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DOE OSTI2014

SU-E-I-97: Smart Auto-Planning Framework in An EMR Environment (SAFEE)

Purpose: Our Radiation Oncology Department uses clinical practice guidelines for patient treatment, including normal tissue sparing and other dosimetric constraints. These practice guidelines were adapted from national guidelines, clinical trials, literature reviews, and practitioner's own experience. Modern treatment planning systems (TPS) have the capability of incorporating these practice guidelines to automatically create radiation therapy treatment plans with little human intervention. We are developing a software infrastructure to integrate clinical practice guidelines and radiation oncology electronic medical record (EMR) system into radiation therapy treatment planning system (TPS) for auto planning. Methods: Our Smart Auto-Planning Framework in an EMR environment (SAFEE) uses a software pipeline framework to integrate practice guidelines,EMR, and TPS together. The SAFEE system starts with retrieving diagnosis information and physician's prescription from the EMR system. After approval of contouring, SAFEE will automatically create plans according to our guidelines. Based on clinical objectives, SAFEE will automatically select treatment delivery techniques (such as, 3DRT/IMRT/VMAT) and optimize plans. When necessary, SAFEE will create multiple treatment plans with different combinations of parameters. SAFEE's pipeline structure makes it very flexible to integrate various techniques, such as, Model-Base Segmentation (MBS) and plan optimization algorithms, e.g., Multi-Criteria Optimization (MCO). In addition, SAFEE uses machine learning, data mining techniques, and an integrated database to create clinical knowledgebase and then answer clinical questions, such as, how to score plan quality or how volume overlap affects physicians' decision in beam and treatment technique selection. Results: In our institution, we use Varian Aria EMR system and RayStation TPS from RaySearch, whose ScriptService API allows control by external programs. These applications are the building blocks of our SAFEE system. Conclusion: SAFEE is a feasible method of integrating clinical information to develop an auto-planning paradigm to improve clinical workflow in cancer patient care.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

RAVEN User Manual

RAVEN is a generic software framework to perform parametric and probabilistic analy- sis based on the response of complex system codes. The initial development was aimed to provide dynamic risk analysis capabilities to the Thermo-Hydraulic code RELAP-7, currently under development at the Idaho National Laboratory (INL). Although the initial goal has been fully accomplished, RAVEN is now a multi-purpose probabilistic and uncer- tainty quantification platform, capable to agnostically communicate with any system code. This agnosticism includes providing Application Programming Interfaces (APIs). These APIs are used to allow RAVEN to interact with any code as long as all the parameters that need to be perturbed are accessible by inputs files or via python interfaces. RAVEN is capable of investigating the system response, and investigating the input space using Monte Carlo, Grid, or Latin Hyper Cube sampling schemes, but its strength is focused to- ward system feature discovery, such as limit surfaces, separating regions of the input space leading to system failure, using dynamic supervised learning techniques. The development of RAVEN has started in 2012, when, within the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the need to provide a modern risk evaluation framework became stronger. RAVEN principal assignment is to provide the necessary software and algorithms in order to employ the concept developed by the Risk Informed Safety Margin Characterization (RISMC) program. RISMC is one of the pathways defined within the Light Water Reactor Sustainability (LWRS) program. In the RISMC approach, the goal is not just the individuation of the frequency of an event potentially leading to a system failure, but the closeness (or not) to key safety-related events. Hence, the approach is in- terested in identifying and increasing the safety margins related to those events. A safety margin is a numerical value quantifying the probability that a safety metric (e.g. for an important process such as peak pressure in a pipe) is exceeded under certain conditions. The initial development of RAVEN has been focused on providing dynamic risk assess- ment capability to RELAP-7, currently under develop-ment at the INL and, likely, future replacement of the RELAP5-3D code. Most the capabilities that have been implemented having RELAP-7 as principal focus are easily deployable for other system codes. For this reason, several side activates are currently ongoing for coupling RAVEN with soft- ware such as RELAP5-3D, etc. The aim of this document is the explaination of the input requirements, focalizing on the input structure.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Enabling a systems biology knowledgebase with gaggle and firegoose

The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is an open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and improve the integration within different environments, and we have created a new tools pipeline for generating EGRIN2 models in a largely automated way.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Personnel Certifications for the Design, Installation and Maintenance of Photovoltaic Systems. Final Technical Report

The North American Board of Certified Energy Practitioners (NABCEP) is the most respected, well-established, and widely recognized national certification organization for professionals in the field of renewable energy. NABCEP’s certifications were created to facilitate consumer protection, improve quality assurance, and help employers judge the skills of existing or potential employees. The certifications also allow individuals to differentiate themselves from others in their field and advance their careers while fostering increased recognition of the profession. Since NABCEP’s founding in 2002, all of its certification exams have been administered in paper-and-pencil format twice per year at 30 exam sites around the United States. The biannual test administration and relatively low number of exam sites make it challenging for many qualified renewable energy professionals to take NABCEP’s certification exams. The rigorous nature of the exam, which leads to many candidates failing the exam on their first and sometimes second attempts, combined with the low number of annual test administrations means that anyone who fails will need to wait another six months for the chance to retake the exam. These factors limited the potential growth of NABCEP’s certification programs and the resultant quality assurance within the renewable energy industry. Thanks to a generous grant by the Department of Energy’s Solar Training and Education for Professional (STEP) program, NABCEP recently began updating its Photovoltaic (PV) Installation Professional Exam and developing three new specialty certifications in PV design, PV installation, and PV commissioning & maintenance. One of the primary objectives of this STEP-funded project was to develop the exams using a computer-based testing (CBT) model to increase the number of exam administrations and available exam sites for NABCEP’s certification exams. To successfully complete this project, NABCEP partnered with Castle Worldwide, Inc. With more than 25 years of experience in test development, test administration, analysis of examinations, and has a staff of 70 experienced personnel, NABCEP was confident that Castle’s team was more than qualified to help NABCEP make the transition to CBT examinations. NABCEP and Castle Worldwide jointly developed a project management plan that included key deliverables, scope management, a work breakdown structure, roles and responsibilities, and a project schedule with milestones. The project schedule was carefully monitored to ensure that activities along the critical path were not delayed and, when deemed necessary, the project was crashed to add resources so that activities could occur in parallel. NABCEP and Castle Worldwide staff met weekly to discuss any potential schedule variances and activities which might delay the closing of the project. NABCEP also recruited 46 subject matter experts (SMEs) to work with Castle’s staff on this project. NABCEP staff, SME’s, and Castle staff worked together to develop the Job Task Analyses that form the basis for the certification exams, create new examination forms, conduct passing score studies, and complete a psychometrical analysis of potential exam items. NABCEP’s SMEs utilized Castle’s item development platform during face-to-face meetings, webinars, and remote item authoring to write, review, and approve exam items. Castle also used their software to psychometrically analyze existing exam items to confirm the reliability and validity of the NABCEP’s certification exams. On January 3rd, 2018, NABCEP’s began offering its PV Installation Professional certification exam via CBT. The exam was available at Castle’s nearly 600 exam sites in the United States. A large number of sites will help to ensure better access for solar professionals in rural and remote areas, which drives down the implicit costs of taking the certification exams. Thanks to the STEP grant and the robust partnership between NABCEP and Castle Worldwide, Inc., personnel certifications will be much more accessible and affordable for renewable energy professionals.

14 SOLAR ENERGY↗
DOE OSTI2019

Advanced Simulation Tools for Muon-Based Accelerators

The project developed new software tools incorporating the most accurate theoretical calculations and experimental data available for crucial and not-yet-considered physics processes specific to muon accelerators. These new tools were applied to modeling muon ionization cooling channels for a muon collider or a neutrino factory, the facilities that have the potential to discover and explore new exciting fundamental physics but require the development of demanding technologies and innovative concepts. G4beamline, COSY Infinity, and WARP computer codes are particularly well-suited for addressing muon accelerator modeling problems. G4beamline was chosen for its flexibility and modularity, and for being one of the de facto standard codes used by the muon accelerator community. COSY was selected for speed, ability to take into account high-order nonlinear effects essential for the large beams under consideration, and availability of built-in optimization tools. WARP was chosen for its space charge calculation capabilities, speed and flexibility of implementing new lattice elements such as RF cavities. This final technical report summarizes the efforts on implementing advanced new tools in these computer codes addressing the shortcomings in modeling muon physics processes and using these tools to model muon ionization cooling channels.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Nanosecond Gated CMOS Camera (NSGCC) ICD (Rev. 2.1)

The Ultra-Fast X-ray Imager (UXI) program is an ongoing effort at Sandia National Laboratories to create high speed, multi-frame, time-gated Read Out Integrated Circuits (ROICs), and a corresponding suite of photodetectors to image a wide variety of High Energy Density (HED) physics experiments on both Sandia’s Z-Machine and LLNL’s National Ignition Facility (NIF). Several cameras have been designed over the length of the program; one of the most recent is the Icarus, which is an improvement on past imagers (Furi and Hippogriff). A second sensor that can be connected is the Daedalus sensor. The Icarus is a 1024 × 512-pixel array with either 25 μm or 8 µm spatial resolution containing four frames of storage per pixel and has improved timing generation and distribution components while achieved 2 ns time gating. The Daedalus sensor is also a 1024 x 512-pixel array with 25 µm special resolution containing three frames of storage per pixel and has an increased set of features for a wider variety of applications from interlacing of rows in each frame to configurability of all shutters. See Section 14 for details regarding the Icarus implementation of the firmware and Section 15 for details regarding the Daedalus implementation. Due to the unique test environments UXI sensors are targeted for, full custom hardware was required to physically mount an Icarus or Daedalus sensor, manage its various functions, and read out pixel data for transfer to a host computer. Beyond experimental functionality, the hardware also needed to accommodate sensor characterization requirements. Lawrence Livermore National Laboratory’s ‘Version 4.0 Board’ was the result of these efforts. It mounts all the components required to fully utilize the Icarus and Daedalus sensors including analog to digital converters to convert pixel data and various system voltages to digital form for readout and analysis, DAC channels for remote configuration of critical bias voltages, static random-access memories to buffer pixel data, RS422 and Gigabit Ethernet communications for remote access, and an FPGA to tie these components together. This document describes the FPGA electrical interfaces in detail to allow the reader a greater understanding of the device, and to facilitate implementation of custom software to control and manage it. The Version 4.0 Board is a continuation of the Nano-second Gated CMOS hardware design that retains much of the functionality of the Version 1.0 Board while adding features including a DAC instead of digital potentiometers, as well as sensors for pressure and radiation. The Version 4.0 board is intended for applications requiring tight form-factor enclosures. It is composed of two stacking boards; one holds the FPGA and regulators to power the various components of the board while the other contains the mating connector to the sensor, image-readoff ADCs, the DAC, and other components.

42 ENGINEERING↗
DOE OSTI2013

An automated voxelized dosimetry tool for radionuclide therapy based on serial quantitative SPECT/CT imaging

Purpose: To create an accurate map of the distribution of radiation dose deposition in healthy and target tissues during radionuclide therapy.Methods: Serial quantitative SPECT/CT images were acquired at 4, 24, and 72 h for 28 {sup 177}Lu-octreotate peptide receptor radionuclide therapy (PRRT) administrations in 17 patients with advanced neuroendocrine tumors. Deformable image registration was combined with an in-house programming algorithm to interpolate pharmacokinetic uptake and clearance at a voxel level. The resultant cumulated activity image series are comprised of values representing the total number of decays within each voxel's volume. For PRRT, cumulated activity was translated to absorbed dose based on Monte Carlo-determined voxel S-values at a combination of long and short ranges. These dosimetric image sets were compared for mean radiation absorbed dose to at-risk organs using a conventional MIRD protocol (OLINDA 1.1).Results: Absorbed dose values to solid organs (liver, kidneys, and spleen) were within 10% using both techniques. Dose estimates to marrow were greater using the voxelized protocol, attributed to the software incorporating crossfire effect from nearby tumor volumes.Conclusions: The technique presented offers an efficient, automated tool for PRRT dosimetry based on serial post-therapy imaging. Following retrospective analysis, this method of high-resolution dosimetry may allow physicians to prescribe activity based on required dose to tumor volume or radiation limits to healthy tissue in individual patients.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2019

Integrated Simulation Capabilities for Analysis of Experiments in the Versatile Test Reactor

The DOE-initiated Versatile Test Reactor (VTR) program aims to establish a domestic fast-neutron irradiation testing capability that meets a variety of domestic and international nuclear energy needs. Currently, integrated tools capable of mechanistic modeling of VTR and a test vehicle do not exist. To address this modeling and analysis deficiency, Argonne's SAS4A/SYSSYS-1 safety analysis code has been coupled with SAM (System Analysis Module) to provide a novel modeling capability that supports VTR and other fast test facilities. This report documents the design, implementation, and testing of this integrated capability. A coupling boundary has been identified at the test vehicle and primary coolant interface, where SAS4A/SASSYS-1 treats primary coolant thermal hydraulics outside the test vehicle, while SAM treats all thermal hydraulic behavior within the test vehicle, including the vehicle walls. Essential to this integrated tool is its newly developed capability to properly model the conjugate heat transfer process which ensures equality of temperatures and heat fluxes at the vehicle wall interface while ensuring energy conservation. A range of testing has been completed to support demonstration of this interface. The testing scope includes steady-state verification using a series of increasingly complex analytical solutions and transient demonstration for a range of design basis accident scenarios using prototypic VTR and test vehicle (i.e. cartridge loop) configurations. Results of this testing confirm verification of the steady-state solutions and provide reasonable and expected transient behavior. The coupling interface has been developed to be robust yet flexible. The implementation within SAS4A/SASSYS-1 supports coupling to any external software or module. The use of decomposed domains and the existing in-core thermal-hydraulic calculational framework within SAS4A/SASSYS-1 enable treatment of arbitrary test vehicle geometries with nonuniform meshing between SAS4A/SASSYS-1 and the coupled code. Modeling of multiple test locations is also supported. Furthermore, computational efficiency is enhanced by utilizing named pipes (or FIFOs), an interface for interprocess communication (IPC).

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2015

Cementitious Barriers Partnership - FY2015 End-Year Report

The DOE-EM Office of Tank Waste Management Cementitious Barriers Partnership (CBP) is chartered with providing the technical basis for implementing cement-based waste forms and radioactive waste containment structures for long-term disposal. Therefore, the CBP ultimate purpose is to support progress in final treatment and disposal of legacy waste and closure of High-Level Waste (HLW) tanks in the DOE complex. This status report highlights the CBP 2015 Software and Experimental Program efforts and accomplishments that support DOE needs in environmental cleanup and waste disposal. DOE needs in this area include: Long-term performance predictions to provide credibility (i.e., a defensible technical basis) for regulator and DOE review and approvals, Facility flow sheet development/enhancements, and Conceptual designs for new disposal facilities. In 2015, the CBP developed a beta release of the CBP Software Toolbox – “Version 3.0”, which includes new STADIUM carbonation and damage models, a new SRNL module for estimating hydraulic properties and flow in fractured and intact cementitious materials, and a new LeachXS/ORCHESTRA (LXO) oxidation module. In addition, the STADIUM sulfate attack and chloride models have been improved as well as the LXO modules for sulfate attack, carbonation, constituent leaching, and percolation with radial diffusion (for leaching and transport in cracked cementitious materials). These STADIUM and LXO models are applicable to and can be used by both DOE and the Nuclear Regulatory Commission (NRC) end-users for service life prediction and long-term leaching evaluations of radioactive waste containment structures across the DOE complex.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2016

Landrush: Rethinking In-Situ Analysis for GPGPU Workflows

In-situ analysis on the output data of scientific simulations has been made necessary by ever-growing output data volumes and increasing costs of data movement as supercomputing is moving towards exascale. With hardware accelerators like GPUs becoming increasingly common in high end machines, new opportunities arise to co-locate scientific simulations and online analysis performed on the scientific data generated by the simulations. However, the asynchronous nature of GPGPU programming models and the limited context-switching capabilities on the GPU pose challenges to co-locating the scientific simulation and analysis on the same GPU. This paper dives deeper into these challenges to understand how best to co-locate analysis with scientific simulations on the GPUs in HPC clusters. Specifically, our 'Landrush' approach to GPU sharing proposes a solution that utilizes idle cycles on the GPU to provide an improved time-to-answer, that is, the total time to run the scientific simulation and analysis of the generated data. Landrush is demonstrated with experimental results obtained from leadership high-end applications on ORNL's Titan supercomputer, which show that (i) GPU-based scientific simulations have varying degrees of idle cycles to afford useful analysis task co-location, and (ii) the inability to context switch on the GPU at instruction granularity can be overcome by careful control of the analysis kernel launches and software-controlled early completion of analysis kernel executions. Results show that Landrush is superior in terms of time-to-answer compared to serially running simulations followed by analysis or by relying on the GPU driver and hardwired thread dispatcher to run analysis concurrently on a single GPU.

Computer Science↗
DOE OSTI2018

Creating an Interprocedural Analyst-Oriented Data Flow Representation for Binary Analysts (CIAO)

National security missions require understanding third-party software binaries, a key element of which is reasoning about how data flows through a program. However, vulnerability analysts protecting software lack adequate tools for understanding data flow in binaries. To reduce the human time burden for these analysts, we used human factors methods in a rolling discovery process to derive user-centric visual representation requirements. We encountered three main challenges: analysis projects span weeks, analysis goals significantly affect approaches and required knowledge, and analyst tools, techniques, conventions, and prioritization are based on personal preference. To address these challenges, we initially focused our human factors methods on an attack surface characterization task. We generalized our results using a two-stage modified sorting task, creating requirements for a data flow visualization. We implemented these requirements partially in manual static visualizations, which we informally evaluated, and partially in automatically generated interactive visualizations, which have yet to be integrated into workflows for evaluation. Our observations and results indicate that 1) this data flow visualization has the potential to enable novel code navigation, information presentation, and information sharing, and 2) it is an excellent time to pursue research applying human factors methods to binary analysis workflows.

42 ENGINEERING↗
DOE OSTI2018

sympl (v. 0.4.0) and climt (v. 0.15.3) – towards a flexible framework for building model hierarchies in Python

sympl (System for Modelling Planets) andclimt (Climate Modelling and Diagnostics Toolkit) are anattempt to rethink climate modelling frameworks from the ground up. The aimis to use expressive data structures available in the scientific Pythonecosystem along with best practices in software design to allow scientists toeasily and reliably combine model components to represent the climate systemat a desired level of complexity and to enable users to fully understandwhat the model is doing. sympl is a framework which formulates the model in terms of astate that gets evolved forward in time or modified within a specifictime by well-defined components. sympl's design facilitates buildingmodels that are self-documenting, are highly interoperable, and providefine-grained control over model components and behaviour. symplcomponents contain all relevant information about the input they expect andoutput that they provide. Components are designed to be easily interchanged,even when they rely on different units or array configurations.sympl provides basic functions and objects which could be used inany type of Earth system model. climt is an Earth system modelling toolkit that contains scientificcomponents built using sympl base objects. These include both purePython components and wrapped Fortran libraries. climt providesfunctionality requiring model-specific assumptions, such as stateinitialization and grid configuration. climt's programming interfacedesigned to be easy to use and thus appealing to a wide audience. Model building, configuration and execution are performed through a Pythonscript (or Jupyter Notebook), enabling researchers to build an end-to-endPython-based pipeline along with popular Python data analysis andvisualization tools.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

OPTIMADE, an API for exchanging materials data

Abstract The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2014

SU-E-T-252: On the Evaluation of Patient Specific IMRT QA Using EPID, Dynalog Files and Patient Anatomy

Purpose: This research, investigates the viability of using the Electronic portal imaging device (EPID) coupled with the treatment planning system (TPS), to calculate the doses delivered and verify agreement with the treatment plan. The results of QA analysis using the EPID, Delta4 and fluence calculations using the multi-leaf collimator (MLC) dynalog files on 10 IMRT patients are presented in this study. Methods: EPID Fluence Images in integrated mode and Dynalog files for each field were acquired for 10 IMRT (6MV) patients and processed through an in house MatLab program to create an opening density matrix (ODM) which was used as the input fluence for dose calculation with the TPS (Pinnacle3, Philips). The EPID used in this study was the aSi1000 Varian on a Novalis TX linac equipped with high definition MLC. The resulting dose distributions were then exported to VeriSoft (PTW) where a 3D gamma was calculated using 3mm-3% criteria. The Scandidos Delta4 phantom was also used to measure a 2D dose distribution for all 10 patients and a 2D gamma was calculated for each patient using the Delta4 software. Results: The average 3D gamma for all 10 patients using the EPID images was 98.2% ± 2.6%. The average 3D gamma using the dynalog files was 94.6% ± 4.9%. The average 2D gamma from the Delta4 was 98.1% ± 2.5%. The minimum 3D gamma for the EPID and dynalog reconstructed dose distributions was found on the same patient which had a very large PTV, requiring the jaws to open to the maximum field size. Conclusion: Use of the EPID, combined with a TPS is a viable method for QA of IMRT plans. A larger ODM size can be implemented to accommodate larger field sizes. An adaptation of this process to Volumetric Arc Therapy (VMAT) is currently under way.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) Software for Depletion and Fuel Management

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) software is being developed in the Research and Test Reactor (RTR) Program at Argonne National Laboratory to meet the reactor design and analysis needs of the Conversion Program. ADDER is a flexible tool that (1) provides a depletion capability through coupling external neutronics codes with a built-in CRAM solver or external depletion code and (2) provides a user-friendly interface to perform fuel management and criticality search operations. The ADDER software is a Python 3 application written using modern software development practices subject to a compliant implementation of NQA-1 and applicable Department of Energy software quality assurance standards. This report is the user guide for the software release referred to as ADDER v1.1.0. The motivation for a software to have flexible capabilities that ADDER possesses is the need to support a wide variety of geometries that are commonly required in analysis of research and test reactors. These reactors can have complex fuel, experiment, or control material shuffling patterns that persist over several years with many fuel management and partial refueling intervals. The scale of fuel management analysis can require tracking of an inventory that is multiple times the core loading. Many reactors, both power and non-power reactors of various types, will find the features of ADDER useful to facilitate key tasks that a fuel or core design engineer must perform with the convenience of concise input and validated functionality.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2016

Status of Electronics Upgrades to the LANL Green is Clean Phoswich Detector Systems - 16419

Los Alamos National Laboratory radiological facilities produce low-density room trash that, in many cases, is not contaminated with radioactivity. It has been estimated that 50 to 90% of low-density room trash is free of radioactive contamination and eligible for inclusion in LANL's Green is Clean (GIC) program. The GIC program is a verification program for non-regulated waste from radiation controlled areas that has been actively segregated as nonradioactive through the use of the waste generator's acceptable knowledge. The GIC program has employed two large area Phoswich gamma ray detector systems (HERCULES and ZEUS) to assay and verify that GIC candidate waste meets free release disposal requirements. The large area (127 cm{sup 2}) Phoswich detectors consist of a thin NaI front crystal (3 mm thick) that is optically coupled to a thick CsI back crystal (50 mm thick). The crystals are set in an oxygen-free high-conductivity copper housing with a very thin (0.025 mm) aluminum entrance window. The scintillation properties of the two crystals are different enough to allow the system's electronic components to identify the origin of any pulse. The original systems utilize Nuclear Instrumentation Module (NIM) electronics to process the detector signals. These electronic modules provide the buffering, amplification, and pulse shape analyzer needed for the proper presentation of signals to the custom Phosmux router module. The router module separates the sodium iodide and cesium iodide signals by their rise times and transfers this information into the computer-mounted multichannel analyzer, a Canberra Model S-100 system. While these NIM Bin counting electronics configurations have been effective for approximately 20 years of operation, they are bulky requiring numerous modules per detector and the important Phosmux module is no longer manufactured by LANL. Modern advancement of commercial counting electronics now offer more compact options for equivalent detector signal processing. A pulse shape discriminator module, the DGF Pixie-4, made by XIA LLC, has been identified that can replace the majority of the original NIM bin electronics in a much more compact chassis - one Pixie-4 replaces four NIM amplifiers and four NIM PSAs and fits in a small National Instruments{sup TM} chassis. Thus, LANL has initiated a system upgrade project to replace the historic NIM electronics with the XIA Pixie4 and associated configuration software. The hardware for one Phoswich systems has been procured for the project and the configuration software, customized for the LANL Phoswich detector application, has been written by the manufacturer. Initial setup and optimization of the Pixie-4 configuration has been performed. Qualitative and quantitative baseline comparisons to the NIM electronics has been performed. Good agreement of key low energy gamma lines between the systems has allowed 'Proof of Concept' to be concluded. Further optimization and performance evaluations are in progress. Modifications to the LabVIEW{sup TM} based operating software (originally written by VI Control Systems Ltd.) are being performed by a LANL LabVIEW{sup TM} programmer to accommodate the electronics upgrade. A new LabVIEW{sup TM} interface to control the Pixie-4 has already been developed. Final optimization and testing, formal software QA, and revisions to operating procedures are in progress to achieve completion of the GIC system upgrade project. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) Software for Depletion and Fuel Management

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) software is being developed in the Research and Test Reactor (RTR) Program at Argonne National Laboratory to meet the reactor design and analysis needs of the Conversion Program. ADDER is a flexible tool that (1) provides a depletion capability through coupling external neutronics codes with a built-in CRAM solver or external depletion code and (2) provides a user-friendly interface to perform fuel management and criticality search operations. The ADDER software is a Python 3 application written using modern software development practices subject to a compliant implementation of NQA-1 and applicable Department of Energy software quality assurance standards. This report is the user guide for the software release referred to as ADDER v1.1.0. The motivation for a software to have flexible capabilities that ADDER possesses is the need to support a wide variety of geometries that are commonly required in analysis of research and test reactors. These reactors can have complex fuel, experiment, or control material shuffling patterns that persist over several years with many fuel management and partial refueling intervals. The scale of fuel management analysis can require tracking of an inventory that is multiple times the core loading. Many reactors, both power and non-power reactors of various types, will find the features of ADDER useful to facilitate key tasks that a fuel or core design engineer must perform with the convenience of concise input and validated functionality.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

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↗