 in the FeMo 2 B 2 -type and CoW 2 B 2 -type structures form a large family of stable/metastable materials of 120 members. Among them, we identify 40 materials with stable magnetic solutions. Further, we discover 11 altermagnets in the FeMo 2 B 2 -type structure. So far, boride altermagnets are rare. In these altermagnets, T = Fe or Mn atoms are arranged in parallel T-chains with strong ferromagnetic intrachain couplings and antiferromagnetic interchain couplings. They simultaneously exhibit electronic band spin splitting, typical of ferromagnetism, and zero net magnetization, typical of antiferromagnetism. They also exhibit magnonic band chiral splitting. Both effects originate from the unique altermagnetic symmetries crucially constrained by the nonmagnetic atoms in the structure. Transport properties of relevance to spintronic applications, including the strain-induced spin-splitter effect and anomalous Hall effect, are predicted. An iodine-assisted synthesis method for TM 2 B 2 is developed, using which 7 of the predicted low-energy phases are experimentally synthesized and characterized, including 4 altermagnets. This work expands the realm of borides by offering new opportunities for studying altermagnetism and altermagnons in borides. It also provides valuable insights into the discovery and design of altermagnets. Here, by demonstrating that altermagnets can exist as families sharing a common motif, this work paves a feasible route for discovering altermagnets by elemental substitutions and high-throughput computations.
Chemical structure↗
Coiled Tube Gas Heaters For Nuclear Gas-Brayton Power Conversion
This project developed an alternative design for heat exchangers for application to heating supercritical carbon dioxide (S-CO 2 ) or air for power conversion. We have identified an annular coiled tube bundle configuration–where hot sodium enters tubes from multiple vertical inlet manifold pipes, flows in a spiral pattern radially inward and downward, and then exits into an equal number of vertical outlet manifold pipes–as a potentially attractive option. The S-CO 2 gas or air flows radially outward through the tube bundle. Coiled tube gas heaters (CTGHs) are expected to have excellent thermal shock, long-term thermal creep, in-service inspection, and reparability characteristics, compared to alternative options. CTGHs have significant commonality with modern nuclear steam generators. Extensive experience exists with the design, manufacture, operation, in-service inspection and maintenance of nuclear steam generators. The U.S. Nuclear Regulatory Commission also has extensive experience with regulatory guidance documented in NUREG 0800. CTGHs leverage this experience and manufacturing capability. The most important difference between steam generators and gas-Brayton cycles such as the S-CO 2 cycle is that the heat exchangers must operate with counter flow with high effectiveness to minimize the pinch-point temperature difference between the hot liquid coolant and the heated gas. S-CO 2 -cycle gas heaters also operate at sufficiently elevated temperatures that time dependent creep is important and allowable stresses are relatively low. Designing heat exchangers to operate in this regime requires configurations that minimize stresses and stress concentrations. The cylindrical tubes and cylindrical manifold pipes used in CTGHs are particularly effective geometries. The first major goal of this research project was to develop and experimentally validate a detailed, 3-D multi-phase (gas-solid-liquid) heat transport model for CTGHs, using methods similar to earlier UCB multi-scale models for PCHEs, which will enable optimization of CTGH designs with respect to the number of manifold pipes, S-CO 2 and sodium circulating power, and other design parameters. CTGHs are relatively novel because the tubes loaded in compression as well as the manifold pipes which form the tube sheets. The second major goal of the experimental and modeling effort was to optimize the assembly and heat treatment of the tube-to-tubesheet joints, using a novel tapered joint configuration, and to develop diffusion-bonded joints with high shear strength and creep resistance, as has been done in other applications for tapered plugs. The project would also conduct creep testing of these tubesheet joints in pressurized furnaces under prototypical conditions of stress and temperature, however this was not feasible due to numerous hinderances. Detailed microstructural investigations was conducted on the diffusion bond interface, while the bond strength was evaluated by tensile testing. The mechanical testing quantified the overall strength of the bond and measured the pull out force as well as long term behavior, which complemented the microstructural analysis and gave a complete understanding of the diffusion bond.
30 DIRECT ENERGY CONVERSION↗
Eigenvector centrality is a metric of elastomer modulus, heterogeneity, and damage
Here, we present an application of eigenvector centrality to encode the connectivity of polymer networks resolved at the micro- and meso-scopic length scales. This method captures the relative importance of different nodes within the network structure and provides a route toward the development of a statistical mechanics model that correlates connectivity with mechanical response. This scheme may be informed by analytical and semi-analytical models for the network structure, or through direct experimental examination. It may be used to predict the reduction in mechanical performance for heterogeneous materials subjected to specific modes of damage. Here, we develop the method and demonstrate that it leads to the prediction of established trends in elastomers. We also apply the model to the case of a self-healing polymer network reported in the literature, extracting insight about the fraction of bonds broken and re-formed during strain and recovery.
36 MATERIALS SCIENCE↗
Developing a laser shockwave model for characterizing diffusion bonded interfaces
The US National Nuclear Security Agency has a Global Threat Reduction Initiative (GTRI) with the goal of reducing the worldwide use of high-enriched uranium (HEU). A salient component of that initiative is the conversion of research reactors from HEU to low enriched uranium (LEU) fuels. An innovative fuel is being developed to replace HEU in high-power research reactors. The new LEU fuel is a monolithic fuel made from a U-Mo alloy foil encapsulated in Al-6061 cladding. In order to support the fuel qualification process, the Laser Shockwave Technique (LST) is being developed to characterize the clad-clad and fuel-clad interface strengths in fresh and irradiated fuel plates. LST is a non-contact method that uses lasers for the generation and detection of large amplitude acoustic waves to characterize interfaces in nuclear fuel plates. However, because the deposition of laser energy into the containment layer on a specimen's surface is intractably complex, the shock wave energy is inferred from the surface velocity measured on the backside of the fuel plate and the depth of the impression left on the surface by the high pressure plasma pulse created by the shock laser. To help quantify the stresses generated at the interfaces, a finite element method (FEM) model is being utilized. This paper will report on initial efforts to develop and validate the model by comparing numerical and experimental results for back surface velocities and front surface depressions in a single aluminum plate representative of the fuel cladding.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
A method of dose reconstruction for moving targets compatible with dynamic treatments
Purpose: To develop a method that allows a commercial treatment planning system (TPS) to perform accurate dose reconstruction for rigidly moving targets and to validate the method in phantom measurements for a range of treatments including intensity modulated radiation therapy (IMRT), volumetric arc therapy (VMAT), and dynamic multileaf collimator (DMLC) tracking. Methods: An in-house computer program was developed to manipulate Dicom treatment plans exported from a TPS (Eclipse, Varian Medical Systems) such that target motion during treatment delivery was incorporated into the plans. For each treatment, a motion including plan was generated by dividing the intratreatment target motion into 1 mm position bins and construct sub-beams that represented the parts of the treatment that were delivered, while the target was located within each position bin. For each sub-beam, the target shift was modeled by a corresponding isocenter shift. The motion incorporating Dicom plans were reimported into the TPS, where dose calculation resulted in motion including target dose distributions. For experimental validation of the dose reconstruction a thorax phantom with a moveable lung equivalent rod with a tumor insert of solid water was first CT scanned. The tumor insert was delineated as a gross tumor volume (GTV), and a planning target volume (PTV) was formed by adding margins. A conformal plan, two IMRT plans (step-and-shoot and sliding windows), and a VMAT plan were generated giving minimum target doses of 95% (GTV) and 67% (PTV) of the prescription dose (3 Gy). Two conformal fields with MLC leaves perpendicular and parallel to the tumor motion, respectively, were generated for DMLC tracking. All treatment plans were delivered to the thorax phantom without tumor motion and with a sinusoidal tumor motion. The two conformal fields were delivered with and without portal image guided DMLC tracking based on an embedded gold marker. The target dose distribution was measured with a radiochromic film in the moving rod and compared with the reconstructed doses using gamma tests. Results: Considerable interplay effects between machine motion and target motion were observed for the treatments without tracking. For nontracking experiments, the mean 2 mm/2% gamma pass rate over all investigated scenarios was 99.6% between calculated and measured doses. For tracking experiments, the mean gamma pass rate was 99.4%. Conclusions: A method for accurate dose reconstruction for moving targets with dynamic treatments was developed and experimentally validated in a variety of delivery scenarios. The method is suitable for integration into TPSs, e.g., for reconstruction of the dose delivered to moving tumors or calculation of target doses delivered with DMLC tracking.
60 APPLIED LIFE SCIENCES↗
Development of a simultaneous Hugoniot and temperature measurement for preheated-metal shock experiments: Melting temperatures of Ta at pressures of 100 GPa
Equations of state of metals are important issues in earth science and planetary science. A major limitation of them is the lack of experimental data for determining pressure-volume and temperature of shocked metal simultaneously. By measuring them in a single experiment, a major source of systematic error is eliminated in determining from which shock pressure release pressure originates. Hence, a non-contact fast optical method was developed and demonstrated to simultaneously measure a Hugoniot pressure-volume (P{sub H}-V{sub H}) point and interfacial temperature T{sub R} on the release of Hugoniot pressure (P{sub R}) for preheated metals up to 1000 K. Experimental details in our investigation are (i) a Ni-Cr resistance coil field placed around the metal specimen to generate a controllable and stable heating source, (ii) a fiber-optic probe with an optical lens coupling system and optical pyrometer with ns time resolution to carry out non-contact fast optical measurements for determining P{sub H}-V{sub H} and T{sub R}. The shock response of preheated tantalum (Ta) at 773 K was investigated in our work. Measured data for shock velocity versus particle velocity at an initial state of room temperature was in agreement with previous shock compression results, while the measured shock data between 248 and 307 GPa initially heated to 773 K were below the Hugoniot evaluation from its off-Hugoniot states. Obtained interfacial temperatures on release of Hugoniot pressures (100-170 GPa) were in agreement with shock-melting points at initial ambient condition and ab initio calculations of melting curve. It indicates a good consistency for shock melting data of Ta at different initial temperatures. Our combined diagnostics for Hugoniot and temperature provides an important approach for studying EOS and the temperature effect of shocked metals. In particular, our measured melting temperatures of Ta address the current controversy about the difference by more than a factor of 2 between the melting temperatures measured under shock and those measured in a laser-heated diamond anvil cell at {approx}100 GPa.
36 MATERIALS SCIENCE↗
Enabling adoption of 2D-NMR for the higher order structure assessment of monoclonal antibody therapeutics
The increased interest in using monoclonal antibodies (mAbs) as a platform for biopharmaceuticals has led to the need for new analytical techniques that can precisely assess physicochemical properties of these large and very complex drugs for the purpose of correctly identifying quality attributes (QA). One QA, higher order structure (HOS), is unique to biopharmaceuticals and essential for establishing consistency in biopharmaceutical manufacturing, detecting process-related variations from manufacturing changes and establishing comparability between biologic products. To address this measurement challenge, two-dimensional nuclear magnetic resonance spectroscopy (2D-NMR) methods were introduced that allow for the precise atomic-level comparison of the HOS between two proteins, including mAbs. Here, an inter-laboratory comparison involving 26 industrial, government and academic laboratories worldwide was performed as a benchmark using the NISTmAb, from the National Institute of Standards and Technology (NIST), to facilitate the translation of the 2D-NMR method into routine use for biopharmaceutical product development. Two-dimensional 1H,15N and 1H,13C NMR spectra were acquired with harmonized experimental protocols on the unlabeled Fab domain and a uniformly enriched-15N, 20%-13C-enriched system suitability sample derived from the NISTmAb. Chemometric analyses from over 400 spectral maps acquired on 39 different NMR spectrometers ranging from 500 MHz to 900 MHz demonstrate spectral fingerprints that are fit-for-purpose for the assessment of HOS. The 2D-NMR method is shown to provide the measurement reliability needed to move the technique from an emerging technology to a harmonized, routine measurement that can be generally applied with great confidence to high precision assessments of the HOS of mAb-based biotherapeutics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗