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At least 811 records · Page 45

A Science Data Gateway for Environmental Management

Science data gateways are effective in providing complex science data collections to the world-wide user Q1 communities. In this paper we describe a gateway for the Advanced Simulation Capability for Environmental Management (ASCEM) framework. Built on top of established web service technologies, the ASCEM data gateway is specifically designed for environmental modeling applications. Its key distinguishing feature sinclude (1) handling of complex spatiotemporal data, (2) offering a variety of selective data access mechanisms, (3) providing state-of-the-art plotting and visualization of spatiotemporal data records, and (4) integrating seamlessly with a distributed workflow system using a RESTful interface. ASCEM projectscientists have been using this data gateway since 2011.

ASCEM, Akuna, Database Management↗

Bringing research findings to the real world is an essential and rewarding experience

The pending changes in the U.S. presidential administration and Congress threaten the ongoing progress being made in lowering U.S. greenhouse gas (GHG) emissions. Yet the need for reducing emissions and directly addressing the energy-climate crisis has never been greater. The energy-climate crisis is defined as the situation created by reliance on fossil fuels for 80% of global energy supply, the combustion of which releases CO 2 , the main greenhouse gas causing global warming. Instead of allowing the U.S. national political situation to be a distraction, scientists, engineers, and policy experts need to push even harder to turn research findings into practical applications so those findings can contribute to actually reducing emissions. In addition, scientists and engineers need to communicate research results to lawmakers and the public to reinforce the urgency of directly addressing the energy-climate crisis. Without giving away still-developing conclusions of the ongoing project, this paper describes that facilitating practical application of research results can be a very rewarding and satisfying experience.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver

Here, we present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators, and students that are more familiar with the APBS framework.

97 MATHEMATICS AND COMPUTING↗

RNA target highlights in CASP15 : Evaluation of predicted models by structure providers

Abstract The first RNA category of the Critical Assessment of Techniques for Structure Prediction competition was only made possible because of the scientists who provided experimental structures to challenge the predictors. In this article, these scientists offer a unique and valuable analysis of both the successes and areas for improvement in the predicted models. All 10 RNA‐only targets yielded predictions topologically similar to experimentally determined structures. For one target, experimentalists were able to phase their x‐ray diffraction data by molecular replacement, showing a potential application of structure predictions for RNA structural biologists. Recommended areas for improvement include: enhancing the accuracy in local interaction predictions and increased consideration of the experimental conditions such as multimerization, structure determination method, and time along folding pathways. The prediction of RNA–protein complexes remains the most significant challenge. Finally, given the intrinsic flexibility of many RNAs, we propose the consideration of ensemble models.

59 BASIC BIOLOGICAL SCIENCES↗

John Grant and the multifaceted nature of true professionalism: Personal perspective

Consideration of the elements that contribute to professional and scientific impact is relevant in a volume honoring John Grant for two reasons. First, John has contributed in many ways to both advancing the methodology and the practical application of surface-analytical tools to understanding surfaces and interfaces of technological importance. The second reason is a little more complex. In an era when there is an effort to quantify contributions in various ways (e.g., citations, H-index, number of publications) and when social media seems, at least anecdotally, to lead a younger generation of scientists to be less involved in traditional professional activities, it is appropriate to examine the nature of the activities that make a lasting contribution to the advancement of science and technology and the professional community that makes progress possible. The multifaceted nature of John’s professional activities provides an appropriate background for exploring the nature of professionalism. With no reservations one can say that the foundation of professionalism is rooted in a scientist’s expertise in some area of research or practice. This expertise might be measured in numerous ways depending upon the field and could include numbers of publications, citations, patents, problems solved, research support obtained, or students produced. These “products” may or may not be readily visible to the community at large. Chuck Wagner – a pioneer in XPS, developer of an empirical set of XPS sensitivity factors and the modified Auger-parameter plot, and winner of the AVS Nerken Award in 1989 – observed that he could not publish or talk about 90% of the work he had done when working for Shell Oil. However, based on XPS capability developments that he could publish, he had a major impact on the development and application of XPS. To some degree John Grant’s research fits this model as well. Much of his early work at the Air Force Materials Research Laboratory was directed at solving materials problems and this important and often ground-breaking work was not published. However, a great deal of creativity and development was required to enable surface-sensitive tools such as AES and XPS to become useful for solving critical problems, and this work could be published.

Baer, Donald R.↗

In Situ Analysis and Visualization of Fusion Simulations: Lessons Learned

The trends in high performance computing, where far more data can be computed that can ever be stored, have made in situ techniques an important area of research and development. Simulation campaigns, where domain scientists work with computer scientists to run a simulation and perform in situ analysis and visualization are important, and complex undertakings. In this paper we report our experiences performing in situ analysis and visualization on two campaigns. The two campaigns were related, but had important differences in terms of the codes that were used, the types of analysis and visualization required, and the visualization tools used. Further, we report the lessons learned from each campaign.

Kim, Mark B.↗

Knowledge Annotations in Scientific Workflows: An Implementation in Kepler

Abstract. Scientic research products are the result of long-term collaborations between teams. Scientic workfows are capable of helping scientists in many ways including the collection of information as to howresearch was conducted, e.g. scientic workfow tools often collect and manage information about datasets used and data transformations. However,knowledge about why data was collected is rarely documented in scientic workflows. In this paper we describe a prototype system built to support the collection of scientic expertise that infuences scientic analysis. Through evaluating a scientic research eort underway at Pacific Northwest National Laboratory, we identied features that would most benefit PNNL scientists in documenting how and why they conduct their research making this information available to the entire team. The prototype system was built by enhancing the Kepler Scientic Work-flow System to create knowledge-annotated scientic workfows and topublish them as semantic annotations.

99 GENERAL AND MISCELLANEOUS↗

Beyond relationships between homogeneous and heterogeneous catalysis

Scientists who regard catalysis as a coherent field have been striving for decades to articulate the fundamental unifying principles. But because these principles seem to be broader than chemistry, chemical engineering, and materials science combined, catalytic scientists commonly interact within the sub-domains of homogeneous, heterogeneous, and bio-catalysis, and increasingly within even narrower domains such as organocatalysis, phase-transfer catalysis, acid-base catalysis, zeolite catalysis, etc. Attempts to unify catalysis have motivated researchers to find relationships between homogeneous and heterogeneous catalysis and to mimic enzymes. These themes have inspired vibrant international meetings and workshops, and we have benefited from the idea exchanges and have some thoughts about a path forward.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coordinative Entities: Forms of Organizing in Data Intensive Science

Scientific collaboration is a long-standing subject of CSCW scholarship that typically focuses on the development and use of computing systems to facilitate research. The research presented in this article investigates the sociality of science by identifying and describing particular, common forms of organizing that researchers in four different scientific realms employ to conduct work in both local contexts and as part of distributed, global projects. This paper introduces five prototypical forms of organizing we categorize as coordinative entities: the Principal Group, Intermittent Exchange, Sustained Aggregation, Federation, and Facility Organization. Coordinative entities as a categorization help specify, articulate, compare, and trace overlapping and evolving arrangements scientists use to facilitate data intensive research. We use this typology to unpack complexities of data intensive scientific collaboration in four cases, showing how scientists invoke different coordinative entities across three types of research activities: data collection, processing, and analysis. Finally, our contribution scrutinizes the sociality of scientific work to illustrate how these actors engage in relational work within and among diverse, dispersed forms of organizing across project, funding, and disciplinary boundaries.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Advancing Fusion with Machine Learning Research Needs Workshop Report

Abstract Machine learning and artificial intelligence (ML/AI) methods have been used successfully in recent years to solve problems in many areas, including image recognition, unsupervised and supervised classification, game-playing, system identification and prediction, and autonomous vehicle control. Data-driven machine learning methods have also been applied to fusion energy research for over 2 decades, including significant advances in the areas of disruption prediction, surrogate model generation, and experimental planning. The advent of powerful and dedicated computers specialized for large-scale parallel computation, as well as advances in statistical inference algorithms, have greatly enhanced the capabilities of these computational approaches to extract scientific knowledge and bridge gaps between theoretical models and practical implementations. Large-scale commercial success of various ML/AI applications in recent years, including robotics, industrial processes, online image recognition, financial system prediction, and autonomous vehicles, have further demonstrated the potential for data-driven methods to produce dramatic transformations in many fields. These advances, along with the urgency of need to bridge key gaps in knowledge for design and operation of reactors such as ITER, have driven planned expansion of efforts in ML/AI within the US government and around the world. The Department of Energy (DOE) Office of Science programs in Fusion Energy Sciences (FES) and Advanced Scientific Computing Research (ASCR) have organized several activities to identify best strategies and approaches for applying ML/AI methods to fusion energy research. This paper describes the results of a joint FES/ASCR DOE-sponsored Research Needs Workshop on Advancing Fusion with Machine Learning, held April 30–May 2, 2019, in Gaithersburg, MD (full report available at https://science.osti.gov/-/media/fes/pdf/workshop-reports/FES_ASCR_Machine_Learning_Report.pdf ). The workshop drew on broad representation from both FES and ASCR scientific communities, and identified seven Priority Research Opportunities (PRO’s) with high potential for advancing fusion energy. In addition to the PRO topics themselves, the workshop identified research guidelines to maximize the effectiveness of ML/AI methods in fusion energy science, which include focusing on uncertainty quantification, methods for quantifying regions of validity of models and algorithms, and applying highly integrated teams of ML/AI mathematicians, computer scientists, and fusion energy scientists with domain expertise in the relevant areas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A Bayesian Machine Learning Model for Estimating Building Occupancy from Open Source Data

Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the art by introducing the Population Data Tables (PDT), a Bayesian based informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000ft2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the art by introducing the Population Data Tables (PDT), a Bayesian model and informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000 ft 2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Inverse regression for ridge recovery: a data-driven approach for parameter reduction in computer experiments

Parameter reduction can enable otherwise infeasible design and uncertainty studies with modern computational science models that contain several input parameters. In statistical regression, techniques for sufficient dimension reduction (SDR) use data to reduce the predictor dimension of a regression problem. A computational scientist hoping to use SDR for parameter reduction encounters a problem: a computer prediction is best represented by a deterministic function of the inputs, so data comprised of computer simulation queries fail to satisfy the SDR assumptions. To address this problem, here we interpret SDR methods sliced inverse regression (SIR) and sliced average variance estimation (SAVE) as estimating the directions of a ridge function, which is a composition of a low-dimensional linear transformation with a nonlinear function. Within this interpretation, SIR and SAVE estimate matrices of integrals whose column spaces are contained in the ridge directions’ span; we analyze and numerically verify convergence of these column spaces as the number of computer model queries increases. Moreover, we show example functions that are not ridge functions but whose inverse conditional moment matrices are low-rank. Consequently, the computational scientist should beware when using SIR and SAVE for parameter reduction, since SIR and SAVE may mistakenly suggest that truly important directions are unimportant.

97 MATHEMATICS AND COMPUTING↗

Cyber Risk Considerations for Nuclear Digital I&C Systems

Many engineers and scientists researching modeling and analysis methods for nuclear energy advancement are focused on proof-of-concept and early-stage development for new reactor designs. Since instrumentation and control (I&C) systems are traditionally developed later in the systems engineering lifecycle, researchers may be unfamiliar with modern digital technology used in these I&C systems. It is even more likely that they are unfamiliar with the cyber risks associated with them. This paper provides a brief overview of nuclear digital I&C systems before examining the importance of cyber risk management at nuclear reactors and the benefits of including Cyber-Informed Engineering throughout the systems engineering lifecycle. The primary goal is for engineers and scientists to develop a mindset that incorporates cybersecurity as another discipline alongside safety when designing and developing new technologies, regardless of technology readiness level.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Integrating continuous atmospheric boundary layer and tower-based flux measurements to advance understanding of land-atmosphere interactions

The atmospheric boundary layer mediates the exchange of energy, matter, and momentum between the land surface and the free troposphere, integrating a range of physical, chemical, and biological processes and is defined as the lowest layer of the atmosphere (ranging from a few meters to 3 km). In this review, we investigate how continuous, automated observations of the atmospheric boundary layer can enhance the scientific value of co-located eddy covariance measurements of land-atmosphere fluxes of carbon, water, and energy, as are being made at FLUXNET sites worldwide. We highlight four key opportunities to integrate tower-based flux measurements with continuous, long-term atmospheric boundary layer measurements: (1) to interpret surface flux and atmospheric boundary layer exchange dynamics and feedbacks at flux tower sites, (2) to support flux footprint modelling, the interpretation of surface fluxes in heterogeneous terrain, and quality control of eddy covariance flux measurements, (3) to support regional-scale modeling and upscaling of surface fluxes to continental scales, and (4) to quantify land-atmosphere coupling and validate its representation in Earth system models. Adding a suite of atmospheric boundary layer measurements to eddy covariance flux tower sites, and supporting the sharing of these data to tower networks, would allow the Earth science community to address new emerging research questions, better interpret ongoing flux tower measurements, and would present novel opportunities for collaborations between FLUXNET scientists and atmospheric and remote sensing scientists.

54 ENVIRONMENTAL SCIENCES↗

Brief history of agricultural systems modeling

Agricultural systems science generates knowledge that allows researchers to consider complex problems or take informed agricultural decisions. The rich history of this science exemplifies the diversity of systems and scales over which they operate and have been studied. Modeling, an essential tool in agricultural systems science, has been accomplished by scientists from a wide range of disciplines, who have contributed concepts and tools over more than six decades. As agricultural scientists now consider the "next generation" models, data, and knowledge products needed to meet the increasingly complex systems problems faced by society, it is important to take stock of this history and its lessons to ensure that we avoid re-invention and strive to consider all dimensions of associated challenges. To this end, we summarize here the history of agricultural systems modeling and identify lessons learned that can help guide the design and development of next generation of agricultural system tools and methods. A number of past events combined with overall technological progress in other fields have strongly contributed to the evolution of agricultural system modeling, including development of process-based bio-physical models of crops and livestock, statistical models based on historical observations, and economic optimization and simulation models at household and regional to global scales. Characteristics of agricultural systems models have varied widely depending on the systems involved, their scales, and the wide range of purposes that motivated their development and use by researchers in different disciplines. Recent trends in broader collaboration across institutions, across disciplines, and between the public and private sectors suggest that the stage is set for the major advances in agricultural systems science that are needed for the next generation of models, databases, knowledge products and decision support systems. Furthermore, the lessons from history should be considered to help avoid roadblocks and pitfalls as the community develops this next generation of agricultural systems models.

60 APPLIED LIFE SCIENCES↗

Process-informed adsorbent design guidelines for direct air capture

Direct air capture using solid adsorbents is a proven technology critical to reducing our net greenhouse gas emissions to zero and beyond. Currently, academic research into the technology mainly focuses on the development of new adsorbents. However, there is a discord between the adsorbent design and process performance. Many materials scientists focus on maximising metrics such as the CO 2 capacity of their adsorbent. Here, we combine detailed process modelling, machine learning, and extensive global sensitivity analysis, which entails varying all of the model parameters together, on a direct air capture process to show that the dry CO 2 adsorption capacity does not influence process performance for an amine-functionalised adsorbent operating in a temperature vacuum swing adsorption (TVSA) process, while it is important in a steam-assisted TVSA (S-TVSA) process. In fact, adsorption kinetics, density, and thermal conductivity are all critical attributes to obtaining a low energy penalty and reduced costs. The analysis also highlights the importance of heat transfer, directing process engineers to (alternative) adsorber designs that maximise this. By an in-depth evaluation of how process performance indicators are affected by materials properties and process operating parameters, this work provides guidance to both material scientists and process engineers towards the design of a “unicorn adsorbent” and intensified DAC processes. This will improve the performance of solid adsorbent direct air capture and help drive down the costs of this vital technology to avert the worst impacts of climate change.

42 ENGINEERING↗

The challenges and opportunities in cumulative effects assessment

The cumulative effects of increasing human use of the ocean and coastal zone have contributed to a rapid decline in ocean and coastal resources. As a result, scientists are investigating how multiple, overlapping stressors accumulate in the environment and impact ecosystems. These investigations are the foundation for the development of new tools that account for and predict cumulative effects in order to more adequately prevent or mitigate negative effects. Despite scientific advances, legal requirements, and management guidance, those who conduct assessments—including resource managers, agency staff, and consultants—continue to struggle to thoroughly evaluate cumulative effects, particularly as part of the environmental assessment process. Even though 45 years have passed since the United States National Environmental Policy Act was enacted, which set a precedent for environmental assessment around the world, defining impacts, baseline, scale, and significance are still major challenges associated with assessing cumulative effects. In addition, we know little about how practitioners tackle these challenges or how assessment aligns with current scientific recommendations. To shed more light on these challenges and gaps, we undertook a comparative study on how cumulative effects assessment (CEA) is conducted by practitioners operating under some of the most well-developed environmental laws around the globe: California, USA; British Columbia, Canada; Queensland, Australia; and New Zealand. We found that practitioners used a broad and varied definition of impact for CEA, which led to differences in how baseline, scale, and significance were determined. We also found that practice and science are not closely aligned and, as such, we highlight opportunities for managers, policy makers, practitioners, and scientists to improve environmental assessment.

54 ENVIRONMENTAL SCIENCES↗

Lessons to be learned from a contentious challenge to mainstream radiobiological science (the linear no-threshold theory of genetic mutations)

There are both statistically valid and invalid reasons why scientists with differing default hypotheses can disagree in high-profile situations. Examples can be found in recent correspondence in this journal, which may offer lessons for resolving challenges to mainstream science, particularly when adherents of a minority view attempt to elevate the status of outlier studies and/or claim that self-interest explains the acceptance of the dominant theory. Edward J. Calabrese and I have been debating the historical origins of the linear no-threshold theory (LNT) of carcinogenesis and its use in the regulation of ionizing radiation. Professor Calabrese, a supporter of hormesis, has charged a committee of scientists with misconduct in their preparation of a 1956 report on the genetic effects of atomic radiation. Specifically he argues that the report mischaracterized the LNT research record and suppressed calculations of some committee members. After reviewing the available scientific literature, I found that the contemporaneous evidence overwhelmingly favored a (genetics) LNT and that no calculations were suppressed. Calabrese's claims about the scientific record do not hold up primarily because of lack of attention to statistical analysis. Ironically, outlier studies were more likely to favor supra-linearity, not sub-linearity. Finally, the claim of investigator bias, which underlies Calabrese's accusations about key studies, is based on misreading of text. Attention to ethics charges, early on, may help seed a counter narrative explaining the community's adoption of a default hypothesis and may help focus attention on valid evidence and any real weaknesses in the dominant paradigm. - Highlights: • Edward J Calabrese has made a contentious challenge to mainstream radiobiological science. • Such challenges should not be neglected, lest they enter the political arena without review. • Key genetic studies from the 1940s, challenged by Calabrese, were found consistent and unbiased. • A 1956 genetics report did not hide estimates and does not need investigation for misconduct. • The scientific record was strong for a no-threshold, linear genetic response to radiation.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗