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Genome-Scale 13 C Fluxomics Modeling for Metabolic Engineering of Saccharomyces cerevisiae .

Synthetic biology is a rapidly developing field that pursues the application of engineering principles and development approaches to biological engineering. Synthetic biology is poised to change the way biology is practiced, and has important practical applications: for example, building genetically engineered organisms to produce biofuels, medicines, and other chemicals. Traditionally, synthetic biology has focused on manipulating a few genes (e.g., in a single pathway or genetic circuit), but its combination with systems biology holds the promise of creating new cellular architectures and constructing complex biological systems from the ground up. Enabling this merge of synthetic and systems biology will require greater predictive capability for modeling the behavior of cellular systems, and more comprehensive data sets for building and calibrating these models. The so-called "-omics" data sets can now be generated via high throughput techniques in the form of genomic, proteomic, transcriptomic, and metabolomic information on the engineered biological system. Of particular interest with respect to the engineering of microbes capable of producing biofuels and other chemicals economically and at scale are metabolomic datasets, and their insights into intracellular metabolic fluxes. Metabolic fluxes provide a rapid and easy to understand picture of how carbon and energy flow throughout the cell. Furthermore, we present a detailed guide to performing metabolic flux analysis and modeling using the open source JBEI Quantitative Metabolic Modeling (jQMM) library. This library allows the user to transform metabolomics data in the form of isotope labeling data from a 13 C labeling experiment into a determination of cellular fluxes that can be used to develop genetic engineering strategies for metabolic engineering.The jQMM library presents a complete toolbox for performing a range of different tasks of interest in metabolic engineering. Various different types of flux analysis and modeling can be performed such as flux balance analysis, 13 C metabolic flux analysis, and two-scale 13 C metabolic flux analysis (2S- 13 C MFA). 2S- 13 C MFA is a novel method that determines genome-scale fluxes without the need of every single carbon transition in the metabolic network. In addition to several other capabilities, the jQMM library can make model based predictions for how various genetic engineering strategies can be incorporated toward bioengineering goals: it can predict the effects of reaction knockouts on metabolism using both the MoMA and ROOM methodologies. In this chapter, we will illustrate the use of the jQMM library through a step-by-step demonstration of flux determination and knockout prediction in a complex eukaryotic model organism: Saccharomyces cerevisiae ( S. cerevisiae ). Included with this chapter is a digital Jupyter Notebook file that provides a computable appendix showing a self-contained example of jQMM usage, which can be changed to fit the user's specific needs. As an open source software project, users can modify and extend the code base to make improvements at will, allowing them to share their development work and contribute back to the jQMM modeling community.

-Omics data↗

Exploratory Nuclear Reactor Safety Analysis and Visualization via Integrated Topological and Geometric Techniques

A recent trend in the nuclear power engineering field is the implementation of heavily computational and time consuming algorithms and codes for both design and safety analysis. In particular, the new generation of system analysis codes aim to embrace several phenomena such as thermo-hydraulic, structural behavior, and system dynamics, as well as uncertainty quantification and sensitivity analyses. The use of dynamic probabilistic risk assessment (PRA) methodologies allows a systematic approach to uncertainty quantification. Dynamic methodologies in PRA account for possible coupling between triggered or stochastic events through explicit consideration of the time element in system evolution, often through the use of dynamic system models (simulators). They are usually needed when the system has more than one failure mode, control loops, and/or hardware/process/software/human interaction. Dynamic methodologies are also capable of modeling the consequences of epistemic and aleatory uncertainties. The Monte-Carlo (MC) and the Dynamic Event Tree (DET) approaches belong to this new class of dynamic PRA methodologies. The major challenges in using MC and DET methodologies (as well as other dynamic methodologies) are the heavier computational and memory requirements compared to the classical ET analysis. This is due to the fact that each branch generated can contain time evolutions of a large number of variables (about 50,000 data channels are typically present in RELAP) and a large number of scenarios can be generated from a single initiating event (possibly on the order of hundreds or even thousands). Such large amounts of information are usually very difficult to organize in order to identify the main trends in scenario evolutions and the main risk contributors for each initiating event. This report aims to improve Dynamic PRA methodologies by tackling the two challenges mentioned above using: 1) adaptive sampling techniques to reduce computational cost of the analysis and 2) topology-based methodologies to interactively visualize multidimensional data and extract risk-informed insights. Regarding item 1) we employ learning algorithms that aim to infer/predict simulation outcome and decide the coordinate in the input space of the next sample that maximize the amount of information that can be gained from it. Such methodologies can be used to both explore and exploit the input space. The later one is especially used for safety analysis scopes to focus samples along the limit surface, i.e. the boundaries in the input space between system failure and system success. Regarding item 2) we present a software tool that is designed to analyze multi-dimensional data. We model a large-scale nuclear simulation dataset as a high-dimensional scalar function defined over a discrete sample of the domain. First, we provide structural analysis of such a function at multiple scales and provide insight into the relationship between the input parameters and the output. Second, we enable exploratory analysis for users, where we help the users to differentiate features from noise through multi-scale analysis on an interactive platform, based on domain knowledge and data characterization. Our analysis is performed by exploiting the topological and geometric properties of the domain, building statistical models based on its topological segmentations and providing interactive visual interfaces to facilitate such explorations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Report on activities and findings under DOE grant “Collaborative research. An Interactive Multi-Model for Consensus on Climate Change”

The project takes a hierarchical approach. The supermodeling scheme was first studied exhaustively with simple systems of ordinary differential equations. Results were described in detail in the previous report. The principal findings were that 1) for highly non-linear systems, such as Lorenz-63, including systems which describe phenomena on very different (atmosphere/ocean) times scales, supermodeling is far superior to any form of output-averaging; 2) negative coefficients can be used to advantage in situations where all models err in the same way, but to different degrees; 3) an interesting variant of supermodeling, “weighted supermodeling”, is the limiting case where inter-model nudging coefficients in the originally conceived “connected supermodel” become infinite, but with fixed ratios, corresponding to a direct combination of the tendencies that appear in corresponding equations for the alternative models; 4) noise is useful for avoiding local optima in training the inter-model coefficients in the supermodel. The supermodeling scheme was then investigated with simple quasigeostrophic (QG) models. As described in the previous report, it was found that QG models on a sphere can be coupled most efficaciously by working in a basis which captures the most variance, rather than the most instability, a somewhat unexpected result that still deserves scrutiny in a broader context. Further studies (since the last report) with QG channel models addressed the central question of when supermodeling is superior to output averaging in situations where nonlinearites are less extreme than with the ODEs initially studied. It was found that for realistic variations in a parameter in the QG model, output averaging is sufficient to capture all but the most subtle quantitative and qualitative behavior. Supermodeling helps when qualitative differences between the models result from unrealistically large parameter differences, or when very detailed spatial structure of the modes of variability are of interest. Therefore, the scheme may still be useful in the case of full climate models with qualitatively different parametrization schemes. A supermodel was constructed from the intermediate-complexity SPEEDO model, a primitive equation model with ocean and land. Versions defined by different parameter choices, in a realistic range, were connected and the coefficients trained. Some improvement was found as compared to output averaging. The learning algorithm used thus far gives sub-optimal, but still useful results when the CO 2 level and other parameters are varied. Spatial structure remains to be studied. The first use of supermodeling with full climate models has been with variants of the ECHAM model that use different convection schemes. As yet the models are only connected at the ocean-atmosphere interface, where weighted combinations of fluxes from the two atmospheres are passed to a common ocean, and the weights adapted during a training period. The supermodel was surprisingly successful at avoiding unrealistic features such as the double-ITCZ (Intertropical Convergence Zone), a problem that arises in both of the two models run separately. The supermodels constructed thus far have not identified dynamical regime shifts in future climate. Thus the planned connection with the work of Tsonis on the relationship between regime shifts and synchronization/de-synchronization among the major climate modes (see U. Wisconsin report) has not yet been made. However the network analysis of the climate system, in observations and models, that was done in conjunction with that study, shows that models differ strongly from one another and from observations in regard to the dynamical structure described by correlation networks [Steinhaeuser and Tsonis 2013], providing a further justification for supermodeling. Toward a general software framework for supermodeling, three versions of CAM (the Community Atmosphere Model) at NCAR were configured for inter-model nudging using the DART (Data Assimilation Research Testbed) capability to stop and re-start models in synchrony. It was clearly established that the inter-model nudging adds almost no computational burden to the runs, but there appears to be a problem with the re-initialization software that is still being debugged. Publications: Several papers were published on the basic idea of the interactive multi-model (supermodel) including demonstrations with low-order ODEs. The last of these, a semi-philosophical review paper on the relevance of synchronization generally, encountered considerable resistance but was finally published in Entropy [Duane 2015]. A paper on the ECHAM/COSMOS supermodel, containing the most promising results so far [Shen et al. 2015] is presently under review.

58 GEOSCIENCES↗

Software-defined Networking for Energy Delivery Systems (SDN4EDS): An Architectural Blueprint (Final Summary Report)

This is the initial version of a reference for suppliers and energy companies of all sizes to deploy networks based on software-defined networking technology (SDN) to improve reliability, reduce cyber security attack surface, and facilitate mitigation of adversarial behavior. It is a living document and will progress over the life cycle of the Software-Defined Networking for Energy Delivery Systems (SDN4EDS) project. Version 2 of this report provides information on the Red Team tabletop assessment performed against the initial reference architecture. Version 3 of this report updates the reference architecture with lessons learned from the Red Team tabletop assessment, as well as provides additional details for the use cases. It also provides information on the decision process that could be used by an organization when considering deploying SDN in their environment. The final version of this report consolidates all the interim reports generated by the project into a final report. It also draws from PNNL’s experience in deploying SDN to make recommendations on how SDN could be deployed in a utility environment, and provides rationale for those decisions allowing individual utilities to make risk-based and knowledge-based decisions on how to best deploy SDN in their own environment. This summary report provides a higher-level overview of the project reports. Readers interested in additional detail, including results of the Red Team assessments and the final configuration, are encouraged to read the full final report.

97 MATHEMATICS AND COMPUTING↗

The SAS4A/SASSYS-1 Version 5.8 Safety Analysis Code System

SAS4A/SASSYS-1 is a software simulation tool used to perform deterministic analysis of anticipated events as well as design basis and beyond design basis accidents for advanced nuclear reactors. Detailed, mechanistic models of steady-state and transient thermal, hydraulic, kinetic, and mechanical phenomena are employed to describe the response of the reactor core, the reactor primary and secondary coolant loops, the reactor control and protection systems, and the balance-of-plant to accidents caused by changes in coolant flow, loss of heat rejection, or reactivity insertion. The consequences of single and double-fault accidents can be modeled, including fuel and coolant heating, fuel and cladding mechanical behavior, core reactivity feedbacks, coolant loop performance including natural circulation, and decay heat removal. Analyses are typically terminated upon demonstration of reactor and plant shutdown to permanently coolable conditions, or upon violation of design basis margins. The objective of the analysis is to quantify accident consequences as measured by the transient behavior of system performance parameters, such as fuel and cladding temperatures, reactivity, and cladding strain. Originally developed for analysis of sodium cooled reactors with oxide fuel clad by stainless steel, the models were subsequently extended and specialized to metallic fuel clad with advanced alloys and to several other coolant options, including lead, LBE, and water.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Analysis of, and defense against, spurious actuations and other incorrect behaviors of digital control systems - 390

Modern digital instrumentation and control (I and C) systems offer nearly unlimited functional capability. However, the complexity of their design (including their system software and application software) is significantly higher than that of conventional, hardwired systems, to the point that it is generally impossible to demonstrate that there are no residual design errors, even when the best development and verification techniques have been applied. When activated by specific conditions, design errors could result in systematic failures, i.e., failures that occur deterministically each time and wherever an activating condition is present. Redundancy could be defeated when the same design error affects multiple channels or systems, and the activating condition affects several of these channels or systems. In the case of safety I and C systems, most of the functions are poised protection functions that must be actuated when and only when a demand situation occurs in the plant. In nuclear power plants, the most dangerous failure mode for such functions generally is failure to actuate, and many measures are taken to protect from such failure mode. This paper considers the other failure modes of safety I and C functions, and also the failure modes of the other I and C functions that are less important to safety. It is not limited to poised functions, and considers other types of functions such as regulation functions or human interface functions. It proposes a framework for analyzing and providing defense against spurious actuations and other incorrect behaviors from digital I and C systems directly interacting with the plant process or with operators: these might be useful for example to justify that design bases for reactor protection are adequate, or to ensure plant performance and availability. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

NanoPSD: A software for automatic detection of Nano-Particle Shape Distribution in electron microscopy images

Accurate quantification of the size and morphology of nanoparticles from electron microscopy (EM) images is essential to understand growth mechanisms, surface reactivity, and functional behavior in nanoscale materials. Manual analysis remains slow, subjective, and difficult to reproduce in large datasets. We introduce NanoPSD (Nano-Particle Shape Distribution), an open-source and fully automated framework for quantitative particle detection and morphology analysis from EM images. NanoPSD integrates adaptive contrast enhancement, polarity-agnostic scale-bar detection, Optical Character Recognition (OCR)-based calibration, and classical segmentation via Otsu thresholding with morphological refinement. Particle contours are used to extract geometric descriptors, including equivalent circular diameter, aspect ratio, circularity, and solidity, enabling automated classification into spherical, rod-like, and aggregate morphologies. The framework supports both single-image and batch processing, generating publication-quality visualizations, LaTeX-ready tables, and structured comma-separated values (CSV) datasets. As a demonstration, we applied NanoPSD to plasma-synthesized nanoparticle samples diagnosed via transmission electron microscopy (TEM). The code produced statistically robust size and morphology distributions spanning a few to tens of nanometers with minimal user supervision. The pipeline demonstrates high reproducibility and scalability, processing large image collections with consistent calibration and output formatting. Its modular design enables seamless integration of future deep-learning-based segmentation models, providing a pathway toward intelligent, data-driven electron microscopy analysis.

36 MATERIALS SCIENCE↗

teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering

Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub.

59 BASIC BIOLOGICAL SCIENCES↗

A Numerical Simulation of Transport Phenomena During the Horizontal Single Belt Casting Process Using an Inclined Feeding System

Horizontal single belt casting (HSBC) has great potential to replace current conventional continuous casting (CCC) processes for sheet metal production, by directly casting 3 to 1 mm sheet for the automobile industry. In the present paper, two-dimensional mathematical models were developed to study transport phenomena, for the case of an inclined wall feeding system for a liquid aluminum wrought alloy (AA6111). Based on the commercial software ANSYS FLUENT 14.5 and user-defined functions, a two-layer turbulence model was used to examine the fluid flow emanating from a slot nozzle set above a water-cooled, high-speed, steel belt. The Volume of Fluid (VOF) method was used to predict the shape of the melt-air interface. A transformed coordinate system (x′, y′) was established in order to analyze the fluid flow on the inclined wall of the feeding system. The total pressure gauge gradient (∂p{sub total}/∂x) was used to describe the behavior of the melt film inside the slot nozzle of the head box. The modeling results show that during the melt film falling process, the total gauge pressure varies within the slot nozzle, which can decrease the stability of the falling film. The first impingement between the falling film and the inclined refractory wall of the feeding system gives rise to a local oscillation, and this influences the stability of the melt film moving downwards. At the rear meniscus position between the inclined wall and the moving belt, there is a clear vibration of the air-melt interface, together with a recirculation zone. The weak vibration of the air-melt interface could be induced by the periodic variation of the melt-air interface. Moreover, the formation of tiny air pockets is predicted. Finally, on the inclined wall of the feeding system, a suitable length of the transition area is needed to avoid over-acceleration of the melt film due to the force of gravity.

36 MATERIALS SCIENCE↗

Annual Report: Carbon Capture Simulation Initiative (CCSI) (30 September 2013)

The Carbon Capture Simulation Initiative (CCSI) is a partnership among national laboratories, industry and academic institutions that is developing and deploying state-of-the-art computational modeling and simulation tools to accelerate the commercialization of carbon capture technologies from discovery to development, demonstration, and ultimately the widespread deployment to hundreds of power plants. The CCSI Toolset will provide end users in industry with a comprehensive, integrated suite of scientifically validated models, with uncertainty quantification (UQ), optimization, risk analysis and decision making capabilities. The CCSI Toolset incorporates commercial and open-source software currently in use by industry and is also developing new software tools as necessary to fill technology gaps identified during execution of the project. Ultimately, the CCSI Toolset will (1) enable promising concepts to be more quickly identified through rapid computational screening of devices and processes; (2) reduce the time to design and troubleshoot new devices and processes; (3) quantify the technical risk in taking technology from laboratory-scale to commercial-scale; and (4) stabilize deployment costs more quickly by replacing some of the physical operational tests with virtual power plant simulations. CCSI is led by the National Energy Technology Laboratory (NETL) and leverages the Department of Energy (DOE) national laboratories’ core strengths in modeling and simulation, bringing together the best capabilities at NETL, Los Alamos National Laboratory (LANL), Lawrence Berkeley National Laboratory (LBNL), Lawrence Livermore National Laboratory (LLNL), and Pacific Northwest National Laboratory (PNNL). The CCSI’s industrial partners provide representation from the power generation industry, equipment manufacturers, technology providers and engineering and construction firms. The CCSI’s academic participants (Carnegie Mellon University, Princeton University, West Virginia University, Boston University and the University of Texas at Austin) bring unparalleled expertise in multiphase flow reactors, combustion, process synthesis and optimization, planning and scheduling, and process control techniques for energy processes. During Fiscal Year (FY) 13, CCSI announced the initial release of its first set of computational tools and models during the October 2012 meeting of its Industry Advisory Board. This initial release led to five companies licensing the CCSI Toolset under a Test and Evaluation Agreement this year. By the end of FY13, the CCSI Technical Team had completed development of an updated suite of computational tools and models. The list below summarizes the new and enhanced toolset components that were released following comprehensive testing during October 2013. 1. FOQUS. Framework for Optimization and Quantification of Uncertainty and Sensitivity. Package includes: FOQUS Graphic User Interface (GUI), simulation-based optimization engine, Turbine Client, and heat integration capabilities. There is also an updated simulation interface and new configuration GUI for connecting Aspen Plus or Aspen Custom Modeler (ACM) simulations to FOQUS and the Turbine Science Gateway. 2. A new MFIX-based Computational Fluid Dynamics (CFD) model to predict particle attrition. 3. A new dynamic reduced model (RM) builder, which generates computationally efficient RMs of the behavior of a dynamic system. 4. A completely re-written version of the algebraic surrogate model builder for optimization (ALAMO). The new version is several orders of magnitude faster than the initial release and eliminates the MATLAB dependency. 5. A new suite of high resolution filtered models for the hydrodynamics associated with horizontal cylindrical objects in a flow path. 6. The new Turbine Science Gateway (Cluster), which supports FOQUS for running multiple simulations for optimization or UQ using a local computer or cluster. 7. A new statistical tool (BSS-ANOVA-UQ) for calibration and validation of CFD models. 8. A new basic data submodel in Aspen Plus format for a representative high viscosity capture solvent, 2-MPZ system. 9. An updated RM tool for CFD (REVEAL) that can create a RM from MFIX. A new lightweight, stand-alone version will be available in late 2013. 10. An updated RM integration tool to convert the RM from REVEAL into a CAPE-OPEN or ACM model for use in a process simulator. 11. An updated suite of unified steady-state and dynamic process models for solid sorbent carbon capture included bubbling fluidized bed and moving bed reactors. 12. An updated and unified set of compressor models including steady-state design point model and dynamic model with surge detection. 13. A new framework for the synthesis and optimization of coal oxycombustion power plants using advanced optimization algorithms. This release focuses on modeling and optimization of a cryogenic air separation unit (ASU). 14. A new technical risk model in spreadsheet format. 15. An updated version of the sorbent kinetic/equilibrium model for parameter estimation for the 1st generation sorbent model. 16. An updated process synthesis superstructure model to determine optimal process configurations utilizing surrogate models from ALAMO for adsorption and regeneration in a solid sorbent process. 17. Validation models for NETL Carbon Capture Unit utilizing sorbent AX. Additional validation models will be available for sorbent 32D in 2014. 18. An updated hollow fiber membrane model and system example for carbon capture. 19. An updated reference power plant model in Thermoflex that includes additional steam extraction and reinjection points to enable heat integration module. 20. An updated financial risk model in spreadsheet format.

01 COAL, LIGNITE, AND PEAT↗

The Cementitious Barriers Partnership (CBP) Software Toolbox Capabilities in Assessing the Degradation of Cementitious Barriers - 13487

The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy (US DOE) Office of Tank Waste and Nuclear Materials Management. The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that help improve understanding and predictions of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program have been used to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to 100 years and longer for operating facilities and longer than 1000 years for waste disposal. The CBP Software Toolbox has produced tangible benefits to the DOE Performance Assessment (PA) community. A review of prior DOE PAs has provided a list of potential opportunities for improving cementitious barrier performance predictions through the use of the CBP software tools. These opportunities include: 1) impact of atmospheric exposure to concrete and grout before closure, such as accelerated slag and Tc-99 oxidation, 2) prediction of changes in K{sub d}/mobility as a function of time that result from changing pH and redox conditions, 3) concrete degradation from rebar corrosion due to carbonation, 4) early age cracking from drying and/or thermal shrinkage and 5) degradation due to sulfate attack. The CBP has already had opportunity to provide near-term, tangible support to ongoing DOE-EM PAs such as the Savannah River Saltstone Disposal Facility (SDF) by providing a sulfate attack analysis that predicts the extent and damage that sulfate ingress will have on the concrete vaults over extended time (i.e., > 1000 years). This analysis is one of the many technical opportunities in cementitious barrier performance that can be addressed by the DOE-EM sponsored CBP software tools. Modification of the existing tools can provide many opportunities to bring defense in depth in prediction of the performance of cementitious barriers over time. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

A Generic and Multifunctional Electromagnetic Transient Model for Grid-Following Inverters

This article presents a generic and multi-functional electromagnetic transient (EMT) dynamic model of grid following (GFL) inverter-based resource (IBR) using the PSCAD software platform. The features of the developed model includes the flexibility in selecting various types and combinations of DC sources covering PV modules, battery modules, ideal DC source module, as well as flexibility in selecting either switched or averaged model of inverter. This model also covers exhaustive lists of controller logic covering open-loop/closed-loop PQ dispatch control, DC voltage and AC terminal voltage control along with the conventional current control designed in dq-domain, ate- domain and positive-negative sequence domain. Moreover, this model is equipped with the flexibility in selecting various types of current limiting schemes that includes saturation-based as well as latching-based current limiter, anti-windup protection. Moreover, the EMT model is agnostic to the MVA rating and is suitable for interfacing transmission systems by being complaint with the IEEE Std. 2800. The generality in the power circuits and the multi-functional options in operation and control of the developed EMT model makes it suitable for both academia and industry to study various power system aspects not limited to but such as fault behavior of GFL IBR and impacts on protection system, transient stability of a system interfaced with large number of GFL IBRs etc.

14 SOLAR ENERGY↗

Development of Integrated Thermal Fluids Modeling Capability for MSRs

The DOE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program supports a full range of computational thermal fluids analysis capabilities and code developments for a broad class of light-water and advanced reactor concepts. The research and development approach under thermal fluids technical area synergistically combines three length and time scales in a hierarchal multi-scale approach. To demonstrate the feasibility and capabilities of a multi-scale thermal fluids capability using these codes, a key joint effort has been pursued to develop an integrated system-and engineering-scale thermal fluids analysis capability with the MOOSE-based codes, through integration of SAM and Pronghorn, both based on the MOOSE framework. This report summarizes the progress in developing an integrated system- and engineering-scale thermal fluids analysis capability based on SAM and Pronghorn for molten salt reactors (MSRs), which gained significant interest in recently years. Two coupling approaches were studied, i.e. separate domain or domain-segregated coupling approach and the domain-overlapping approach. A series of coupled multi-physics models have been developed for a common reference molten salt fast reactor (MSFR) concept, ranging from standalone SAM system model to integrated SAM-Pronghorn-Griffin models. Both the steady state and the transient simulations are performed to the state-of-the-art simulation capabilities of NEAMS software suite in MSFR system applications. This report also covers further development and testing of the gas transport model in SAM for MSR modeling support. The presence of noncondensable gas in MSR systems would have strong impacts on fission gas removal and transport of noble metals throughout the system. Fission products removed through the off-gas system can also impact reactivity and can act as an additional point of heat removal. To ensure that the gas transport model is adequately tested, the supported modeling capabilities and features of SAM were identified, and a suite of tests were developed to test the model for each identified feature. Validation and UQ testing were also performed for the model and demonstrated that the buoyancy term, which was originally developed using non-salt/helium gas experimental data, can capture the experimental gas bubble velocity and diameter to within experimental and code uncertainty. An existing MSRE model was also modified in this work to include the gas transport model and to demonstrate the gas model behavior for realistic conditions of interest.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

CBP Toolbox Version 3.0 “Beta Testing” Performance Evaluation

One function of the Cementitious Barriers Partnership (CBP) is to assess available models of cement degradation and to assemble suitable models into a “Toolbox” that would be made available to members of the partnership, as well as the DOE Complex. To this end, SRNL and Vanderbilt University collaborated to develop an interface using the GoldSim software to the STADIUM @ code developed by SIMCO Technologies, Inc. and LeachXS/ORCHESTRA developed by Energy research Centre of the Netherlands (ECN). Release of Version 3.0 of the CBP Toolbox is planned in the near future. As a part of this release, an increased level of quality assurance for the partner codes and the GoldSim interface has been developed. This report documents results from evaluation testing of the ability of CBP Toolbox 3.0 to perform simulations of concrete degradation applicable to performance assessment of waste disposal facilities. Simulations of the behavior of Savannah River Saltstone Vault 2 and Vault 1/4 concrete subject to sulfate attack and carbonation over a 500- to 1000-year time period were run using a new and upgraded version of the STADIUM @ code and the version of LeachXS/ORCHESTRA released in Version 2.0 of the CBP Toolbox. Running both codes allowed comparison of results from two models which take very different approaches to simulating cement degradation. In addition, simulations of chloride attack on the two concretes were made using the STADIUM @ code. The evaluation sought to demonstrate that: 1) the codes are capable of running extended realistic simulations in a reasonable amount of time; 2) the codes produce “reasonable” results; the code developers have provided validation test results as part of their code QA documentation; and 3) the two codes produce results that are consistent with one another. Results of the evaluation testing showed that the three criteria listed above were met by the CBP partner codes. Therefore, it is concluded that the codes can be used to support performance assessment. This conclusion takes into account the QA documentation produced for the partner codes and for the CBP Toolbox.

97 MATHEMATICS AND COMPUTING↗

The Next Generation System Analysis Model: Capabilities for Simulating a Waste Management System - 19131

The U.S. Department of Energy (DOE) Office of Nuclear Energy Office of Spent Fuel and Waste Disposition's Integrated Waste Management System (IWMS) program is applying integrated waste management system architecture analysis, system engineering, and decision analysis principles to inform potential future decisions regarding potential nuclear waste management system architectures. Architecture analyses of the IWMS are being conducted to support the future deployment of a comprehensive system for managing nuclear waste that considers all major aspects of the back end of the nuclear fuel cycle (i.e., transportation, storage, and disposal). The system architecture analyses consider alternative disposition pathways for commercial spent nuclear fuel (SNF) being stored dry in at-reactor Independent Spent Fuel Storage Installations (ISFSIs) or wet in spent-fuel pools. One method for evaluating these alternatives is simulating the movement of SNF throughout the system components. Successfully simulating a system on the scale of a national waste management system requires - accurate baseline information (e.g., historic fuel discharges from reactors and dry storage loadings at reactor sites), - modeling all logistic interactions between components of the proposed system, and - tracking and reporting all relevant details regarding the simulation's execution. The Next Generation System Analysis Model (NGSAM) is an agent-based simulation software tool designed for the express purpose of modeling the IWMS. It is based on the Performance Analysis Tool, a simulation platform that has been used to model logistics for the Department of Defense and the Federal Emergency Management Agency. Using existing, government-owned software allows NGSAM developers to modify the software at the level of source code and to develop flexible usability and modeling solutions for developing and running simulations of the IWMS. NGSAM imports data from the Oak Ridge National Laboratory (ORNL) Unified Database (e.g., historic assembly information, thermal profiles for assembly heat, at-reactor dry storage loadings) to ensure that the simulation initializes with a realistic representation of the state of commercial SNF in the United States. NGSAM is designed with the flexibility to model and track the behavior of virtually any IWMS architecture assumptions or design considerations. For example, NGSAM can model multiple interim storage facilities or repositories or none at all. Similarly, all assumptions regarding shipment schedules, operating schedules, and reactor operation assumptions can be modeled and adjusted in NGSAM with relative ease. The development of NGSAM was targeted to waste management system analysts as the primary users. With that in mind, analysts from ORNL, Sandia National Laboratories (SNL), and Argonne National Laboratory (ANL) were intimately involved in the development process. That involvement extended beyond merely defining requirements. System analysts have been involved with design decisions and software benchmarking and tests, and they have provided subject-matter expertise where necessary. The result is a high degree of interaction between professional software developers and system analysts, with a multitude of benefits to both groups. This paper explores some of the underlying methodology of the agile software development process used in the creation of NGSAM. It illustrates the capabilities of NGSAM. Some example use cases are discussed as well, with relevant results providing context for how NGSAM is used by system analysts to gain a greater understanding of alternative waste management system architectures. This is a technical paper that does not take into account the contractual limitations under the Standard Contract for Disposal of Spent Nuclear Fuel and/or High-Level Radioactive Waste (Standard Contract) (10 CFR Part 961). Under the provisions of the Standard Contract, DOE does not consider spent nuclear fuel in multi-assembly canisters to be an acceptable waste form, absent a mutually agreed-to contract amendment. To the extent discussions or recommendations in this paper conflict with the provisions of the Standard Contract, the Standard Contract provisions prevail. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

PSA 2025 DPRA for Cyber Optimization

Cyberattacks can have many different attack paths, durations, and goals. There are also many different mitigation options involving hardware, software, and/or humans. Evaluating defense options should include quantitative evaluation of overall effectiveness to make cost and risk-informed decisions. Typical cyberattack modeling methods only provide a qualitative evaluation and have difficulty with time dependent scenarios. The main areas of cybersecurity are confidentiality, integrity, and availability. For companies with cyber-physical systems such as advanced nuclear reactors, cyber-related integrity is a requirement set by the U.S. Nuclear Regulatory Commission. But companies are also concerned about availability or reliability as a business case. As cyber threats are evolving to a business-for-hire structure, more attacks focus on disrupting business success and reliability, causing financial and economic stability risk. Companies want reliability analysis while optimizing cost, which requires more than safety modeling methods. Dynamic-state-based and Markov-based modeling provides a method for better cyber scenario modeling with timing and conditional features not found in other numerical evaluation methods. EMRALD (Event Modeling Risk Assessment using Lined Diagrams) is a dynamic risk analysis modeling and simulation tool and has features that reduce modeling issues such as state-base explosion found in Markov-based tools. It has been used to model different time-dependent events including plant behavior and operator procedures. As a general modeling tool, EMRALD can also be used to model cyberattack scenarios with varying mitigation options and quantify effectiveness, producing numerical data for risk-informed decisions. This paper uses EMRALD to demonstrate that dynamic risk analysis can be used for cyber threat modeling to provide insights for design decision-making and optimize defense strategies.

97 - MATHEMATICS AND COMPUTING↗

Performing Numerical Analysis of Cybersecurity Options Using Dynamic Risk Analysis Tool EMRALD

Cyberattacks can have many different attack paths, durations, and goals. There are also many different mitigation options involving hardware, software, and/or humans. Considering a cyber threat should involve defense-in-depth methods and a quantitative or numerical evaluation of overall effectiveness against dynamic, time-dependent attacks to make cost and risk-informed decisions. Typical cyberattack modeling methods only provide a qualitative evaluation. The main areas of cybersecurity are confidentiality, integrity, and availability. For companies with cyber-physical systems such as advanced nuclear reactors, cyber-related safety is a requirement set by North American Electric Reliability and the U.S. Nuclear Regulatory Commission. They are also concerned about availability or reliability as a business case. As cyber threats are evolving to a business-for-hire structure, more attacks may focus on disrupting business success and reliability, causing financial and economic stability risk. Companies want to know business reliability and recovery from those threats, and that requires modeling physical behavior of the targets. Dynamic-state-based and Markov-based modeling provides a method for better cyber scenario modeling with different tools having issues such as state-base explosion. Dynamic modeling enables time and conditional features not found in other numerical evaluation methods. EMRALD (Event Modeling Risk Assessment using Lined Diagrams) is a dynamic risk analysis modeling and simulation tool and has features that reduce modeling issues. It has been used to model different time-dependent events including plant behavior and operator procedures. As a general modeling tool, EMRALD can also be used to model cyberattack scenarios with varying mitigation options and quantify effectiveness, producing numerical data for risk-informed decisions. This paper uses EMRALD to demonstrate that dynamic numerical risk analysis can be used for cyber threat modeling to provide insights for design decision-making and optimize defense strategies. Keywords: cyber modeling; cyber-physical systems; numerical cyber modeling

97 - MATHEMATICS AND COMPUTING↗

Involute Working Group – FSI Analysis of Fuel Plates Using Finite Volume and Finite Element Methods

The three involute plate research reactors RHF, HFIR, and FRM II have expressed an interest in using computational software to carry their steady-state safety analysis. Since these tools represent a significant departure from the methods used currently (one-dimensional), the acceptability of the new approach by regulators requires thorough verification and validation of these tools. Therefore, Argonne National Laboratory and the three involute-plate reactors formed an informal group called the Involute Working Group aiming at qualifying computational tools to perform steady-state safety analysis. The present report focuses on a comparison of finite volume and finite element methods to model solids in fluid-structure interaction problems with the goal to estimate the coolant flow-induced fuel plate deflections obtained with the two methods. The finite volume method will be obsoleted in STARCCM+ by the end of 2021, nevertheless, this evaluation is important because the method was used by ANL researchers to model the response of the fuel plates, despite its drawbacks, which are discussed in the report. It was essential to check how those estimates compare to the results obtained with the finite element method that is considered superior for structural analysis. Various geometries, i.e., flat, cylindrical and circle-involute fuel plates, as well as coolant flow speed, were considered. The comparison shows that, independently of the plate geometry, the finite volume method significantly underestimates the deflection as compared to finite element method for coarser meshes. When the discretization is developed as a result of a mesh sensitivity study using finite element method, the result obtained using finite volume method can be a few times smaller than the corresponding finite element method solution. A code-to-code comparison , between STAR-CCM+ and LS-DYNA was included in the analysis. Within the LS-DYNA models, two types of finite element formulations were used: solid and shell finite elements. Mesh sensitivity study showed that both approaches converge to a similar value that was obtained with STAR-CCM+ finite element solver. The evaluation of the computational solvers was extended by adding two benchmark cases from the STAR-CCM+ Verification Suite and presented in the Appendix A. The selected cases are: (1) bending of a cantilever beam under external load, and (2) cylindrical shell deformation analysis, known in the literature as ‘Scordelis-Lo roof’. The problems were solved with finite volume, and finite element methods, and the results confirmed the previously discussed findings. The analysis shows that the finite element solver is superior to the finite volume solver in terms of representation of model geometry and estimating the structural behavior of fuel plates. Depending on the ratio of the load to the flexibility of the plate, the finite volume solver can greatly under- or overestimate the structural response if a very carefully selected mesh is not used.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗