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At least 1,063 records · Page 59

Visualization of yeast chromosomal DNA

The DNA molecule is the most significant life molecule since it codes the blue print for other structural and functional molecules of all living organisms. Agarose gel electrophoresis is now being widely used to separate DNA of virus, bacteria, and lower eukaryotes. The task was undertaken of reviewing the existing methods of DNA fractionation and microscopic visualization of individual chromosonal DNA molecules by gel electrophoresis as a basis for a proposed study to investigate the feasibility of separating DNA molecules in free fluids as an alternative to gel electrophoresis. Various techniques were studied. On the molecular level, agarose gel electrophoresis is being widely used to separate chromosomal DNA according to molecular weight. Carl and Olson separate and characterized the entire karyotype of a lab strain of Saccharomyces cerevisiae. Smith et al. and Schwartz and Koval independently reported the visualization of individual DNA molecules migrating through agarose gel matrix during electrophoresis. The techniques used by these researchers are being reviewed in the lab as a basis for the proposed studies.

Lubega, Seth↗

Genetic Algorithm Optimization of a Cost Competitive Hybrid Rocket Booster

Performance, reliability and cost have always been drivers in the rocket business. Hybrid rockets have been late entries into the launch business due to substantial early development work on liquid rockets and solid rockets. Slowly the technology readiness level of hybrids has been increasing due to various large scale testing and flight tests of hybrid rockets. One remaining issue is the cost of hybrids versus the existing launch propulsion systems. This paper will review the known state-of-the-art hybrid development work to date and incorporate it into a genetic algorithm to optimize the configuration based on various parameters. A cost module will be incorporated to the code based on the weights of the components. The design will be optimized on meeting the performance requirements at the lowest cost.

Story, George↗

Collaborative Host Facility for Lunar Operations

This project establishes a new collaborative simulation connectivity capability for JSC utilizing existing facilities. The principal collaborating organizations are Safety & Mission Assurance (Code NA) and Engineering Directorate (Code EA), but the capability is open for any JSC user. The core of the connectivity resides in Code ER7’s Concept Exploration Laboratory (CEL) and is part of ER7’s Systems Engineering Simulator (SES) complex. NA Subject Matter Experts (SMEs) work proactively in situ with EA and commercial crew counterparts to evaluate Safety Review Panel (SRP) protocols for landers, habitation modules, and lunar roving systems using the same tools, terrain models and data as the designers. NA software initiated under two JSC Center Innovation Fund (CIF) and Innovation Charge account (ICA) funded projects will be used to configure the CEL to function as an EA maintained facility. Collaboration via the CEL with the U.S. Space Force (USSF) provides visibility for USSF. The potential for commercial crew and vehicle suppliers will require IT security and associated security architecture to be implemented in additional CIF based proposals.

Collaborative Simulation Hosting↗

Changes to virus taxonomy, the international code of virus classification and nomenclature, and the ICTV statutes ratified by the International Committee on Taxonomy of Viruses (2025)

Abstract The 56th meeting of the Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) was held in Bari, Italy, in July/August, 2024, and 115 submitted taxonomy proposals were reviewed. A total of 112 were subsequently ratified by the ICTV membership. An additional 9 error correction proposals were also approved in August 2025. This article lists the taxonomy proposals that have now been incorporated into release 40 version v2 of the Master Species List ( https://ictv.global/msl ), the Virus Metadata Resource ( https://ictv.global/vmr ), and associated ICTV databases. In addition to the assignments of 1,563 new virus species, 243genera, 55 families, 11 orders, and 8 classes, there were substantial additions to higher taxonomic ranks. These include the creation of a new realm ( Singelaviria ), which is based on the recognition of a separate evolutionary origin for the hallmark capsid genes of members of the kingdom Helvetiavirae. These express capsid proteins forming a single jelly-roll fold that is structurally and evolutionarily distinct from those of members of the family Bamfordvirae , assigned to the realm Varidnaviria . Furthermore, the realm Varidnaviria underwent a major reorganization, including the addition of a new kingdom, Abadenavirae . Another notable change was the classification of the vertebrate-infecting single-stranded DNA anellovirids into a new phylum Commensaviricota (kingdom Shotokuvirae , realm Monodnaviria ). Archaeal viruses infecting the hyperthermophilic Archaeoglobi were assigned to a new phylum Calorviricota , in the kingdom Trapavirae (realm Monodnaviria ), whereas RNA viruses infecting hyperthermophilic bacteria were classified into a new phylum Artimaviricota (realm Riboviria ). In recognition of his extensive and valuable contributions to virus taxonomic developments in Study Groups and over the period of his EC membership, Stuart Siddell was honoured as a new life member of the ICTV. The ICTV has created a new strategy for disseminating information on taxonomy advances through annual open-access publication of citeable taxonomy proposal summaries from each ICTV Subcommittee. A collective total of 354 co-authors of the seven summaries were drawn from members of each Subcommittee, the EC, and a very large number of contributors from the wider virology community.

Simmonds, Peter (ORCID:0000000279644700)↗

Literature Review of Advanced Reactor Cost Estimates

This report provides a comprehensive review of existing literature on advanced reactor cost estimations in the form of a ‘meta-study’. Over 30 references were evaluated and considered as part of this effort. The information is then distilled into different tiers, each with varying levels of detail and granularity. The recommendations consist of low/medium/high estimates for capital and operating costs that can be adjusted using various correction factors (based on learning, numbers of plants per site, etc.). In addition, reference breakdown in costs based on a code of account structure is provided for the main four types of advanced reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Validation for 233U-Fueled Systems in KENO V.a in SCALE 6.2

Validation of the KENO V.a Monte Carlo code has been performed in recent years using benchmark experiments contained in the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook. The models used in these recent validation efforts have been drawn from the Verified, Archived Library of Inputs and Data (VALID). Models must be generated and reviewed by qualified individuals to be added to the VALID library, which leads to high confidence in the models and reduces the probability that apparent validation issues are a result of modeling errors. The contents of the VALID library are somewhat limited because of the effort involved in generating and reviewing models, so no 233U-fueled experiments are included in VALID. A large number of models of 233U experiments have been modeled in the past in support of the criticality safety of 233U in storage at Oak Ridge National Laboratory (ORNL). In June 2016, two midshipmen from the United States Naval Academy were assigned to ORNL, and they reviewed and updated these models for execution in SCALE 6.2. The validation of 233U is of interest because some discrepancies in SCALE results were identified by a beta tester at the Nuclear Energy Agency modeling these systems. These discrepancies were related to a data thinning procedure in the continuous-energy nuclear data process, and had been resolved prior to the release of SCALE 6.2

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.

59 BASIC BIOLOGICAL SCIENCES↗

Contingency Contractor Optimization Phase 3 Sustainment Verification and Validation V&V) Report - Contingency Contractor Optimization Engineering - Prototype

The reports and test plans contained within this document serve as supporting materials to the activities listed within the “Contingency Contractor Optimization Tool – Prototype (CCOT-P) Verification & Validation Plan” [1]. The activities included test development, testing, peer reviews, and expert reviews. The engineering prototype reviews were done for both the software and the mathematical model used in CCOT-P. Section 2 includes the peer and expert review reports, which summarize the findings from each of the reviews and document the resolution of any issues. Section 3 details the test plans that were followed for functional testing of the application through the interface. Section 4 describes the unit tests that were run on the code.

97 MATHEMATICS AND COMPUTING↗

33 Shafts Category of Transuranic Waste Stored Below Ground within Area G

This report compiles information to support the evaluation of alternatives and analysis of regulatory paths forward for the 33 shafts. The historical information includes a form completed by waste generators for each waste package (Reference 6) that included a waste description, estimates of Pu-239 and uranium-235 (U-235) based on an accounting technique, and calculations of mixed fission products (MFP) based on radiation measurements. A 1979 letter and questionnaire (Reference 7) provides information on waste packaging of hot cell waste and the configuration of disposal shafts as storage in the 33 Shafts was initiated. Tables of data by waste package were developed during a review of historical documents that was performed in 2005 (Reference 8). Radiological data was coupled with material-type data to estimate the initial isotopic content of each waste package and an Oak Ridge National Laboratory computer code was used to calculate 2009 decay levels. Other sources of information include a waste disposal logbook for the 33 shafts (Reference 9), reports that summarize remote-handled waste generated at the CMR facility (Reference 10) and placement of waste in the 33 shafts (Reference 11), a report on decommissioning of the LAMPRE reactor (Reference 12), interviews with an employee and manager involved in placing waste in the 33 shafts (References 13 and 14), an interview with a long-time LANL employee involved in waste operations (Reference 15), a 2002 plan for disposition of remote-handled TRU waste (Reference 16), and photographs obtained during field surveys of several shafts in 2007. The WIPP Central Characterization Project (CCP) completed an Acceptable Knowledge (AK) summary report for 16 canisters of remote-handled waste from the CMR Facility that contains information relevant to the 33 Shafts on hot-cell operations and timeline (Reference 17).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DayCent_CABBI_energy_farm_sorghum_BNI_Ecosphere

This repository contains call source code and input files that are part of the DayCent_CABBI BNI model experiments described in the manuscript below. Hartman et al. 2022. In Silico Evaluation of Plant Nitrification Suppression Effects on Agroecosystem Nitrogen Loss. Ecosphere . In Review.

70101 Agricultural Land Management↗

Numerical simulation of transverse fuel injection

A review of recent work at NASA Langley Research Center to compare the predictions of transverse fuel injector flow fields and mixing performance with experimental results is presented. Various cold (non-reactive) mixing studies were selected for code calibration which include the effects of boundary layer thickness and injection angle for sonic hydrogen injection into supersonic air. Angled injection of helium is also included. This study was performed using both the three-dimensional elliptic and the parabolized Navier-Stokes (PNS) versions of SPARK. Axial solution planes were passed from PNS to elliptic and elliptic to PNS in order to efficiently generate solutions. The PNS version is used both upstream and far downstream of the injector where the flow can be considered parabolic in nature. The comparisons are used to identify experimental deficiencies and computational procedures to improve agreement.

Mao, Marlon↗

Time and position accuracy using codeless GPS

The Global Positioning System has allowed scientists and engineers to make measurements having accuracy far beyond the original 15 meter goal of the system. Using global networks of P-Code capable receivers and extensive post-processing, geodesists have achieved baseline precision of a few parts per billion, and clock offsets have been measured at the nanosecond level over intercontinental distances. A cloud hangs over this picture, however. The Department of Defense plans to encrypt the P-Code (called Anti-Spoofing, or AS) in the fall of 1993. After this event, geodetic and time measurements will have to be made using codeless GPS receivers. However, there appears to be a silver lining to the cloud. In response to the anticipated encryption of the P-Code, the geodetic and GPS receiver community has developed some remarkably effective means of coping with AS without classified information. We will discuss various codeless techniques currently available and the data noise resulting from each. We will review some geodetic results obtained using only codeless data, and discuss the implications for time measurements. Finally, we will present the status of GPS research at JPL in relation to codeless clock measurements.

Dunn, C. E.↗

Multimedia Information eXchange for I-NET, Inc. at the Kennedy Space Center: A continuing study of the application of worldwideweb technology

Multimedia Information eXchange (MIX) is a multimedia information system that accommodates multiple data types and provides consistency across platforms. Information from all over the world can be accessed quickly and efficiently with the Internet-based system. I-NET's MIX uses the World Wide Web and Mosaic graphical user interface. Mosaic is available on all platforms used at I-NET's Kennedy Space Center (KSC) facilities. Key information system design concepts and benefits are reviewed. The MIX system also defines specific configuration and helper application parameters to ensure consistent operations across the entire organization. Guidelines and procedures for other areas of importance in information systems design are also addressed. Areas include: code of ethics, content, copyright, security, system administration, and support.

Metcalf, David↗

A Comparison of EAST Shock-Tube Radiation Measurements with a New Air Radiation Model

This paper presents a comparison between the recent EAST shock tube radiation measurements (Grinstead et al., AIAA 2008-1244) and the HARA radiation model. The equilibrium and nonequilibrium radiation measurements are studied for conditions relevant to lunar-return shock-layers; specifically shock velocities ranging from 9 to 11 kilometers per second at initial pressures of 0.1 and 0.3 Torr. The simulated shock-tube flow is assumed one-dimensional and is calculated using the LAURA code, while a detailed nonequilibrium radiation prediction is obtained in an uncoupled manner from the HARA code. The measured and predicted intensities are separated into several spectral ranges to isolate significant spectral features, mainly strong atomic line multiplets. The equations and physical data required for the prediction of these strong atomic lines are reviewed and their uncertainties identified. The 700-1020 nm wavelength range, which accounts for roughly 30% of the radiative flux to a peak-heating lunar return shock-layer, is studied in detail and the measurements and predictions are shown to agree within 15% in equilibrium. The plus or minus 1.5% uncertainty on the measured shock velocity is shown to cause up to a plus or minus 30% difference in the predicted radiation. This band of predictions contains the measured values in almost all cases. For the highly nonequilibrium 0.1 Torr cases, the nonequilibrium radiation peaks are under-predicted by about half. This under-prediction is considered acceptable when compared to the order-of-magnitude over-prediction obtained using a Boltzmann population of electronic states. The reasonable comparison in the nonequilibrium regions provides validation for both the non-Boltzmann modeling in HARA and the thermochemical nonequilibrium modeling in LAURA. The N2 (+)(1-) and N2(2+) molecular band systems are studied in the 290 480 nm wavelength range for both equilibrium and nonequilibrium regimes. The non-Boltzmann rate models for these systems, which have significant uncertainties, are tuned to improve the comparison with measurements.

Johnston, Christopher O.↗

Physics and Algorithm Enhancements for a Validated MCNP/X Monte Carlo Simulation Tool, Phase VII

Currently the US lacks an end-to-end (i.e., source-to-detector) radiation transport simulation code with predictive capability for the broad range of DHS nuclear material detection applications. For example, gaps in the physics, along with inadequate analysis algorithms, make it difficult for Monte Carlo simulations to provide a comprehensive evaluation, design, and optimization of proposed interrogation systems. With the development and implementation of several key physics and algorithm enhancements, along with needed improvements in evaluated data and benchmark measurements, the MCNP/X Monte Carlo codes will provide designers, operators, and systems analysts with a validated tool for developing state-of-the-art active and passive detection systems. This project is currently in its seventh year (Phase VII). This presentation will review thirty enhancements that have been implemented in MCNPX over the last 3 years and were included in the 2011 release of version 2.7.0. These improvements include 12 physics enhancements, 4 source enhancements, 8 tally enhancements, and 6 other enhancements. Examples and results will be provided for each of these features. The presentation will also discuss the eight enhancements that will be migrated into MCNP6 over the upcoming year.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Flammable Gas Generation and Control at the Idaho Completion Project Legacy Combustible Gas Generation - 20191

On April 11, 2018, four drums containing transuranic waste at the Idaho National Laboratory underwent over-pressurization, ejecting their lids and spreading radiological waste within a facility. An investigation has found that waste in the drums generated methane gas, which contributed to the event. Subsequent to the investigation, the potential for drums to have methane and other flammable analytes whose concentrations could approach or exceed the lower flammability limit (LFL) and the adequacy of the controls to prevent or mitigate a possible deflagration was evaluated. An extensive review of the historical records was performed to determine how many drums exceed the LFL. The historical record identified a small quantity of drums that exceeded the LFL for xylene, hydrogen, and methane. The primary codified applicable code or standard for handling drums is 29 CFR 1910.120 (j) 'Handling Drums and Containers.' It is used throughout the commercial and government sector. This code is integrated throughout the Fluor Idaho safety management programs and procedures to control the Standard Industrial Hazards (SIHs) associated with drum and container handling. Example requirements include: - Drums and containers are inspected, and their integrity assured prior to being moved. - Site operations are organized to minimize the amount of drum or container movement. - When there is a reasonable possibility of flammable atmospheres being present, material handling equipment and hand tools are of the type to prevent sources of ignition. Drums and containers under pressure, as evidenced by bulging or swelling, are not moved until the cause for excess pressure is determined and appropriate containment procedures have been implemented to protect employees from explosive relief of the drum. Drums which exceed the WIPP FGA limit have NCRs associated with them. Once a drum fails flammable gas sampling, an NCR is initiated. The NCR drives placement into NCR dense pack rows. A standing order drives placement of the FGA failures to a single planer segregation location. These drums are not allowed for further processing or shipment until the NCR has been cleared. Once in the single planer rows, follow-up FGA testing is performed by CCP. The NCR is dispositioned by follow-up sampling occurring after adequate time has been provided for the gas to diffuse through the filter assembly, or, in some cases, the drums are repackaged into additional drums to reduce the source term. To date, the ICP project has performed approximately 1.5 million drums moves without a deflagration event due to combustible gas generation. Flammable gas generation in a transuranic waste drum is not unique to the ICP but is common across the DOE complex. Based on the experience at Idaho, application of industry standards is sufficient to control the risk of drum deflagration due to drum movements. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

SAS4A/SASSYS-1 Commercial Grade Dedication Example Report for a Generic Sodium Pool-Type Fast Reactor Application

In the U.S., a key component of the commercialization of advanced reactors is completion of a license application, which must ultimately be approved by the Nuclear Regulatory Commission (NRC). The approval of the license application by the NRC is contingent on satisfactory demonstration of the design basis and the response of the advanced reactor design to transient and accident scenarios using accepted codes and methods. This report describes the qualification and dedication requirements that the advanced reactor safety analysis system software SAS4A/SASSYS-1 are expected to need to fulfill to be used for sodium-cooled pool-type fast reactor licensing. The qualification and dedication requirements are identified through performance critical characteristics and evaluation model acceptance criteria representative of the advanced reactor design considered for licensing. This document captures, additionally, the verification process developed to demonstrate that the software fulfills the qualification and dedication requirements for a generic sodium-cooled pool-type fast reactor as part of the commercial grade dedication process. Like most software that has primarily existed in the research and development space, the most significant challenge facing SAS4A/SASSYS-1 for use in a licensing framework is the availability of a documentation basis describing the code pedigree. SAS4A/SASSYS-1 has been used for licensing of the fast flux test facility (FFTF) and the JOYO sodium-cooled fast reactor in Japan, as well as the design of the CRBR Plant. However, the historical verification and validation (V&V) activities supporting SAS4A/SASSYS-1 development do not align with modern software quality assurance (SQA) and V&V requirements. Two approaches to use of SAS4A/SASSYS-1 in a commercial licensing framework have been identified: commercial-grade dedication (CGD) and software qualification. The methods and requirements prescribed in the ASME NQA-1-2008/2009 Standard and Regulatory Guide 1.203 on the evaluation model development and assessment process (EMDAP) have been used as guidance to define the CGD and qualification processes, respectively. A qualification and dedication requirements matrix has been developed which utilizes fundamental software verification. In this process, software verification is defined as a software quality process aimed at defining software requirement specifications, developing software design documentation, and performing and documenting acceptance testing of the code against requirements. A key element of software qualification and dedication includes determination of software acceptance with respect to critical characteristics relevant to the functional requirements of the software. To assist with identification of cross-cutting transient phenomena and functional requirements, domestic SFR vendor designs have been reviewed to identify a reference SFR design. For this report, the reference design is defined as a pool-type reactor with metal alloy fuel, a liquid-metal intermediate heat transport system, and passive decay heat rejection systems. Given this reference, a series of high-level cross-cutting phenomena was identified for a general class of single-fault undercooling or reactivity insertion transients that scopes the design basis space, with the goal of assisting with prioritization of documentation development efforts for key transient models in SAS: 1) Reactivity feedback response prior to scram; 2) System-wide thermal inertia; 3) Transition in natural circulation flow regime in heat removal systems; 4) Decay heat generation; 5) Steady-state fuel characterization; 5) Clad/fuel behavior at elevated temperatures; 6) Point kinetics and decay heat; 7) Pump coastdown behavior; 8) Core flow redistribution in loss of forced convection; 9) Pool stratification. As a demonstration of CGD of SAS4A/SASSYS-1 for a sodium pool reactor, a software qualification and dedication gap analysis as it relates to code documentation has been performed. This effort leverages the framework established as part of the SAS4A/SASSYS-1 SQA Program. This CGD demonstration provides a framework that vendors can build upon to demonstrate the applicability of the SAS4A/SASSYS-1 software for licensing a sodium-cooled pool-type fast reactor.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Analyzing Stochastic Computer Models: A Review with Opportunities

In modern science, computer models are often used to understand complex phenomena and a thriving statistical community has grown around analyzing them. This review aims to bring a spotlight to the growing prevalence of stochastic computer models-providing a catalogue of statistical methods for practitioners, an introductory view for statisticians (whether familiar with deterministic computer models or not), and an emphasis on open questions of relevance to practitioners and statisticians. Gaussian process surrogate models take center stage in this review, and these, along with several extensions needed for stochastic settings, are explained. The basic issues of designing a stochastic computer experiment and calibrating a stochastic computer model are prominent in the discussion. Instructive examples, with data and code, are used to describe the implementation of, and results from, various methods.

agent based model↗