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SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences

Background Synthetic biology involves combining different DNA fragments, each containing functional biological parts, to address specific problems. Fundamental gene-function research often requires cloning and propagating DNA fragments, such as those from the iGEM Parts Registry or Addgene, typically distributed as circular plasmids. Addgene’s repository alone offers around 150,000 plasmids. To ensure data integrity, cryptographic checksums can be calculated for the sequences. Each sequence has a unique checksum, making checksums useful for validation and quick lookups of associated annotations. For example, the SEGUID checksum uniquely identifies protein sequences with a 27-character string. Objectives The original SEGUID, while effective for protein sequences and single-stranded DNA (ssDNA), is not suitable for circular DNA since there is no natural starting position nor for double-stranded DNA (dsDNA) since two separate sequences are present. Challenges include how to uniquely represent linear dsDNA, circular ssDNA, and circular dsDNA. To meet these needs, we propose SEGUID v2, which extends the original SEGUID to handle additional types of sequences. Conclusions SEGUID v2 produces orientation and rotation invariant checksums for single-stranded, double-stranded, possibly staggered, linear, and circular DNA and RNA sequences. Customizable alphabets allow for other types of sequences. In contrast to the original SEGUID, which uses Base64, SEGUID v2 uses Base64url to encode the SHA-1 hash. This ensures SEGUID v2 checksums can be used as-is in filenames, regardless of platform, and in URLs, with minimal friction. Availability SEGUID v2 is readily available for major programming languages, distributed under the MIT license. JavaScript package seguid is available on npm, Python package seguid on PyPi, R package seguid on CRAN, and a Tcl script on GitHub. These tools, along with documentation, examples, and an online SEGUID Calculator , can be found at https://www.seguid.org .

Pereira, Humberto↗

DIY Affordable Window Shading

This document shows how you can easily and affordably shade your windows to keep your home from getting too hot on sunny days. This phenomenon (what researchers call “solar heat gain”) can threaten occupant comfort and safety, especially during heatwaves. Still, many homes lack adequate protection. All of these solutions can be implemented inexpensively using common household items or items that can easily be purchased online. Additionally, you don’t need specialized tools or expertise to install them. Note that these are ideally temporary fixes, so households with sufficient means should still pursue permanent ones (e.g.,shades—preferably on the outside—or specialized windows or films). In their absence, the stopgap measures described below can help protect you and your loved ones during heatwaves and other exceptional events.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Contribution to the IRPHEP handbook since Physor 2018

The Organisation for Economic Co-operation and Development (OECD), the Nuclear Energy Agency (NEA), the International Reactor Physics Experiment Evaluation Project (IRPhEP) continue to preserve and evaluate integral reactor physics experiment data to support nuclear energy and technology needs. International contributions are collated within the International Handbook of Evaluated Reactor Physics Benchmark Experiments (IRPhEP Handbook). The 2021 edition of the IRPhEP Handbook now contains data for 57 unique nuclear facilities with benchmark specifications for 169 experimental series, of which four are draft evaluations. Distributed with the IRPhEP Handbook and available online is the IRPhEP Database and Analysis Tool (IDAT), allowing users to search and interrogate the data. Since Physor 2018, there have been 11 minor revisions to existing benchmark evaluations, significant revisions to two evaluations, one draft evaluation, and nine new evaluations. The corona virus pandemic has delayed international activities supporting the production of additional content for the IRPhEP Handbook. However, efforts continue for numerous endeavors to complete new reactor physics benchmark evaluations to support current and future validation needs. Those interested in serving as evaluators and/or reviewers are strongly encouraged to participate. This paper provides a summary of IRPhEP content and activities since Physor 2018. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Advanced Reactor Control and Operations (ARCO): A University Research Facility for Developing Optimized Digital Control Rooms

The Advanced Reactor Control and Operations (ARCO) facility was constructed in January 2018 to serve as a test bed for advanced reactor control rooms and operator support systems. Since then, it has supported human-machine interface user experience research, fault detection and mitigation technology development, control room concept of operations development, and remote operations research. ARCO serves as the control room for the Compact Integral Effects Test (CIET) facility, which replicates the primary-side flow paths and thermal-hydraulic behavior of a fluoride-salt-cooled high-temperature reactor (FHR) using simulant fluids and scaling principles. New reactor designs feature different operating conditions and scenarios than those in existing reactors. ARCO supports the research and development of digital tools for operator communications, intuitive real-time data analysis, online health monitoring and prognostics, and control room cybersecurity. By integrating these different technologies, ARCO acts as a prototypical control system to iteratively develop methods and tools of operation in advanced small modular nuclear reactors. This paper describes the features of and challenges to operating advanced small modular reactors underlying the design basis for ARCO and its operator support systems.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

eLog analysis for accelerators: status and future outlook

This work demonstrates electronic logbook (eLog) systems leveraging modern AI-driven information retrieval capabilities at the accelerator facilities of Fermilab, Jefferson Lab, Lawrence Berkeley National Laboratory (LBNL), SLAC National Accelerator Laboratory. We evaluate contemporary tools and methodologies for information retrieval with Retrieval Augmented Generation (RAGs), focusing on operational insights and integration with existing accelerator control systems. The study addresses challenges and proposes solutions for state-of-the-art eLog analysis through practical implementations, demonstrating applications and limitations. We present a framework for enhancing accelerator facility operations through improved information accessibility and knowledge management, which could potentially lead to more efficient operations.

Accelerator Physics↗

Using Parameter Sweep in WaterTAP to Analyze New Water Treatment Technologies

We describe a powerful and generalized parameter sweep tool in this report that was originally developed to analyze the performance of existing and novel water treatment models being developed in WaterTAP. Since WaterTAP is built upon IDAES and Pyomo, the parameter sweep tool can be used to systematically explore and debug the behavior of most Pyomo and IDAES numerical models. In order to enable meaningful analyses, the parameter sweep tool has been designed with the following features: 1) Model flexibility: The parameter sweep tool does not enforce any restrictions on the types of models that can be used with it. As long as a Pyomo model can be solved and the parameter is active and mutable, the tool only needs functions that describe how to run the model, the sweep parameters, and the output quantities of interest. 2) Flexible sampling: The parameter sweep tool has inbuilt functions to generate samples from a random distribution or a multidimensional Euclidean space. Furthermore, the users have to ability to supply samples generated from a tool of their choice. 3) Multiple sweep types: A user can choose from one of 3 types of parameter sweeps depending on their needs. 4) Detailed outputs: Outputs generated by the parameter sweep tool can be stored in detailed H5 file or user-friendly CSV files for post processing. 5) Parallel computing: The parameter sweep supports shared and distributed memory parallel computing to enable the use of high performance computers (HPC) for large-scale analyses. 6) Modular: The parameter sweep tool is self-contained and can easily be integrated within an outer-loop analysis or as desired by the user. 7) Ease of use: The tool is well documented and a simple sweep can be easily executed by following the online documentation in a few lines of code. We demonstrate the use of the parameter sweep tool on a simple water treatment system from the WaterTAP repository and show its parallel scaling performance on an Apple laptop and NREL's Eagle HPC. The parameter sweep tool is actively being used with models currently being developed within WaterTAP and we expect its use to grow beyond it to other IDAES and Pyomo models.

97 MATHEMATICS AND COMPUTING↗

Cross-platform analysis of public responses to the 2019 Ridgecrest earthquake sequence on Twitter and Reddit

Online social networks (OSNs) have become a powerful tool to study collective human responses to extreme events such as earthquakes. Most previous research concentrated on a single platform and utilized users’ behaviors on a single platform to study people’s general responses. In this study, we explore the characteristics of people’s behaviors on different OSNs and conduct a cross-platform analysis of public responses to earthquakes. Our findings support the Uses and Gratification theory that users on Reddit and Twitter are engaging with platforms that they may feel best reflect their sense of self. Using the 2019 Ridgecrest earthquakes as our study cases, we collected 510,579 tweets and 45,770 Reddit posts (including 1437 submissions and 44,333 comments) to answer the following research questions: (1) What were the similarities and differences between public responses on Twitter and Reddit? (2) Considering the different mechanisms of Twitter and Reddit, what unique information of public responses can we learn from Reddit as compared with Twitter? By answering these research questions, we aim to bridge the gap of cross-platform public responses research towards natural hazards. Our study evinces that the users on the two different platforms have both different topics of interest and different sentiments towards the same earthquake, which indicates the necessity of investigating cross-platform OSNs to reveal a more comprehensive picture of people’s general public responses towards certain disasters. Our analysis also finds that r/conspiracy subreddit is one of the major venues where people discuss the 2019 Ridgecrest earthquakes on Reddit and different misinformation/conspiracies spread on Twitter and Reddit platforms (e.g., “Big one is coming” on Twitter and “Nuclear test” on Reddit).

58 GEOSCIENCES↗

PDB‐101: Molecular Explorations through Biology and Medicine

PDB‐101 is an online portal for teachers, students, and the general public to promote exploration of the structural biology of proteins and nucleic acids ( pdb101.rcsb.org ). Learning about the diverse shapes and functions of these biological macromolecules helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy. Why PDB‐101? Researchers around the world are studying these molecules at the atomic level. These 3D structures are freely available at the Protein Data Bank (PDB), the central storehouse of biomolecular structures. This website builds introductory materials to help beginners get started in the basics of biomolecular structure and function (“101”, as in an entry level course) as well as resources for extended learning. Since 2011, PDB‐101 has been developed by the RCSB PDB , a global resource for the advancement of research and education in biology and medicine. Along with our Worldwide PDB collaborators, RCSB PDB curates, annotates, and makes publicly available the PDB data deposited by scientists around the globe. The RCSB PDB then provides a window to these data through a rich online resource with powerful searching, reporting, and visualization tools for researchers. This information is then streamlined for students and teachers at PDB‐101. Features include the ongoing Molecule of the Month series, educational materials such as paper models, posters, molecular animations, educational curricula and more. The section “Guide to Understanding PDB Data” is a primer for detailed PDB‐specific information: PDB Data, Visualizing Structures, Reading Coordinate Files, scientific methods for structure determination, and more. PDB‐101 also runs annual Video Challenges for high school students. Participants create short videos that tell molecular stories that connect structural biology and medicine. Previous topics have included HIV/AIDS, diabetes, and antimicrobial resistance. The 2022 challenge will focus on Molecular Mechanisms of Cancer. PDB‐101 activities are evaluated using user surveys, feedback from in‐person activities, and website analytics. In 2020, PDB‐101 hosted >850,000 users and >2.6 million page views.

Zardecki, Christine↗

Normal or abnormal? Machine learning for the leakage detection in carbon sequestration projects using pressure field data

The international commitments for atmospheric carbon reduction will require a rapid increase in carbon capture and storage (CCS) projects. The key to any successful CCS project lies in the long term storage and prevention of leakage of stored carbon dioxide (CO 2 ). In addition to being a greenhouse gas, CO 2 leaks reaching the surface can accumulate in low-lying areas resulting in a serious health risk. Among several alternatives, some of the more promising CCS storage formations are depleted oil and gas reservoirs, where the reservoirs had good geological seals prior to hydrocarbon extraction. With more CCS wells coming online, it is imperative to implement permanent, automated monitoring tools. We apply machine learning models to automate the leakage detection process in carbon storage reservoirs using rates of (CO 2 ) injection and pressure data measured by simple harmonic pulse testing (HPT). To validate the feasibility of this machine learning based workflow, we use data from HPT experiments carried out in the Cranfield oil field, Mississippi, USA. The data consist of a series of pulse tests conducted with baseline parameters and with an artificially introduced leak. Here, in this study, we pose the leakage detection task as an anomaly detection problem where deviation from the predicted behavior indicates leaks in the reservoir. Results show that different machine learning architectures such as multi-layer feed forward network, Long Short-Term Memory, and convolutional neural network are able to identify leakages and can provide early warning. These warnings can then be used to take remedial measures.

58 GEOSCIENCES↗

Practical Multi-Cycle Refueling Simulation of Stable Salt Reactors Based on REBUS Depletion Calculation

A Python software tool ReloadPy has been developed to assistant in formulating online refueling strategies for a family of stable salt reactors. ReloadPy wraps over the legacy fast reactor analysis codes REBUS, DIF3D, and PERSENT. These codes are used to perform single cycle depletion analysis and calculate reactivity worth and power density. ReloadPy determines a refueling assembly position to achieve the user-specified primary objective while satisfying constraints on various performance parameters such as the maximum power density, the maximum reactivity worth of reloaded assembly, and the minimum cycle length. Various capabilities of prescribing refueling sequence or a range of candidate refueling positions and restarting a previous simulation with altered options are implemented to reduce the required user’s efforts to investigate different refueling strategies. This report presents the computational models and methods and also serves as a user guide. Long-term simulation capabilities with different refueling strategies are demonstrated by a series of sample SSR refueling calculations with two-dimensional surrogate core models.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Evaluating the Nation's Pipeline Infrastructure with NETL's Advanced Infrastructure Integrity Model (AIIM)

This poster is a part of BIL-EDX4CCS Task 36: Advanced Infrastructure Integrity Modeling to Evaluate Existing Energy Infrastructure Reusability and Risk, the goal of which is to produce a smart tool that will assess existing energy infrastructure reusability and risk using the Advanced Infrastructure Integrity Model (AIIM). This model forecasts lifespan and potential risk using a multitude of factors such as incidents reports, structural characteristics, and the surrounding environment. The project aims to provide scientific insights for a better understanding of carbon storage (CS), potential to support CS stakeholder needs, national decarbonization, and mitigating climate change. AIIM will utilize an energy infrastructure database as its input, developed by acquiring publicly available data as well as NETL derived products. These resources include incidents, geohazards, and infrastructure variables. Soil data in the form of rasters and pipeline incident reports were processed and a script was developed to count the number of times features such as roads, railroads, and rivers intersected with pipeline segments which were then converted to points. Distance to oil and natural gas wells, petroleum ports, intermodal freight facilities, and geologic structures were also calculated. After data preparation and quality control was completed, the data was integrated into the pipeline points. Once models are complete, a smart tool will be created in the form of an online dashboard.

Malay, Caleb↗

Engaging the Regulatory Community to Aid Environmental Consenting/Permitting Processes for Marine Renewable Energy

Regulators involved in consenting/permitting marine renewable energy (MRE) have faced multiple challenges due to relatively new, unfamiliar technologies and uncertainty surrounding potential environmental impacts. This has resulted in slow progress for the MRE industry, including long consenting timeframes and extensive and expensive monitoring requirements, which increase financial risk for investors. OES-Environmental has surveyed regulators internationally to understand their key knowledge gaps and perspectives to support the development of the MRE industry. From the results of these surveys a data transferability process and a risk retirement pathway have been developed to assess consenting and monitoring requirements in proportion to risk. A tool for discovering existing data sets by using an online matrix has been developed, along with training materials, regulatory guidance documents, and a strategic outreach plan to engage regulators and advisers. his engagement and the application of these products should lead to a better understanding of the environmental effects of marine energy, and more efficient consenting processes.

16 TIDAL AND WAVE POWER↗

Multi-Unit Dwelling Plug-in EV Charging Innovation Pilots (Final Report)

Nearly one-third of residences in the U.S. are multi-unit dwellings (MUDs), e.g., apartments and condominiums, and MUDs with five or more units account for approximately 45% of rental households. While 80% of EV charging takes place at home, less than 5% of home charging takes place at MUDs. With public electric vehicle (EV) charging still underdeveloped, lack of access to reliable home charging is a major barrier to EV adoption for MUD residents. Challenges to siting electric vehicle supply equipment (EVSE) at MUDs include the high upfront cost of EVSE installation, physical and/or electrical infrastructure constraints, a lack of clear incentives for property managers to invest in installing EV charging for tenants, and a limited number of EV charging service providers that offer solutions adapted to the unique needs of MUDs. Through award DE-EE0008473 from the U.S. Department of Energy’s Office of Energy Efficiency and Renewable Energy (EERE), Center for Sustainable Energy (CSE), Energetics, and Forth, along with a diverse team of partners, led a three-year project to address barriers to EV charging at MUDs by developing an online toolkit geared toward residents, homeowner associations (HOAs), and property managers. The project, referred to as Vehicle Charging Innovations – Multi-Unit Dwellings (VCI-MUD project), engaged stakeholders across the country to identify real and perceived barriers to EV charging at MUDs and explored innovative technologies that attempt to alleviate the identified barriers. Over the course of three and a half years, the project conducted 60 interviews with industry stakeholders, compiled findings in an easy-to-use toolkit, and disseminated the toolkit across national, regional, state, and local channels. Key findings and outcomes of the VCI-MUD project include: Identifying six primary barriers to the installation of EV charging at MUDs; Developing five fact sheets and eight case studies highlighting innovative charging solutions to address barriers, including real-world operational and financial data; Developing a user-friendly, online empowerment toolkit with five important points for “making your pitch” to support EV charging to assist residents, property managers, building managers, and HOAs explore options for MUD charging. The VCI-MUD online toolkit was designed with replicability in mind. It includes general tools and guides to evaluate EV charging demand, gauge readiness for EV charging installation, and develop actionable plans. The fact sheets and case studies highlight the diversity of emerging MUD EV charging solutions, featuring different geographic and structural installation scenarios and providing interested parties with a menu of options, rather than prescribing a one-size-fits-all solution. The following resources are included in the toolkit to provide MUD stakeholders with all the information needed to navigate EV charging installation at their MUD location: Empowerment Toolkit – Easy-to-read FAQ overview, stakeholder roles and responsibilities, and additional resources for MUD EV charging installations; Charging Basics – Glossary of terms and descriptions of charging features, installation and operating expenses; EV Charging Survey Templates – Resident-to-Resident, Property Manager-to-Resident and HOA-to-Resident template letters with pre-populated template questions; Technology Selection Tool – Charging barrier fact sheets and case study examples; Installation Checklist – Submittal document requirements for EVSE installations; MUD Building Self-Evaluation Survey – Self-guided evaluation of potential barriers to EV charging installation at MUD locations; Curbside Resources – Case studies and fact sheets for curbside charging options; Find a Certified Electrician – Approved list of certified EV charging installers; “Right-to-Charge” State Legal References – Legal requirements for charging equipment at MUD locations. The online toolkit was promoted extensively in the final six months of the project and will continue to be disseminated by the Clean Cities Coalitions and other partners after the end of the VCI-MUD project to encourage, support, and demonstrate viable solutions for vehicle charging infrastructure in MUDs.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Implementing Online Oscillation Monitoring and Forced Oscillation Source Locating at Peak Reliability

This paper introduces a framework of online oscillation monitoring systems and forced oscillation detection & source location tools that Peak Reliability ('PEAK') has implemented for the Reliability Coordinator (RC) function of the Western Interconnection. The framework consists of four main components: (1) Montana Tech's Modal Analysis Software (MAS) engine; (2) Washington State University's Oscillation Monitor System (OMS) software; (3) Forced Oscillation Detection and Source Location Algorithms (FODSL); and (4) PEAK in-house visualization tool and alarming logic built in PI Processbook. The framework has been validated and applied for real system oscillation studies successfully. Implementation experience and lessons learned will be discussed in the paper.

14 SOLAR ENERGY↗

Physiological Characterization of Language Comprehension

In this project, our goal was to develop methods that would allow us to make accurate predictions about individual differences in human cognition. Understanding such differences is important for maximizing human and human-system performance. There is a large body of research on individual differences in the academic literature. Unfortunately, it is often difficult to connect this literature to applied problems, where we must predict how specific people will perform or process information. In an effort to bridge this gap, we set out to answer the question: can we train a model to make predictions about which people understand which languages? We chose language processing as our domain of interest because of the well- characterized differences in neural processing that occur when people are presented with linguistic stimuli that they do or do not understand. Although our original plan to conduct several electroencephalography (EEG) studies was disrupted by the COVID-19 pandemic, we were able to collect data from one EEG study and a series of behavioral experiments in which data were collected online. The results of this project indicate that machine learning tools can make reasonably accurate predictions about an individual?s proficiency in different languages, using EEG data or behavioral data alone.

42 ENGINEERING↗

Online Interactive Platform for COVID-19 Literature Visual Analytics: Platform Development Study

Background Papers on COVID-19 are being published at a high rate and concern many different topics. Innovative tools are needed to aid researchers to find patterns in this vast amount of literature to identify subsets of interest in an automated fashion. Objective We present a new online software resource with a friendly user interface that allows users to query and interact with visual representations of relationships between publications. Methods We publicly released an application called PLATIPUS (Publication Literature Analysis and Text Interaction Platform for User Studies) that allows researchers to interact with literature supplied by COVIDScholar via a visual analytics platform. This tool contains standard filtering capabilities based on authors, journals, high-level categories, and various research-specific details via natural language processing and dozens of customizable visualizations that dynamically update from a researcher’s query. Results PLATIPUS is available online and currently links to over 100,000 publications and is still growing. This application has the potential to transform how COVID-19 researchers use public literature to enable their research. Conclusions The PLATIPUS application provides the end user with a variety of ways to search, filter, and visualize over 100,00 COVID-19 publications.</:p>

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Open Chemistry, JupyterLab, REST, and quantum chemistry

Quantum chemistry must evolve if it wants to fully leverage the benefits of the internet age, where the worldwide web offers a vast tapestry of tools that enable users to communicate and interact with complex data at the speed and convenience of a button press. The Open Chemistry project has developed an open-source framework that offers an end-to-end solution for producing, sharing, and visualizing quantum chemical data interactively on the web using an array of modern tools and approaches. These tools build on some of the best open-source community projects such as Jupyter for interactive online notebooks, coupled with 3D accelerated visualization, state-of-the-art computational chemistry codes including NWChem and Psi4, and emerging machine learning and data mining tools such as ChemML and ANI. They offer flexible formats to import and export data, along with approaches to compare computational and experimental data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Utilization of Additive Manufacturing for the Rapid Prototyping of C-Band Radiofrequency Loads

Additive manufacturing is a versatile technique that shows promise in providing quick and dynamic manufacturing for complex engineering problems. Research has been ongoing into the use of additive manufacturing for potential applications in radiofrequency (RF) component technologies. Here, we present a method for developing an effective prototype load produced from 316L stainless steel on a direct metal laser sintering machine. The model was tested using simulation software to verify the validity of the design. The load structure was manufactured by an online digital manufacturing company, showing the viability of using easily accessible tools to manufacture RF structures. The produced load was able to produce an S11 value of −22.8 dB at a C-band frequency of 5.712 GHz while under a vacuum. In a high-power test, the load was able to terminate a peak power of 8.1 MW. The discussion includes future applications of the present method and how it will help to improve the implementation of future accelerator concepts.

36 MATERIALS SCIENCE↗