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All sources NASA NTRS DOE OSTI

DOE OSTI2016

The unexpected confluence of plasma physics and climate science: On the lives and legacies of Norman Rostoker and Sherry Rowland

The Norman Rostoker Memorial Symposium brought together approximately 150 attendees to share their recent work and to reflect on the contributions of Norman Rostoker to the field of plasma physics and the advancement of fusion as a source of renewable clean energy. The field has changed considerably in a few short decades, with theoretical advances and technological innovations evolving in lock step. Over those same decades, our understanding of human induced climate change has also evolved; measurable changes in Earth’s physical, chemical, and biological processes have already been observed, and these will likely intensify in the coming decades. Never before has the need for clean energy been more pronounced, or the need for transformative solutions more pressing. As scientists work with legislators, journalists, and the public to take actions to address the threat of climate change, there is much to be learned from the legacies of innovators like Norman Rostoker, who have tackled complex problems with scientific insight and determination even when the odds were stacked against them. I write this from the perspective on an Earth system scientist who studies photosynthesis and the biogeochemistry of the oceans, and my statements about plasma physics and Norman Rostoker are based on information I gathered from the colloquium and from many enjoyable conversations with his friends and colleagues.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Cinema:Snap: Real-time tools for analysis of dynamic diamond anvil cell experiment data

We report we developed tools and a workflow for real-time analysis of data from dynamic diamond anvil cell experiments performed at user light sources. These tools allow users to determine the phases of matter observed during the compression of materials in order to make decisions during an experiment to improve the quality of experimental results and maximize the use of scarce experimental facility time. The tools fill a gap in dynamic compression data analysis tools that are real-time, are flexible to the needs of high-pressure scientists, connect to automated processing of results, can be easily incorporated into workflows with existing tools and data formats, and support remote experimental data analysis workflows. Specific analytics developed include novel automated two-peak analysis for overlapping peaks and multiple phases, coordinated views of pressure and temperature values, full-compression contour plots, and configurable views of integrated x-ray diffraction. We present an experimental use case to show how the tools produce real-time analytics that help the scientists revise parameters for the next compression

47 OTHER INSTRUMENTATION↗

DOE OSTI2015

Choosing experiments to accelerate collective discovery

Scientists perform a tiny subset of all possible experiments. What characterizes the experiments they choose? What are the consequences of those choices for the pace of scientific discovery? We model scientific knowledge as a network and science as a sequence of experiments designed to gradually uncover it. By analyzing millions of biomedical articles published over 30 y, we find that biomedical scientists pursue conservative research strategies exploring the local neighborhood of central, important molecules. Although such strategies probably serve scientific careers, we show that they slow scientific advance, especially in mature fields, where more risk and less redundant experimentation would accelerate discovery of the network. Lastly, we also consider institutional arrangements that could help science pursue these more efficient strategies.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2011

Advancing Science through Mining Libraries, Ontologies, and Communities

Life scientists today cannot hope to read everything relevant to their research. Emerging text-mining tools can help by identifying topics and distilling statements from books and articles with increased accuracy. Researchers often organize these statements into ontologies, consistent systems of reality claims. Like scientific thinking and interchange, however, text-mined information (even when accurately captured) is complex, redundant, sometimes incoherent, and often contradictory: it is rooted in a mixture of only partially consistent ontologies. We review work that models scientific reason and suggest how computational reasoning across ontologies and the broader distribution of textual statements can assess the certainty of statements and the process by which statements become certain. With the emergence of digitized data regarding networks of scientific authorship, institutions, and resources, we explore the possibility of accounting for social dependences and cultural biases in reasoning models. Computational reasoning is starting to fill out ontologies and flag internal inconsistencies in several areas of bioscience. In the not too distant future, scientists may be able to use statements and rich models of the processes that produced them to identify underexplored areas, resurrect forgotten findings and ideas, deconvolute the spaghetti of underlying ontologies, and synthesize novel knowledge and hypotheses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Automated Resonance Fitting for Nuclear Data Evaluation

Global and national efforts to deliver high-quality nuclear data to users have a wide-ranging impact, affecting applications in national security, reactor operations, basic science, medicine, and more. Cross section evaluation is a major part of this effort, combining theory and experimentation to produce recommended values and uncertainties for reaction probabilities. Resonance region evaluation is a specialized type of nuclear data evaluation that can require significant manual effort and months of time from expert scientists. In this article, non-convex non-linear optimization methods are combined with concepts of inferential statistics to infer a resonance model from experimental data in an automated manner that is not dependent on prior evaluation(s). This methodology aims to enhance the workflow of a resonance evaluator by minimizing time, effort, and the potential for bias from prior assumptions, while enhancing reproducibility and documentation, thereby addressing well-known challenges in the field.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2014

Open-access databases as unprecedented resources and drivers of cultural change in fisheries science

Open-access databases with utility in fisheries science have grown exponentially in quantity and scope over the past decade, with profound impacts to our discipline. The management, distillation, and sharing of an exponentially growing stream of open-access data represents several fundamental challenges in fisheries science. Many of the currently available open-access resources may not be universally known among fisheries scientists. We therefore introduce many national- and global-scale open-access databases with applications in fisheries science and provide an example of how they can be harnessed to perform valuable analyses without additional field efforts. We also discuss how the development, maintenance, and utilization of open-access data are likely to pose technical, financial, and educational challenges to fisheries scientists. Such cultural implications that will coincide with the rapidly increasing availability of free data should compel the American Fisheries Society to actively address these problems now to help ease the forthcoming cultural transition.

data↗

DOE OSTI2017

Modeling organic electronic materials: bridging length and time scales

Organic electronics is a popular and rapidly growing field of research. The optical, electrical and mechanical properties of organic molecules and materials can be tailored using increasingly well controlled synthetic methods. The challenge and fascination with this field of research is derived from the fact that not only the chemical identity, but also the spatial arrangement of the molecules critically affects the performance of the material. Thus synthetic, fabrication, characterisation and computational scientists need to work closely to relate a materials performance in a device to the molecular details that cause and optimise that performance. For computational scientists in particular, the need to relate macroscopic device performance to details of molecular electronic structure brings challenges in methodology due to the need to bridge many orders of time and length scales. Furthermore, this article provides a survey of computational methods applied to multiple-length and time scale problems in organic electronic materials. Here we seek to highlight a few particular approaches that expand the simulation toolbox.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Second user workshop on high-power lasers at the Linac Coherent Light Source

The second international workshop on the physics enabled by the unique combination of high-power lasers with the world-class Linac Coherent Light Source (LCLS) free-electron X-ray laser beam was held in Stanford, CA, on October 7–8, 2014. The workshop was co-organized by UC Berkeley, Lawrence Berkeley, Lawrence Livermore, and SLAC National Accelerator Laboratories. More than 120 scientists, including 40 students and postdoctoral scientists who are working in high-intensity laser-matter interactions, fusion research, and dynamic high-pressure science came together from North America, Europe, and Asia. The focus of the second workshop was on scientific highlights and the lessons learned from 16 new experiments that were performed on the Matter in Extreme Conditions (MEC) instrument since the first workshop was held one year ago.

43 PARTICLE ACCELERATORS↗

DOE OSTI2017

CompNanoTox2015: novel perspectives from a European conference on computational nanotoxicology on predictive nanotoxicology

A first European Conference on Computational Nanotoxicology, CompNanoTox, was held in November 2015 in Benahavís, Spain with the objectives to disseminate and integrate results from the European modeling and database projects (NanoPUZZLES, ModENPTox, PreNanoTox, MembraneNanoPart, MODERN, eNanoMapper and EU COST TD1204 MODENA) as well as to create synergies within the European NanoSafety Cluster. This conference was supported by the COST Action TD1204 MODENA on developing computational methods for toxicological risk assessment of engineered nanoparticles and provided a unique opportunity for crossfertilization among complementary disciplines. The efforts to develop and validate computational models crucially depend on high quality experimental data and relevant assays which will be the basis to identify relevant descriptors. The ambitious overarching goal of this conference was to promote predictive nanotoxicology, which can only be achieved by a close collaboration between the computational scientists (e.g. database experts, modeling experts for structure, (eco) toxicological effects, performance and interaction of nanomaterials) and experimentalists from different areas (in particular toxicologists, biologists, chemists and material scientists, among others). The main outcome and new perspectives of this conference are summarized here.

nanoqsar↗

DOE OSTI2018

TomoBank: a tomographic data repository for computational x-ray science

There is a widening gap between the fast advancement of computational methods for tomographic reconstruction and their successful implementation in production software at various synchrotron facilities. This is due in part to the lack of readily available instrument datasets and phantoms representative of real materials for validation and comparison of new numerical methods. Recent advancements in detector technology made sub-second and multi-energy tomographic data collection possible [1], but also increased the demand to develop new reconstruction methods able to handle in-situ [2] and dynamic systems [3] that can be quickly incorporated in beamline production software [4]. The X-ray Tomography Data Bank, tomoBank, provides a repository of experimental and simulated datasets with the aim to foster collaboration among computational scientists, beamline scientists, and experimentalists and to accelerate the development and implementation of tomographic reconstruction methods for synchrotron facility production software by providing easy access to challenging dataset and their descriptors.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2022

Cryo-FIB for TEM Investigation of Soft Matter and Beam Sensitive Energy Materials

Primarily driven by structural biology, the rapid advances in cryogenic electron microscopy techniques are now being adopted and applied by materials scientists. Samples that inherently have electron transparency can be rapidly frozen (vitrified) in amorphous ice and imaged directly on a cryogenic transmission electron microscopy (cryo-TEM), however this is not the case for many important materials systems, which can consist of layered structures, embedded architectures, or be contained within a device. Cryogenic focused ion beam (cryo-FIB) lift-out procedures have recently been developed to extract intact regions and interfaces of interest, that can then be thinned to electron transparency and transferred to the cryo-TEM for characterization. Several detailed studies have been reported demonstrating the cryo-FIB lift-out procedure, however due to its relative infancy in materials science improvements are still required to ensure the technique becomes more accessible and routinely successful. Here, we review recent results on the preparation of cryo-TEM lamellae using cryo-FIB and show that the technique is broadly applicable to a range of soft matter and beam sensitive energy materials. We then present a tutorial that can guide the materials scientist through the cryo-FIB lift-out process, highlighting recent methodological advances that address the most common failure points of the technique, such as needle attachment, lift-out and transfer, and final thinning.

36 MATERIALS SCIENCE↗

DOE OSTI2021

2020 roadmap on plasma accelerators

Abstract Plasma-based accelerators use the strong electromagnetic fields that can be supported by plasmas to accelerate charged particles to high energies. Accelerating field structures in plasma can be generated by powerful laser pulses or charged particle beams. This research field has recently transitioned from involving a few small-scale efforts to the development of national and international networks of scientists supported by substantial investment in large-scale research infrastructure. In this New Journal of Physics 2020 Plasma Accelerator Roadmap, perspectives from experts in this field provide a summary overview of the field and insights into the research needs and developments for an international audience of scientists, including graduate students and researchers entering the field.

43 PARTICLE ACCELERATORS↗

DOE OSTI2010

Neutron Science TeraGrid Gateway

The unique contributions of the Neutron Science TeraGrid Gateway (NSTG) are the connection of national user facility instrument data sources to the integrated cyberinfrastructure of the National Science FoundationTeraGrid and the development of a neutron science gateway that allows neutron scientists to use TeraGrid resources to analyze their data, including comparison of experiment with simulation. The NSTG is working in close collaboration with the Spallation Neutron Source (SNS) at Oak Ridge as their principal facility partner. The SNS is a next-generation neutron source. It has completed construction at a cost of $1.4 billion and is ramping up operations. The SNS will provide an order of magnitude greater flux than any previous facility in the world and will be available to all of the nation's scientists, independent of funding source, on a peer-reviewed merit basis. With this new capability, the neutron science community is facing orders of magnitude larger data sets and is at a critical point for data analysis and simulation. There is a recognized need for new ways to manage and analyze data to optimize both beam time and scientific output. The TeraGrid is providing new capabilities in the gateway for simulations using McStas and a fitting service on distributed TeraGrid resources to improved turnaround. NSTG staff are also exploring replicating experimental data in archival storage. As part of the SNS partnership, the NSTG provides access to gateway support, cyberinfrastructure outreach, community development, and user support for the neutron science community. This community includes not only SNS staff and users but extends to all the major worldwide neutron scattering centers.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2012

UNEDF: Advanced Scientific Computing Collaboration Transforms the Low-Energy Nuclear Many-Body Problem

The demands of cutting-edge science are driving the need for larger and faster computing resources. With the rapidly growing scale of computing systems and the prospect of technologically disruptive architectures to meet these needs, scientists face the challenge of effectively using complex computational resources to advance scientific discovery. Multi-disciplinary collaborating networks of researchers with diverse scientific backgrounds are needed to address these complex challenges. The UNEDF SciDAC collaboration of nuclear theorists, applied mathematicians, and computer scientists is developing a comprehensive description of nuclei and their reactions that delivers maximum predictive power with quantified uncertainties. This paper describes UNEDF and identifies attributes that classify it as a successful computational collaboration. Finally, we illustrate significant milestones accomplished by UNEDF through integrative solutions using the most reliable theoretical approaches, most advanced algorithms, and leadership-class computational resources.

Nam, H.↗

DOE OSTI2016

Thinking in three dimensions: discovering reciprocal signaling between the extracellular matrix and nucleus and the wisdom of microenvironment and tissue architecture

I thought long and hard whether I could avoid talking about family and personal life, and just share the excitement of being a scientist and how science continues to sustain us all. But so many people, especially younger scientists, want to know-and always ask-How did you do it? A woman from Iran, a Middle Eastern country and essentially Muslim, now considered backwards and misguided if not downright scary, traveling very young and alone to the United States, finishing college and graduate school together with having children, first-year graduate school and second-year post doc-years ago, going against a number of entrenched dogmas, and yet succeeding against many odds and obstacles, and all the while on soft money? Below is my personal narrative answering some of these questions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Biophysics at the coffee shop: lessons learned working with George Oster

Over the past 50 years, the use of mathematical models, derived from physical reasoning, to describe molecular and cellular systems has evolved from an art of the few to a cornerstone of biological inquiry. George Oster stood out as a pioneer of this paradigm shift from descriptive to quantitative biology not only through his numerous research accomplishments, but also through the many students and postdocs he mentored over his long career. Those of us fortunate enough to have worked with George agree that his sharp intellect, physical intuition, and passion for scientific inquiry not only inspired us as scientists but also greatly influenced the way we conduct research. We would like to share a few important lessons we learned from George in honor of his memory and with the hope that they may inspire future generations of scientists.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Skills and Knowledge for Data-Intensive Environmental Research

The scale and magnitude of complex and pressing environmental issues lend urgency to the need for integrative and reproducible analysis and synthesis, facilitated by data-intensive research approaches. However, the recent pace of technological change has been such that appropriate skills to accomplish data-intensive research are lacking among environmental scientists, who more than ever need greater access to training and mentorship in computational skills. Here, we provide a roadmap for raising data competencies of current and next-generation environmental researchers by describing the concepts and skills needed for effectively engaging with the heterogeneous, distributed, and rapidly growing volumes of available data. We articulate five key skills: (1) data management and processing, (2) analysis, (3) software skills for science, (4) visualization, and (5) communication methods for collaboration and dissemination. We provide an overview of the current suite of training initiatives available to environmental scientists and models for closing the skill-transfer gap.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Spotlight on… Janet K. Jansson

Janet Jansson is Chief Scientist for Biology in the Earth and Biological Sciences Directorate at the Pacific Northwest National Laboratory (PNNL) and President of the International Society for Microbiology (ISME). She obtained her Ph.D. in 1988 at Michigan State University and then established a successful research career in Sweden. From 2000-2006, she was Professor of Environmental Microbiology at the Swedish University of Agricultural Sciences and Vice Dean of the Natural Sciences Faculty. From 2007-2013, she was a senior staff scientist at Lawrence Berkeley National Laboratory, and from 2012-2014 an Adjunct Professor at UC Berkeley and the University of Copenhagen.

59 BASIC BIOLOGICAL SCIENCES↗