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DOE OSTI2014

TH-A-19A-01: An Open Source Software for Proton Treatment Planning in Heterogeneous Medium

Purpose: Due to its success in Radiation Oncology during the last decade, interest in proton therapy is on the rise. Unfortunately, despite the global enthusiasm in the field, there is presently no free, multiplatform and customizable Treatment Planning System (TPS) providing proton dose distributions in heterogenous medium. This restricts substantially the progress of clinical research for groups without access to a commercial Proton TPS. The latest implementation of our pencil beam dose calculation algorithm for proton beams within the 3D Slicer open-source environment fulfills all the conditions described above. Methods: The core dose calculation algorithm is based on the Hong algorithm (1), which was upgraded with the Kanematsu theory describing the evolution of the lateral scattering of proton beamlets in heterogeneous medium. This algorithm deals with both mono-energetic beams and Spread Out Bragg Peak (SOBP). In order to be user-friendly, we provide a graphical user interface implemented with the Qt libraries, and visualization with the 3D Slicer medical image analysis software. Two different pencil beam algorithms were developed, and the clinical proton beam line at our facility was modeled. Results: The dose distributions provided by our algorithms were compared to dose distributions coming from both commercialized XiO TPS and literature (dose measurements, GEANT4 and MCNPx) and turned out to be in a good agreement, with maximum dose discrepancies of 5% in homogeneous phantoms and 10% in heterogeneous phantoms. The algorithm of SOBP creation from an optimized weigthing of mono-energetic beams results in flat SOBP. Conclusion: We hope that our efforts in implementing this new, open-source proton TPS will help the research groups to have a free access to a useful, reliable proton dose calculation software.(1) L. Hong et al., A pencil beam algorithm for proton dose calculations, Phys. Med. Biol. 41 (1996) 1305–1330. This project is paid for by NCI/MGH Federal share as a research grant.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2013

Finite unified theories and their predicitions

All-loop Finite Unified Theories (FUTs) are very interesting N = 1 supersymmetric Grand Unified Theories (GUTs) realising an old field theory dream, and moreover have a remarkable predictive power due to the required reduction of couplings. The reduction of the dimensionless couplings in N = 1 GUTs is achieved by searching for renormalization group invariant (RGI) relations among them holding beyond the unification scale. Finiteness results from the fact that there exist RGI relations among dimensional couplings that guarantee the vanishing of all beta-functions in certain N = 1 GUTs even to all orders. Additional developments in the soft supersymmetry breaking sector of N = 1 GUTs and FUTs lead to exact RGI relations, i.e. reduction of couplings, in this dimensionful sector of the theory, too. Based on the above theoretical framework phenomenologically consistent FUTs have been constructed. Here we review two FUT models based on the SU(5) gauge group. Confronting their predictions with the top and bottom quark masses and other experimental constraints a light Higgs-boson mass in the range M{sub H} ∼ 121–126 GeV has been predicted, in striking agreement with the recent experimental results from ATLAS and CMS. Furthermore naturally a relatively heavy s-spectrum emerged with coloured supersymmetric particles above ∼1.5 TeV in agreement with the non-observation of those particles at the LHC. Restricting further the parameter space of the best version of the SU(5) FUT according to the reported accuracy of the Higgs boson mass and B-physics observables we find predictions for the rest of the Higgs masses and the s-spectrum.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

jialiu232/MetaFunPrimer_paper_info

Genes belonging to the same functional group may include numerous and variable gene sequences, making characterizing and quantifying difficult. Therefore, high-throughput design tools are needed to simultaneously create primers for improved quantification of target genes. We developed MetaFunPrimer, a bioinformatic pipeline, to design primers for numerous genes of interest. This tool also enables gene target prioritization based on ranking the presence of genes in user-defined references, such as environment-specific metagenomes. Given inputs of protein and nucleotide sequences for gene targets of interest and an accompanying set of reference metagenomes or genomes, MetaFunPrimer generates primers for ranked genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 publicly available soil metagenomes. We demonstrate computationally that these amoA-AOB primers can cover 94% of the amoA-AOB genes observed in the 1,550 soil metagenomes compared with a 49% estimated coverage by previously published primers. Finally, we verified the utility of these primer sets in incubation experiments that used long-term nitrogen fertilized or unfertilized soils. High-throughput quantitative PCR (qPCR) results and statistical analyses showed significant differences in relative quantification patterns between the two soils, and subsequent absolute quantifications also confirmed that target genes enumerated by six selected primer pairs were significantly more abundant in the nitrogen-fertilized soils. This new tool gives microbial ecologists a new approach to assess functional gene abundance and related microbial community dynamics quickly and affordably.

Liu, Jia↗

DOE OSTI2026

Virtual Growth of SRF Materials

Niobium's native surface oxide affects SRF cavity and superconducting qubit performance, motivating interest in controlling its crystalline structure. We combine a literature-derived machine-learning analysis with temperature-dependent XRD to study crystalline ordering in Nb2O5. Random Forest models, trained on 74 processing conditions from 17 papers and validated by leave-one-group-out cross-validation, predicted broad crystallinity outcomes well (balanced accuracy 0.809), but struggled with specific polymorph identity (0.577). Annealing temperature was the dominant predictor across all targets; oxygen partial pressure showed negligible importance, reflecting narrow literature coverage rather than physical irrelevance. Temperature-dependent XRD on anodized and H2O2-treated Niobium showed structural evolution consistent with the machine learning predictions. Our model and overall approach provide a data-driven framework for identifying and optimizing conditions that promote crystallization in initially amorphous oxides. This framework can guide the selection of growth and post-annealing conditions for Nb surfaces by narrowing the experimental parameter space, thereby reducing trial-and-error efforts in developing oxide structures relevant to SRF applications.

Tilkin, Anthony [Fermilab]↗

NASA NTRS1980

Brazilian stone meteorites

A survey of Brazilian meteorites is presented, along with basic premises of meteoritics, including classification, naming, and analytic procedures. Meteorites are noted to be of interest as representative samples of ancient rocks, perhaps half as old as the universe, as sometimes originating from outside the solar system, containing early solar material, and containing evidence of cosmic ray interactions or collisions. The characteristics which make up the achondrite and chondrite group are reviewed, and a listing of the primary characteristics of known Brazilian meteorites is provided.

Gomes, C. B.↗

NASA NTRS1986

Hydromagnetic waves at low latitudes - A symposium review from the fifth IAGA assembly

The aim of the symposium was to bring together investigators with interests in low latitude hydromagnetic waves in order to review the present state of knowledge in this area of magnetospheric physics. Of particular importance is the means by which wave energy is transferred to low latitudes to produce geomagnetic pulsations on the ground. The group of contributed papers reviewed shows that definitive experiments are underway and new theories capable of providing resonant wave energy at low latitudes are being developed. Particular topics covered by the review include solar wind control, wave spectra, array studies of wave parameters, storm time waves, and global wave resonance theory involving the coupling of compressional and transverse waves in the magnetosphere.

Fraser, B. J.↗

NASA NTRS1994

Center for modeling of turbulence and transition: Research briefs, 1993

This research brief contains the progress reports of the research staff of the Center for Modeling of Turbulence and Transition (CMOTT) from June 1992 to July 1993. It is also an annual report to the Institute for Computational Mechanics in Propulsion located at Ohio Aerospace Institute and NASA Lewis Research Center. The main objectives of the research activities at CMOTT are to develop, validate, and implement turbulence and transition models for flows of interest in propulsion systems. Currently, our research covers eddy viscosity one- and two-equation models, Reynolds-stress algebraic equation models, Reynolds-stress transport equation models, nonequilibrium multiple-scale models, bypass transition models, joint scalar probability density function models, and Renormalization Group Theory and Direct Interaction Approximation methods. Some numerical simulations (LES and DNS) have also been carried out to support the development of turbulence modeling. Last year was CMOTT's third year in operation. During this period, in addition to the above mentioned research, CMOTT has also hosted the following programs: an eighteen-hour short course on 'Turbulence--Fundamentals and Computational Modeling (Part I)' given by CMOTT at the NASA Lewis Research Center; a productive summer visitor research program that has generated many encouraging results; collaborative programs with industry customers to help improve their turbulent flow calculations for propulsion system designs; a biweekly CMOTT seminar series with speakers from within and without the NASA Lewis Research Center including foreign speakers. In addition, CMOTT members have been actively involved in the national and international turbulence research activities. The current CMOTT roster and organization are listed in Appendix A. Listed in Appendix B are the abstracts of the biweekly CMOTT seminar. Appendix C lists the papers contributed by CMOTT members.

Liou, William W.↗

NASA NTRS1998

The NPG 7120.5A Electronic Review Process

The use of electronics to review a document is well within the technical realm of today's state-of-the-art workplace. File servers and web site interaction are common tools for many NASA employees. The electronic comment processing described here was developed for the NPG 7120.5A review to augment the existing NASA Online Directives Information System (NODIS). The NODIS system is NASA's official system for formal review, approval and storage of NASA Directives. The electronic review process worked so well that NASA and other agencies may want to consider it as one of our "best practices." It was participatory decision making at its very best, a process that attracted dozens of very good ideas to improve the document as well as the way we can be managing projects far more effectively. The revision of NPG 7120.5A has significant implications for the way all elements of the Agency accomplish program and project management. Therefore, the review of NPG 7120.5A was an Agencywide effort with high visibility, heavy participation and a short schedule. The level of involvement created interest in supplementing the formal NODIS system with a system to collect comments efficiently and to allow the Centers and Codes to review and consolidate their comments into the official system in a short period of time. In addition, the Program Management Council Working Group (PMCWG), responsible for the revision of the document and the disposition of official comments, needed an electronic system to manage the disposition of comments, obtain PMCWG consensus on each disposition, and coordinate the disposition with the appropriate Headquarters Code that had submitted the official comment. The combined NASA and contractor talents and resources provided a system that supplemented the NODIS system and its operating personnel to produce a thorough review and approval of NPG 7120.5A on April 3, 1998, 7.5 months from the start of the process. The original six-month schedule is indicated. All milestones occurred on time, except for completion of comment disposition, which required an additional 30 days. Approval of the document occurred sixteen days after completion of the "Purple Package."

McBrayer, Robert↗

NASA NTRS2003

The Study of Biomass Emissions for Defining Radiative Forcing of Climate

Accurate quantification of the amounts of trace gases and particulate matter emitted from vegetation fires and other sources of biomass burning (agricultural waste and biofuels) on a regional and global basis is required by a number of users, including scientists studying a wide range of atmospheric processes, national governments who are required to report greenhouse gas emissions, and those interested in quantifying the sources of air pollution that affect human health at regional scales. Over the past decade, improvements in the ability to detect and map fires using a number of different satellite systems have been achieved, largely through efforts coordinated through working groups organized by the IGBP Data and Information System and Global Observation of Forest Cover (GOFC) projects. In addition, significant advances and improvement in or understanding of the emissions factors for biomass burning in different biomes has resulted through efforts by the Biomass Burning Experiment (BIBEX) organized through the International Global Atmospheric Chemistry project. A number of satellite-based fire data products have been generated, and a number of new products will shortly be available. These new data products will provide the basis for estimating emissions from biomass burning on a global basis. However, a number of issues remain concerning the availability of other data sets needed to generate these estimates. Recognizing these issues, the GOFC-Fire Satellite Validation Workshop (held in Lisbon, Portugal on 9-11 July 2001), recommended that a workshop focusing on Improving Global Estimates of Atmospheric Emissions from Biomass Burning be organized. This workshop was held from 17- 19 July 2002 on the campus of the University of Maryland, College Park, Maryland. This workshop served as the annual meeting of the GOFC/GOLD-Fire Program. The overall goals of the meeting were to review the information products generated from satellite imagery and other sources that are currently available for developing emission estimates from biomass burning, evaluate areas where improved or additional products would be beneficial, and recommend products for use by the atmospheric science community.

Penner, Joyce↗

NASA NTRS2009

Orion Landing Simulation Eight Soil Model Comparison

LS-DYNA finite element simulations of a rigid Orion Crew Module (CM) were used to investigate the CM impact behavior on eight different soil models. Ten different landing conditions, characterized by the combination of CM vertical and horizontal velocity, hang angle, and roll angle were simulated on the eight different soils. The CM center of gravity accelerations, pitch angle, kinetic energy, and soil contact forces were the outputs of interest. The simulation results are presented, with comparisons of the CM behavior on the different soils. The soils analyzed in this study can be roughly categorized as soft, medium, or hard, according to the CM accelerations that occur when landing on them. The soft group is comprised of the Carson Sink Wet soil and the Kennedy Space Center (KSC) Low Density Dry Sand. The medium group includes Carson Sink Dry, the KSC High Density In-Situ Moisture Sand and High Density Flooded Sand, and Cuddeback B. The hard soils are Cuddeback A and the Gantry Unwashed Sand. The softer soils were found to produce lower peak accelerations, have more stable pitch behavior, and to be less sensitive to the landing conditions. This investigation found that the Cuddeback A soil produced the highest peak accelerations and worst stability conditions, and that the best landing performance was achieved on the KSC Low Density Dry Sand.

Mark, Stephen D.↗

DOE OSTI2026

Virtual Growth of SRF Materials: A Machine Learning Approach to Predict the Crystalline Structural Ordering in Nb Surface Oxides

Tilkin, Anthony [Unlisted, US, IL; Fermilab]↗

NASA NTRS2004

Using Trained Pixel Classifiers to Select Images of Interest

We present a machine-learning-based approach to ranking images based on learned priorities. Unlike previous methods for image evaluation, which typically assess the value of each image based on the presence of predetermined specific features, this method involves using two levels of machine-learning classifiers: one level is used to classify each pixel as belonging to one of a group of rather generic classes, and another level is used to rank the images based on these pixel classifications, given some example rankings from a scientist as a guide. Initial results indicate that the technique works well, producing new rankings that match the scientist's rankings significantly better than would be expected by chance. The method is demonstrated for a set of images collected by a Mars field-test rover.

Mazzoni, D.↗

NASA NTRS1991

The 1991 International Conference on Aging Aircraft and Structural Airworthiness

Civil aviation serves a strategic interest to the United States. Thus, the need to maintain a high standard of aviation safety is axiomatic. While the industry has witnessed phenomenal growth in the past two decades, the proportion of aging aircraft in air carrier fleets has been ever increasing-a trend that is projected to continue. Certain events which occurred in 1988 and previous years and public concern about the safety of the high time aircraft led to an International Conference on Aging Aircraft in Washington, D.C., during which a number of aviation safety related issues applicable to aging aircraft were raised and discussed among the conference participants. Various groups that have a vital stake in commercial aviation made certain recommendations which led to the formation of a task force and a broad undertaking involving the Federal Aviation Administration (FAA), the National Aeronautics and Space Administration (NASA), industry and international organizations to insure continued airworthiness of aging airplanes. At the same time, significant research and development programs were initiated by the FAA and NASA to complement the broader effort. In view of the success of the 1988 conference, the FAA desired that conferences be held annually to disseminate information on the status of the task force's activities on aircraft certification and airline maintenance related issues and to offer a forum for participation by all interested parties. Thus, the 2nd International Conference was held in 1989 in Baltimore and the third in the series in 1990 in Bordeaux, France. Both of them, like the first conference, attracted rousing attendance and interest. Thus, the stage was set for organizing the 4th International Conference in 1991. By 1991, the FAA and NASA research programs were yielding significant results, a consideration that led to a larger segment of the 4th International Conference Program being devoted to presentations about the impact of the research on the other activities of the task group. Agreement had also been reached between the FAA and NASA to coordinate and integrate their respective program activities. Hence, NASA was co-opted as a sponsor of the conference. A group consisting of Mr. Stephen Erickson of the Air Transport Association of America, Mr. Jesse Lewis and Mr. Richard Johnson of the FAA, and Mr. Thomas Crooker of NASA was formed to organize the conference. The members of the group are owed special thanks for their efforts that ensured the success of the conference.

Aging Aircraft↗

DOE OSTI2019

Multi-Phenotype Association Decomposition: Unraveling Complex Gene-Phenotype Relationships

Various patterns of multi-phenotype associations (MPAs) exist in the results of Genome Wide Association Studies (GWAS) involving different topologies of single nucleotide polymorphism (SNP)-phenotype associations. These can provide interesting information about the different impacts of a gene on closely related phenotypes or disparate phenotypes (pleiotropy). In this work we present MPA Decomposition, a new network-based approach which decomposes the results of a multi-phenotype GWAS study into three bipartite networks, which, when used together, unravel the multi-phenotype signatures of genes on a genome-wide scale. The decomposition involves the construction of a phenotype powerset space, and subsequent mapping of genes into this new space. Clustering of genes in this powerset space groups genes based on their detailed MPA signatures. We show that this method allows us to find multiple different MPA and pleiotropic signatures within individual genes and to classify and cluster genes based on these SNP-phenotype association topologies. We demonstrate the use of this approach on a GWAS analysis of a large population of 882 Populus trichocarpa genotypes using untargeted metabolomics phenotypes. This method should prove invaluable in the interpretation of large GWAS datasets and aid in future synthetic biology efforts designed to optimize phenotypes of interest.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Machine Learning meets Algebraic Combinatorics: A Suite of Benchmark Datasets to Accelerate AI for Mathematics Research

The use of benchmark datasets has become an important engine of progress in machine learning (ML) over the past 15 years. Recently there has been growing interest in utilizing machine learning to drive advances in research-level mathematics. However, off-the-shelf solutions often fail to deliver the types of insights required by mathematicians. This suggests the need for new ML methods specifically designed with mathematics in mind. The question then is: what benchmarks should the community use to evaluate these? On the one hand, toy problems such as learning the multiplicative structure of small finite groups have become popular in the mechanistic interpretability community whose perspective on explainability aligns well with the needs of mathematicians. While toy datasets are a useful benchmark for initial work, they lack the scale, complexity, and sophistication of many of the principal objects of study in modern mathematics. To address this, we introduce a new collection of benchmark datasets, Algebraic Combinatorics Benchmarks (ACBench), representing either classic or open problems in algebraic combinatorics, a subfield of mathematics that studies discrete structures arising from abstract algebra. After describing the datasets, we discuss the challenges involved in constructing “good” mathematics benchmarks, describe baseline model performance, and discuss some of the insights these datasets can provide that may be of interest even to those who are not interested in mathematics research itself.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

An inverse Ruddlesden-Popper nitride Ca 7 (Li 1–x Fe x )Te 2 N 2 grown from Ca flux

Nitridoferrates containing monovalent iron ions are a class of materials of recent interest as potentially novel magnetic materials. Aiming at the exploration of nitridoferrates of calcium, we report the single crystal growth from Ca flux and crystal structure of the first member ( n = 2) of a series of inverse Ruddlesden-Popper nitrides with a general formula of A n–1 A' 2 B n X 3 n +1 , where A = Li/Fe, A' = Te, B = N, and X = Ca. Single crystal X-ray diffraction analyses indicate the crystal with a composition of Ca 7 (Li 0.32(1) Fe 0.68(1) )Te 2 N 2 and the tetragonal space group I 4/mmm (a = 4.7884(1) Å, c = 25.3723(4) Å, Z = 2). The structure features alternately stacking NaCl-type A'X slabs and the perovskite-type ABX 3 slabs along the c axis. The Li/Fe atoms are located in cuboctahedral cavities surrounded by eight Ca 6 N octahedra in the ABX 3 slab. As a result, this work demonstrates the viability of the Ca-rich flux as a suitable solvent for the exploration of new complex nitrides with interesting crystal structure and properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Submodels of model of nonlinear diffusion in the inhomogeneous medium involving absorption

We study the five-parameter model, describing the process of nonlinear diffusion in an inhomogeneous medium in the presence of absorption, for which the differential equation of the model admits a continuous Lie group of transformations, acting on the set of its solutions. We found six submodels of the original model of nonlinear diffusion, with different symmetry properties. Of these six submodels, the five submodels with transient absorption, for which the absorption coefficient depends on time according to a power law, represent the greatest interest with a mathematical point of view and with the point of view of physical applications. For each of these nonlinear submodels, we obtained formulas for producing new solutions that contain arbitrary constants, and we found all invariant submodels. All essentially distinct invariant solutions describing these invariant submodels are found in an explicit form or are reduced to finding the solution of nonlinear integral equations. The presence of the arbitrary constants in the integral equations that determine these solutions provide new opportunities for analytical and numerical study of boundary value problems for the received submodels and, thus, for the original model of nonlinear diffusion. For the received invariant submodels, we studied diffusion processes for which at the initial moment of the time at a fixed point is specified as a concentration and its gradient or as a concentration and its velocity. Solving of boundary value problems describing these processes is reduced to the solving of nonlinear integral equations. We established the existence and uniqueness of solutions of these boundary value problems under some additional conditions. The obtained results can be used to study the diffusion of substances, diffusion of conduction electrons and other particles, diffusion of physical fields and propagation of heat in inhomogeneous medium, and also to study a turbulence (Leith model, differential approximation to wave turbulence)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1999

The Conference Proceedings of the 1999 Air Transport Research Group (ATRG) of the WCTR Society

Issues around direct flights across Taiwan Strait are always one of the hottest topics in eastern Asia transport market. Although the direct links have not been connected yet, they are still highly concerned by different disciplines of politics, laws, and management. Airlines and related business also watch closely to these issues for policy changes will easily affect their interests in Chinese market which the future of the air transportation in eastern Asia is heavily depending on. In the past decades, Hong Kong was the most important hub in this market; it will still be an important one in the future. It is proved, however, traffic on the link between Hong Kong and Taiwan can be shifted to the link between Macau and Taiwan, so can it be shifted to the links across Taiwan Strait. Moreover, outgoing passengers from China transferred in Hong Kong can also find transit services in Taiwan. These movements will possibly cause a big change in eastern Asian air transport system for there are millions of passengers travelling in this area. The uncertainties of direct links across Taiwan Strait are still leaving, some problems unsolved. Whether the direct links will be defined as international routes or domestic' routes are not clear; the selection of hubs and airlines to provide direct services are not yet made; even the type of freedoms and bilateral agreements can also change the market and network quite a lot. A much bigger volume of passengers can also be found if further travelling deregulation for Chinese to travel across Taiwan Strait can be made. All these variables are making issues around direct flights worthy of continuous observant.

Zhang, Anming↗