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At least 1,351 records · Page 75

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

IslandViewer is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer’s integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.

59 BASIC BIOLOGICAL SCIENCES↗

Elga v.1

SAND2021-4635 O Elga is a software system that provides distributed and elastic computation for temporal graph algorithms. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Gabert, Kasimir↗

Fast and robust strategies for large-scale mixed-integer SCOPF

This project develops scalable, computationally efficient algorithms to solve realistic large-scale power system optimization problems, including systems with more than 8,000 buses, as part of a larger series of competitions run by ARPA-E. These problems are critical because the secure and reliable operation of the power grid is becoming increasingly challenging, especially under conditions of increased uncertainty and variability. The economic feasibility of our methods is high, given that they are purely software-based solutions designed to operate power grids more efficiently. The technical effectiveness balances heuristics and approximations to provide a trade-off between speed and accuracy.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Physical Processes Governing Atmospheric Trace Constituents Measured from an Aircraft on PEM-Tropics

Before the mission, the PI (principal investigator) was instrumental in securing real-time use of the new 51-level ECMWF (European Centre for Medium Range Weather Forecasts) meteorological data. During the mission, he provided flight planning and execution guidance as meteorologist for the P-3B. Mr. Yong Zhu computed and plotted meteorological forecast maps using the ECMWF data and transmitted them to the field from MIT (Massachusetts Institute of Technology). Dr. John Cho was in the field for the Christmas Island portion to extract data from the on-site NOAA (National Oceanic and Atmospheric Administration) radars for local wind profiles that were used at the flight planning meetings. When the power supply for the VHF radar failed, he assisted the NOAA engineer in its repair. After the mission, Mr. Zhu produced meteorological data memos, which were made available to the PEM (Pacific Exploratory Mission)-Tropics B science team on request. An undergraduate student, Ms. Danielle Morse, wrote memos annotating the cloud conditions seen on the aircraft external monitor video tapes. Dr. Cho and the PI circulated a memo regarding the status (and associated problems) of the meteorological measurement systems on the DC-8 and P-3B to the relevant people on the science team. Several papers by members of our project were completed and accepted by JGR (Journal of Geophysical Research) for the first special section on PEM-Tropics B. These papers included coverage of the following topics: 1) examination of boundary layer data; 2) water vapor transport; 3) tropospheric trace constituent layers; 4) summarizations of the meteorological background and events during PEM-Tropics B; 5) concomitant lidar measurements of ozone, water vapor, and aerosol.

Newell, Reginald E.↗

Symbology Development for General Aviation Synthetic Vision Primary Flight Displays for the Approach and Missed-Approach Modes of Flight

Spatial disorientation induced by inadvertent flight into instrument meteorological conditions (IMC) continues to be a leading cause of fatal accidents in general aviation. The Synthetic Vision Systems General Aviation (SVS-GA) research element, an integral part of NASA s Aviation Safety and Security Program (AvSSP), is investigating a revolutionary display technology designed to mitigate low visibility events such as controlled flight into terrain (CFIT) and low-visibility loss of control (LVLoC). The integrated SVS Primary Flight Display (SVS-PFD) utilizes computer generated 3-dimensional imagery of the surrounding terrain augmented with flight path guidance symbology. This unique combination will provide GA pilots with an accurate representation of their environment and projection of their flight path, regardless of time of day or out-the-window (OTW) visibility. The initial Symbology Development for Head-Down Displays (SD-HDD) simulation experiment examined 16 display configurations on a centrally located high-resolution PFD installed in NASA s General Aviation Work Station (GAWS) flight simulator. The results of the experiment indicate that situation awareness (SA) can be enhanced without having a negative impact on flight technical error (FTE), by providing a general aviation pilot with an integrated SVS display to use when OTW visibility is obscured.

Bartolone, Anthony P.↗

Stockpile Stewardship: How We Ensure the Nuclear Deterrent Without Testing

In the 1990s, the U.S. nuclear weapons program shifted emphasis from developing new designs to dismantling thousands of existing weapons and maintaining a much smaller enduring stockpile. The United States ceased underground nuclear testing, and the Department of Energy created the Stockpile Stewardship Program to maintain the safety, security, and reliability of the U.S. nuclear deterrent without full-scale testing. This video gives a behind the scenes look at a set of unique capabilities at Lawrence Livermore that are indispensable to the Stockpile Stewardship Program: high performance computing, the Superblock category II nuclear facility, the JASPER a two stage gas gun, the High Explosive Applications Facility (HEAF), the National Ignition Facility (NIF), and the Site 300 contained firing facility.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Multiple social platforms reveal actionable signals for software vulnerability awareness: A study of GitHub, Twitter and Reddit

Software vulnerabilities are flaws in computer systems that leave users open to attack. In many cases, these vulnerabilities go unnoticed and remain unresolved in codebases. Thus, awareness of software vulnerabilities among the public is crucial to ensure effective cybersecurity practices, the development of high quality software, and ultimately national security. This awareness can be better understood by studying the spread and evolution of software vulnerability discussions in online communities. This work is the first to evaluate and contrast how discussions about software vulnerabilities spread on three social platforms -- Twitter, GitHub, and Reddit. To lay the groundwork, we showcase a novel fundamental framework for measuring information spread that identifies the spread mechanisms and observables across platforms, the units of information, and the groups of measurements that can be applied to focus on a specific phenomena e.g., information cascades. We then analyze and contrast social network topologies for three example social networks and measure the scale and speed of the spread of discussion of specific vulnerabilities to understand how far and how widely they spread, how many users participate in discussions, and the duration of their spread. To demonstrate the awareness of more impactful software vulnerabilities, a subset of our analysis focuses on vulnerabilities targeted during recent major cyber attacks as well as vulnerabilities exploited by advanced persistent threat groups. We discover that usually, vulnerability discussions start on GitHub, before occurring on Twitter and Reddit. While studying how some user-level and content-level characteristics influence vulnerability spread, we observe that Twitter discussions started by users predicted to be humans have larger size, breadth, depth, adoption rate, lifetime, and structural virality compared to those started by users predicted to be bots. On Reddit, we contrast the differences in thread structure that originate from posts with positive, negative and neutral polarity. We find that posts that are positive have larger, deeper and wider discussions compared to negative and neutral posts. We anticipate the results of our analysis to not only increase the understanding of software vulnerability awareness but also inform models for simulating information spread across multiple social environments online.

97 MATHEMATICS AND COMPUTING↗

Universal Polarization Transformations: Spatial Programming of Polarization Scattering Matrices Using a Deep Learning‐Designed Diffractive Polarization Transformer

Abstract Controlled synthesis of optical fields having nonuniform polarization distributions presents a challenging task. Here, a universal polarization transformer is demonstrated that can synthesize a large set of arbitrarily‐selected, complex‐valued polarization scattering matrices between the polarization states at different positions within its input and output field‐of‐views (FOVs). This framework comprises 2D arrays of linear polarizers positioned between isotropic diffractive layers, each containing tens of thousands of diffractive features with optimizable transmission coefficients. After its deep learning‐based training, this diffractive polarization transformer can successfully implement N i N o = 10 000 different spatially‐encoded polarization scattering matrices with negligible error, where N i and N o represent the number of pixels in the input and output FOVs, respectively. This universal polarization transformation framework is experimentally validated in the terahertz spectrum by fabricating wire‐grid polarizers and integrating them with 3D‐printed diffractive layers to form a physical polarization transformer. Through this set‐up, an all‐optical polarization permutation operation of spatially‐varying polarization fields is demonstrated, and distinct spatially‐encoded polarization scattering matrices are simultaneously implemented between the input and output FOVs of a compact diffractive processor. This framework opens up new avenues for developing novel devices for universal polarization control and may find applications in, e.g., remote sensing, medical imaging, security, material inspection, and machine vision.

Optical neural networks↗

Distributed Energy Systems: Security Implications of the Grid of the Future

Distributed Energy Resources (DER) are being added to the nation's electric grid, and as penetration of these resources increases, they have the potential to displace or offset large-scale, capital-intensive, centralized generation. Integration of DER into operation of the traditional electric grid requires automated operational control and communication of DER elements, from system measurement to control hardware and software, in conjunction with a utility's existing automated and human-directed control of other portions of the system. Implementation of DER technologies suggests a number of gaps from both a security and a policy perspective.

24 POWER TRANSMISSION AND DISTRIBUTION↗

V-INT: Automated Vulnerability Intelligence and Risk Assessment

The project team, including the University of Arkansas (UA) as the lead, the University of Arkansas at Little Rock (UALR), Network Perception (NP), and Bastazo, has successfully researched, developed, and demonstrated the V-INT toolset, and also integrated it into the commercial products of NP (i.e., NP-View) and Bastazo (i.e., Spartan). The end product is a cybersecurity software tool for energy utilities that can automatically assess the risks of software vulnerabilities in an organization’s assets considering the organization’s firewall policies. It allows security operators to identify the small portion of vulnerabilities that poses true threats to their system (i.e., those that are not protected by firewall policies) and prioritize the mitigation of these vulnerabilities to minimize risks. It also allows security operators to identify the vulnerability-induced attack paths under their organization’s firewall policy, providing effective decision supports for mitigating potential attacks.

97 MATHEMATICS AND COMPUTING↗

Invensys Foxboro Control Software Security Assessment

Idaho National Laboratory, in collaboration with Invensys, performed a laboratory assessment on Invensys Foxboro Control Software. During this assessment, vulnerabilities were discovered, evaluated, and mitigation strategies developed.

97 MATHEMATICS AND COMPUTING↗

Stabilizer Rank Strong Simulation v.0.1

This software improves upon the Clifford gate+T gate magic state strong simulation algorithm by Brayvi and Gosset. It provides a better stabilizer state decomposition that scales as 2^{0.463t}, an improvement over 2^{0.468t}, for t T gate magic states. This code enables simulations of universal quantum computing with that asymptotic scaling cost. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525 SAND2020-14293 O

SciDAC↗

2009.3 Revision of the Evaluated Nuclear Data Library (ENDL2009.3)

LLNL's Computational Nuclear Data and Theory Group have created a 2009.3 revised release of the Evaluated Nuclear Data Library (ENDL2009.3). This library is designed to support LLNL's current and future nuclear data needs and will be employed in nuclear reactor, nuclear security and stockpile stewardship simulations with ASC codes. The ENDL2009 database was the most complete nuclear database for Monte Carlo and deterministic transport of neutrons and charged particles. It was assembled with strong support from the ASC PEM and Attribution programs, leveraged with support from Campaign 4 and the DOE/Office of Science's US Nuclear Data Program. This document lists the revisions and fixes made in a new release called ENDL2009.3, by com- paring with the existing data in the previous release ENDL2009.2. These changes are made in conjunction with the revisions for ENDL2011.3, so that both the .3 releases are as free as possible of known defects.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Next-Generation Analysis and Visualization Platform for Manufacturing and Engineering Workflows (Final Report)

Advanced manufacturing and engineering are fundamental to the economic strength and national security of the United States. With the introduction of advanced modeling and simulation practices in manufacturing and engineering over the last several decades, we are producing better products, more quickly, and at decreased cost. Through the adoption of high-performance computing (HPC) enabled workflows, in small- to medium-sized manufacturers and engineering firms, which employ fewer than 500 people, is renewing United States manufacturing and engineering. Despite successes, there are significant barriers to widespread adoption of these tools. Our Phase I SBIR project, Next-Generation Analysis and Visualization Platform for Manufacturing and Engineering Workflows, aims to address several of these barriers. Our project helped us evaluate the feasibility and benefits and mitigate risks of asynchronous processing for analysis and visualization workflows. We evaluated the impact of asynchronous, non-blocking communication can have on the user experience in a complex visualization application. Besides the impact on users, we wanted to understand the impacts on developers (development application programming interfaces (APIs))and generated applications (robustness and stability). Any asynchronous platform implementation is bound to rely on multiple threads which can make the programming model extraordinarily complex and prone to bugs. If not managed carefully, the complexity and resulting instability would be an unacceptable evolution for widely used production tools like ParaView and putting the success of the Phase II project at risk.

42 ENGINEERING↗

Current Needs in Radiochemistry

There are a number of current needs in the development of the Pu and Am separations that underpin larger interest areas including nuclear waste issues, nuclear weapons, nuclear forensics, nuclear fuels and similarly related fields. In the large areas of interest, there are a number of sub-fields that include corrosion chemistry, pyrochemistry, solution-phase chemistry, rapid separations, environmental speciation, and other similar efforts. However, in all of the these fields it is important to realize that the underlying chemistry that underpins these efforts is similar in that Pu and Am are bound to ligands that can be in the solid, aqueous, or gas phase and separations occurs due to the preferential binding of the ligand to Pu or Am based on a number of factors that include pH, concentration, oxidation state, etc. In the past, most of the Pu and Am chemistry has occurred in limited scope within universities where micro-scale and bench-top scale chemistry are the dominate investigative theme. At US national laboratory and their international counterparts, larger scale reactions have been attempted such that industrial scale chemistry has been completed. Some of this technology has been harnessed in radiopharmaceuticals and nuclear fuel reprocessing. However, such bench-top research is expensive to due to the safety and security that is concerned when dealing with Pu, and scale-up of reactions is even more resource intensive. In an effort to offset this expensive, it would be of interest to explore the ability to predict selectivity based on the computational modeling of actinide chemistry. This has historically been limited by the abilities of large supercomputers, but with the emphasis on developing exascale computers within the US and similar efforts by other countries this predictive modeling has potential to produce significant results that would yield improved understanding of actinide chemistry.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗