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All sourcesNASA NTRSDOE OSTI
NASA NTRS2006

Implementing Access to Data Distributed on Many Processors

A reference architecture is defined for an object-oriented implementation of domains, arrays, and distributions written in the programming language Chapel. This technology primarily addresses domains that contain arrays that have regular index sets with the low-level implementation details being beyond the scope of this discussion. What is defined is a complete set of object-oriented operators that allows one to perform data distributions for domain arrays involving regular arithmetic index sets. What is unique is that these operators allow for the arbitrary regions of the arrays to be fragmented and distributed across multiple processors with a single point of access giving the programmer the illusion that all the elements are collocated on a single processor. Today's massively parallel High Productivity Computing Systems (HPCS) are characterized by a modular structure, with a large number of processing and memory units connected by a high-speed network. Locality of access as well as load balancing are primary concerns in these systems that are typically used for high-performance scientific computation. Data distributions address these issues by providing a range of methods for spreading large data sets across the components of a system. Over the past two decades, many languages, systems, tools, and libraries have been developed for the support of distributions. Since the performance of data parallel applications is directly influenced by the distribution strategy, users often resort to low-level programming models that allow fine-tuning of the distribution aspects affecting performance, but, at the same time, are tedious and error-prone. This technology presents a reusable design of a data-distribution framework for data parallel high-performance applications. Distributions are a means to express locality in systems composed of large numbers of processor and memory components connected by a network. Since distributions have a great effect on the performance of applications, it is important that the distribution strategy is flexible, so its behavior can change depending on the needs of the application. At the same time, high productivity concerns require that the user be shielded from error-prone, tedious details such as communication and synchronization.

James, Mark↗
NASA NTRS2012

A Comprehensive Structural Dynamic Analysis Approach for Multi Mission Earth Entry Vehicle (MMEEV) Development

The anticipated NASA Mars Sample Return Mission (MSR) requires a simple and reliable method in which to return collected Martian samples back to earth for scientific analysis. The Multi-Mission Earth Entry Vehicle (MMEEV) is NASA's proposed solution to this MSR requirement. Key aspects of the MMEEV are its reliable and passive operation, energy absorbing foam-composite structure, and modular impact sphere (IS) design. To aid in the development of an EEV design that can be modified for various missions requirements, two fully parametric finite element models were developed. The first model was developed in an explicit finite element code and was designed to evaluate the impact response of the vehicle and payload during the final stage of the vehicle's return to earth. The second model was developed in an explicit code and was designed to evaluate the static and dynamic structural response of the vehicle during launch and reentry. In contrast to most other FE models, built through a Graphical User Interface (GUI) pre-processor, the current model was developed using a coding technique that allows the analyst to quickly change nearly all aspects of the model including: geometric dimensions, material properties, load and boundary conditions, mesh properties, and analysis controls. Using the developed design tool, a full range of proposed designs can quickly be analyzed numerically and thus the design trade space for the EEV can be fully understood. An engineer can then quickly reach the best design for a specific mission and also adapt and optimize the general design for different missions.

Perino, Scott↗
NASA NTRS2013

The Geospace Dynamics Observatory; A Paradigm Changing Geospace Mission

The Geospace Dynamics Observatory (GDO) mission observes the near-Earth region in space called Geospace with unprecedented resolution, scale and sensitivity. At a distance of 60 Earth Radii (Re) in a near-polar circular orbit and a approx. 27-day period, GDO images the earth's full disk with (1) a three-channel far ultraviolet imager, (2) an extreme ultraviolet imager of the plasmasphere, and (3) a spectrometer in the near to far ultraviolet range that probes any portion of the disk and simultaneously observes the limb. The exceptional capabilities of the GDO mission include (1) unprecedented improvement in signal to noise for globalscale imaging of Earth's space environment that enable changes in the Earth's space environment to be resolved with orders of magnitude higher in temporal and spatial resolution compared to existing data and other approaches, and (2) unrivaled capability for resolving the temporal evolution, over many days, in local time or latitude with a continuous view of Earth's global-scale evolution while simultaneously capturing the changes at scales smaller than are possible with other methods. This combination of new capabilities is a proven path to major scientific advances and discoveries. The GDO mission (1) has the first full disk imagery of the density and composition variability that exist during disturbed "storm" periods and the circulation systems of the upper atmosphere, (2) is able to image the ionosphere on a global and long time scale basis, (3) is able to probe the mechanisms that control the evolution of planetary atmospheres, and (4) is able to test our understanding of how the Earth is connected to the Sun. This paper explores the optical and technical aspects of the GDO mission and the implementation strategy. Additionally, the case will be made that GDO addresses a significant portion of the priority mission science articulated in the recent Solar and Space Physics Decadal Survey.

Spann, James↗
DOE OSTI2012

MueLu Multigrid Preconditioning Package

MueLu is intended for the research and development of multigrid algorithms used in the solution of sparse linear systems arising from systems of partial differential equations. The software provides multigrid source code, test programs, and short example programs to demonstrate the various interfaces for creating, accessing, and applying the solvers. MueLu currently provides an implementation of smoothed aggregation algebraic multigrid method and interfaces to many commonly used smoothers. However, the software is intended to be extensible, and new methods can be incorporated easily. MueLu also allows for advanced usage, such as combining multiple methods and segregated solves. The library supports point and block access to matrix data. All algorithms and methods in MueLu have been or will be published in the open scientific literature.

Source record↗
DOE OSTI2017

Peer Review Lessons Learned - DOE and Regulator Perspectives - 17140

The DOE NNSA Nevada Field Office (NFO) Underground Test Area (UGTA) Activity requires an external peer review to complete an extensive stage of site characterization and groundwater flow and contaminant transport model(s) development. The external peer review evaluates whether assumptions, methods, and conclusions derived from model(s) outputs are based on sound scientific principles and examines the scientific appropriateness of the model(s) outputs for informing the regulatory decision. The regulatory decision which is made by the Nevada Division of Environmental Protection (NDEP) is whether the model is acceptable to advance to the next UGTA strategy stage. Depending on the specific corrective action unit, the next stage is a Corrective Action Decision Document/Corrective Action Plan or Closure Stage. Three external peer reviews have taken place to date for the UGTA Activity. The first one resulted in a second phase of characterization and model development. The second external peer review resulted in advancement to the next UGTA strategy stage. While advancement to the next strategy stage was recommended by the third external peer review, a series of supplemental data collection and analyses and model simulation activities to address external peer review comments, including drilling three new wells and sampling multiple wells, occurred before moving into the next UGTA strategy stage. Twelve participants representing different aspects of the peer reviews (NDEP, NNSA/NFO, science advisors, presenters, and external peer reviewers) were interviewed to generate a combined lessons learned. Questions were asked regarding their experience with the process including panel selection, focused questions, presentations, interactions between UGTA Activity participants and reviewers, and results. The interview results were combined with the outcome of a published lessons learned report developed following the first external peer review. In general, those interviewed believed that all three external peer reviews were satisfactory and met the goals of the FFACO process. The following seven lessons learned were identified: (1) Ensure the panel is not biased and has a balance of technical and regulatory background; (2) Clearly state the review objective(s) at the start of the review; (3) Ask focused questions that support the peer review objective(s) but that do not ask the specific regulatory question; (4) Establish a peer review panel earlier in the strategy process; (5) Establish one point of contact for the entire review and conduct periodic meetings with the peer review panel to ensure focus remains on the review objective(s) and to ensure that pertinent information is provided; (6) Ensure that presentations are well coordinated, anomalous data or analysis results are addressed, and are focused on supporting the peer review objective(s); and (7) Carefully consider the panel's recommendations prior to embarking on a particular path forward. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS2023

Neural-Based Compression Scheme for Solar Image Data

Studying the solar system and especially the Sun relies on the data gathered daily from space missions. These missions are data-intensive and compressing this data to make them efficiently transferable to the ground station is a twofold decision to make. Stronger compression methods, by distorting the data, can increase data throughput at the cost of accuracy which could affect scientific analysis of the data. On the other hand, preserving subtle details in the compressed data requires a high amount of data to be transferred, reducing the desired gains from compression. In this work, we propose a neural network-based lossy compression method to be used in NASA’s data-intensive imagery missions. We chose NASA’s Solar Dynamics Observatory (SDO) mission which transmits 1.4 terabytes of data each day as a proof of concept for the proposed algorithm. In this work, we propose an adversarially trained neural network, equipped with local and non-local attention modules to capture both the local and global structure of the image resulting in a better trade-off in rate-distortion (RD) compared to conventional hand-engineered codecs. The RD variational autoencoder used in this work is jointly trained with a channel-dependent entropy model as a shared prior between the analysis and synthesis transforms to make the entropy coding of the latent code more effective. We also studied how optimizing perceptual losses could help our neural compressor to preserve high-frequency details of the data in the reconstructed compressed image. Our neural image compression algorithm outperforms currently-in-use and state-of-the-art codecs such as JPEG and JPEG-2000 in terms of the RD performance when compressing extreme-ultraviolet (EUV) data. As a proof of concept for use of this algorithm in SDO data analysis, we have performed coronal hole (CH) detection using our compressed images, and generated consistent segmentations, even at a compression rate of ∼ 0.1 bits per pixel (compared to 8 bits per pixel on the original data) using EUV data from SDO.

Image coding↗
NASA NTRS1992

Sonic boom acceptability studies

The determination of the magnitude of sonic boom exposure which would be acceptable to the general population requires, as a starting point, a method to assess and compare individual sonic booms. There is no consensus within the scientific and regulatory communities regarding an appropriate sonic boom assessment metric. Loudness, being a fundamental and well-understood attribute of human hearing was chosen as a means of comparing sonic booms of differing shapes and amplitudes. The figure illustrates the basic steps which yield a calculated value of loudness. Based upon the aircraft configuration and its operating conditions, the sonic boom pressure signature which reaches the ground is calculated. This pressure-time history is transformed to the frequency domain and converted into a one-third octave band spectrum. The essence of the loudness method is to account for the frequency response and integration characteristics of the auditory system. The result of the calculation procedure is a numerical description (perceived level, dB) which represents the loudness of the sonic boom waveform.

Shepherd, Kevin P.↗
NASA NTRS2018

NASA Guidelines for Promoting Scientific and Research Integrity

The National Aeronautics and Space Administration (NASA) seeks to explore and expand human knowledge of the Earth, solar system, and universe and to enable the development of aeronautical and space exploration systems. NASA's ability to achieve these purposes depends on the integrity of the research and technology activities the agency conducts and supports. The NASA workforce - as well as all external entities who review proposals for or receive NASA funding - must maintain the highest standards of scientific integrity. These responsibilities include selecting the most meritorious research activities through open and fair competition, peer review and other appropriate merit review processes, and avoidance of actual and perceived conflicts of interest; avoiding fabrication, falsification, or plagiarism in proposing, performing, or reviewing research, or in reporting research results; openly sharing results and methods not subject to classification or privacy standards; disclosing assumptions and biases in sharing and applying scientific information and data; and acting honestly and transparently in using and serving on advisory committees and in engaging in professional development activities.

Guidelines↗
DOE OSTI2020

Numerical methods for nonlocal and fractional models

Partial differential equations (PDEs) are used with huge success to model phenomena across all scientific and engineering disciplines. However, across an equally wide swath, there exist situations in which PDEs fail to adequately model observed phenomena, or are not the best available model for that purpose. On the other hand, in many situations, nonlocal models that account for interaction occurring at a distance have been shown to more faithfully and effectively model observed phenomena that involve possible singularities and other anomalies. Here, we consider a generic nonlocal model, beginning with a short review of its definition, the properties of its solution, its mathematical analysis and of specific concrete examples. We then provide extensive discussions about numerical methods, including finite element, finite difference and spectral methods, for determining approximate solutions of the nonlocal models considered. In that discussion, we pay particular attention to a special class of nonlocal models that are the most widely studied in the literature, namely those involving fractional derivatives. The article ends with brief considerations of several modelling and algorithmic extensions, which serve to show the wide applicability of nonlocal modelling.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

TH-D-16A-01: Medical Physics Workshop: Editorial Vision and Guidance On Writing and Reviewing Papers

On January 1, 2014, editorial leadership of Medical Physics passed from esteemed long-time Editor Bill Hendee to a collective editorial group composed of the three presenters listed above. In this presentation, we would like to outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. Vision for Medical Physics and current initiatives: Jeff Williamson, Editor-in-Chief We cannot improve on Dr. Hendee's succinct vision statement “to continue the Journal's tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be s the preeminent forum for electronic exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; or (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities we face are: are electronic-only and open access publishing; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. To address these issues over the next 3 years, we have reduced the size of our Editorial Board and focused its efforts on improving the Journal's impact through 4 working groups (WGs): WG-1: Review process quality and selectivity Creation of 120 member Board of Associate Editors to improve review uniformity by placing Ms. management in fewer hands New reviewer guidelines and templates Answer: “what is the scope of medical physics research?” Recursive taxonomy for tagging review expertise and article contents WG-2 Improving reader experience Redesigning http://MedPhys.org to host interactive features and gateway to electronic issue archive Experimentation with interactive features beginning with “Point/Counterpoint” Data mining and Journal quality evaluation Find out who are audiences are Identify characteristics of high impact articles Measure effectiveness of innovations Outreach to related communities Special issues presenting high-impact work in designated subcommunities Addressing the needs of new research constituencies: engineers, biophysicists, clinicians Guidelines and templates for reviewers and associate editors: Shiva Das, Therapy Physics Editor We will discuss the Med. Phys. review process and a new initiative to create review templates that attempts to address current shortcomings. Template design is informed by the literature on of the review process effectiveness and practices of other journals. Its goals are to provide authors more constructive criticism to improve the manuscript; quantifying perceived importance and potential impact; and providing structured sections that prompt the reviewer to addresses important technical and editorial elements. While the template is recommended to be used, reviewers could alternatively enter their comments in the older free-form style. The expectations of the template are that it will enable consistently thorough, high quality reviews that accurately separate acceptable vs. substandard submissions but continue our tradition of helping authors to enhance papers with high potential. Ultimately, the goal is to reduce variability and subjectivity in the peer-review process, in turn leading to articles with higher research and clinical impact. We will also discuss interesting perspectives from several journals on aspects of the peer-review process such as public input via comments, influence of author-suggested reviewers, and bias in reviewer selection. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics Ms. must include a clear and concise statement of the novelty and clinical and/or scientific importance of their work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; or first demonstration that an existing engineering solution solves a clinical problem. Authors must also include: sufficient background information and rationale; enough detail that the work can be reproduced by others; sufficient statistical analysis to refute or validate their hypothesis, how it compares to; is distinct from, and improves upon others' work; and the limitations of their study. When the authors receive critiques from the referees and associate editor, the authors should provide a detailed point-bypoint response to each comment. We now ask that the authors' rebuttal include the text of the original criticism, the authors' response, and the modified text along with the line numbers in the revised article. We also ask that the new text be highlighted in a different font color in the revised submission. These changes and others will be discussed. Their purpose is to facilitate the review process.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2016

TH-C-204-00: Medical Physics Workshop: An Update On the Journal’s Improvement Activities and Guidance On Writing and Reviewing Papers

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-C-204-01: Vision for Medical Physics and Status of Current Initiatives

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-C-204-02: Improving Manuscript Quality Via Structured Reviews, Enhanced Scientific Category Taxonomy, and Outreach

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-C-204-03: Writing Good Scientific Papers and Responding to Critiques

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Electronic structure simulations in the cloud computing environment

The transformative impact of modern computational paradigms and technologies, such as high-performance computing, quantum computing, and cloud computing, has opened up profound new opportunities for scientific simulations. Scalable computational chemistry is one beneficiary of this technological progress. The main focus of this paper is on the performance of various quantum chemical formulations, ranging from low-order methods to high-accuracy approaches, implemented in different computational chemistry packages, such as NWChem, NWChemEx, SPEC, ExaChem, and FLOSIC codes on the Azure Quantum Element (AQE) Microsoft cloud services. We pay particular attention to the intricate workflows for performing composite chemistry simulations, associated data curation, and mechanisms for accuracy assessment, as defined by the enabling cloud Computational Chemistry as a Service (CCaaS). Our focus also extends to Arrows' automated workflow for high throughput simulations. Finally, we provide a perspective on the role of cloud computing in supporting the mission of leadership computational facilities (LCFs).

computational chemistry, electronic structure, Clo↗
NASA NTRSDate not supplied

A Novel Machine Learning Method for Surface PM2.5 Estimations from Geostationary Satellites

Particulate matter (PM) with a diameter of less or equal to 2.5 μm, known as PM , affects human health as it penetrates the respiratory system. The Environmental Protection Agency (EPA) measures the atmospheric concentration of PM using air quality monitors stationed throughout the Continental United States (CONUS). Such measurements are points on a spatial domain and therefore, might not be representative of the air quality at nearby areas considering that the composition of the atmosphere is highly variable from place to place. Satellite based AOD permits a spatially uniform means of estimating PM and new geostationary satellites provide high temporal and spatial resolution estimation of AOD. However, the concentration of PM is non-linearly dependent on other atmospheric parameters that include relative humidity, temperature, and height of the planetary boundary layer. This information may be estimated at similar spatial and temporal resolutions as AOD from numerical modeling such as from the National Oceanic and Atmospheric Administration’s (NOAA) High Resolution Rapid Refresh (HRRR) model which resolves near real-time atmospheric conditions over the CONUS. The estimation of PM concentration is a multi-parametric problem that considers the effect of temporal dependencies among the different parameters. Deep learning approaches are appropriate for such complex estimation problems as they intrinsically capture relations among multiple non-linear parameters. This study compares deep-learning methods to traditional regression analysis to demonstrate the capabilities of these methods in predicting PM2.5 concentrations. Additionally, a novel ensemble learning approach is employed to identify scientific processes that could further improve the estimation of PM concentration. Utilizing Long Short-Term Memory (LSTM) neural networks, which are suitable for multivariate time series estimation problems as they are capable of learning long-term dependencies, individual models are created for each EPA station and trained on the aforementioned dataset collocated over each station. Individual station models are merged if the model's performance is improved by reducing the root mean squared error (RMSE) metric. This ensemble training method ultimately reduces the RMSE value. Evaluation of these results provide insights into physical processes and related observable parameters that may contribute to PM concentrations. Identified parameters evaluated to be statistically different between the merged and unmerged models are expected to improve overall performance. These new parameters are then utilized for reevaluation of the deep learning methods with an extreme gradient boosting model with an RMSE of 5.5 providing the best results.

George Priftis↗
DOE OSTI2023

Progressive Tree-Based Compression of Large-Scale Particle Data

Scientific simulations and observations using particles have been creating large datasets that require effective and efficient data reduction to store, transfer, and analyze. However, current approaches either compress only small data well while being inefficient for large data, or handle large data but with insufficient compression. Toward effective and scalable compression/decompression of particle positions, we introduce new kinds of particle hierarchies and corresponding traversal orders that quickly reduce reconstruction error while being fast and low in memory footprint. Our solution to compression of large-scale particle data is a flexible block-based hierarchy that supports progressive, random-access, and error-driven decoding, where error estimation heuristics can be supplied by the user. For low-level node encoding, we introduce new schemes that effectively compress both uniform and densely structured particle distributions. Our proposed methods thus target all three phases of a tree-based particle compression pipeline, namely tree construction, tree traversal, and node encoding. In conclusion, the improved efficacy and flexibility of these methods over existing compressors are demonstrated through extensive experimentation, using a wide range of scientific particle datasets.

97 MATHEMATICS AND COMPUTING↗