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At least 1,153 records · Page 64

Microbial Taxonomy Run Amok

DNA sequencing has led to an explosion in discovery of microbial phylogenetic novelty, especially that represented by uncultivated taxa, to which the traditional system of prokaryotic taxonomy has not adapted. A lack of expansion of the International Code of Nomenclature of Prokaryotes (ICNP, 'the Code') to effectively capture this information has created a 'wild west' situation where names are published or appear in popular reference databases without further verification or validation. The rapid propagation of variant and questionable naming methods has led to widespread confusion and undermines prior accomplishments. Furthermore, we exemplify inconsistencies that have arisen from this practice and endanger the interoperability of scientific findings. The immediate solution to this problem is to develop and adopt universal best practices that are accepted by expert researchers, major publishers, the International Committee on Systematics of Prokaryotes (ICSP), and international microbiological societies.

59 BASIC BIOLOGICAL SCIENCES↗

Introducing the embedded random phase approximation: H 2 dissociative adsorption on Cu(111) as an exemplar

The random phase approximation (RPA) as a means of treating electron correlation recently has been shown to outperform standard density functional theory (DFT) approximations in a variety of cases. However, the computational cost of the RPA is substantially more than DFT, especially when aiming to study extended surfaces. Properly accounting for sufficient surface ensemble size, Brillouin zone sampling, and vacuum separation of periodic images in standard periodic-planewave-based DFT code raises the cost to achieve converged results. Here, we show that sub-system embedding schemes enable use of the RPA for modeling heterogeneous reactions at reduced computational cost. Further, we explore two different embedded RPA (emb-RPA) approaches, periodic emb-RPA and cluster emb-RPA. We use the (experimentally and theoretically) well-studied H 2 dissociative adsorption on Cu(111) as our exemplar, and first perform full periodic RPA calculations as a benchmark. The full RPA results match well the semi-empirical barrier fit to experimental observables and others derived from high-level computations, e.g., from recent embedded n-electron valence second order perturbation theory [Zhao et al., J. Chem. Theory Comput. 16(11), 7078–7088 (2020)] and quantum Monte Carlo [Doblhoff-Dier et al., J. Chem. Theory Comput. 13(7), 3208–3219 (2017)] simulations. Among the two emb-RPA approaches tested, the cluster emb-RPA accurately reproduces the energy profile (maximum error of 50 meV along the reaction pathway) while reducing the computational cost by approximately two orders of magnitude. We therefore expect that the embedded cluster approach will enable wider RPA implementation in heterogeneous catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Certification Validation Libraries

“The code “Certificate Validation Libraries” provides the ability to validate x509 certificates in python using a simple library. These libraries validate certificates in 3 ways: 1) validation that certificate has not expired. 2) validation that certificate has not been revoked and 3) validation of certificate's digital signature. The benefits of this code is that one can properly validate x509 certificates, thus strengthening the security of systems using these libraries.”

Maerz, StefanA↗

kessel

Kessel is a tool to create and drive continuous integration (CI) and developer workflows through a unified interface across multiple code projects and environments. It serves as a driver and integration layer for build systems and package managers, providing a flexible library of reusable components to build and execute complex workflows consistently.

Berger, Richard [@lanl]↗

FLASSH 1.0: Full Law Analysis Scattering System Hub

Nuclear technologies, such as thermal reactors and critical systems, are driven by reaction rates which are directly dependent on thermal neutrons. The ability to calculate reaction rates is directly linked to the capability to predict and understand the cross sections. For atoms bound within a material structure, the available modes of energy exchange are captured in the Thermal Scattering Law (TSL, i.e. S(α,β)). The TSL is fundamentally a material property and can be defined explicitly to account for the excitation and deexcitation of the lattice energy states. This work describes the development of the Full Law Analysis Scattering System Hub (FLASSH) which calculates the TSL and cross sections. FLASSH is a modern code which has been designed to produce accurate TSL evaluations, remove historical approximations, and improve formulations while making advance physics accessible and simple to use.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Data Arrays for Microearthquake (MEQ) Monitoring using Deep Learning for the Newberry EGS Sites

The 'Machine Learning Approaches to Predicting Induced Seismicity and Imaging Geothermal Reservoir Properties' project looks to apply machine learning (ML) methods to Microearthquake (MEQ) data for imaging geothermal reservoir properties and forecasting seismic events, in order to advance geothermal exploration and safe geothermal energy production. As part of the project, this submission provides data arrays for 149 microearthquakes between the year 2012 and 2013 at the Newberry EGS Site for use with the Deep Learning Algorithm that has been developed. The data provided includes raw waveform data, location data, normalized waveform data, and processed waveform data. Penn State Geothermal Team has shared the following files from the project: - 149 microearthquakes (MEQs) between 2012 and 2013 at Newberry EGS sites, 'Normalized Waveform Inputs.npz' are normalized waveforms. - labels of 149 MEQs: Processed Waveform Inputs.npz - location labels of 149 MEQs: Location Data.npz Note: .npz is the python file format by NumPy that provides storage of array data.

15 GEOTHERMAL ENERGY↗

Design of a Transport System for the PIP-II HB650 Cryomodule

The PIP-II Project at FNAL requires the assembly of 3 high-beta 650MHz cryomodules at STFC Daresbury (DL) in the UK. These modules must be safely transported from DL to FNAL in the USA. Previous experience with cryomodule transport was leveraged at both labs to design a transport system to protect the cryomodules during transit. Requirements for the system included mitigation of shocks, drops, and vibrations, and acting as a lifting fixture. It is comprised of a tessellated steel frame which encompasses the module with a wire rope isolator arrangement which the module mounts to. The frame was designed to withstand the weight of the 12.5 tonne cryomodule in various load cases. Details of shock and vibration profiles were obtained from MIL-STD-810H and were used to guide the sizing of the isolators. The frame and the isolation system were analysed via FEA using the shock and vibration profiles as an input. The transport system was found to be suitable for the given isolation, frame stiffness, and lifting code requirements. The frame has been fabricated and successfully load tested at FNAL. It will now be road tested with a dummy cryomodule before undergoing a trial run to DL.

43 PARTICLE ACCELERATORS↗

SimpleMass (Version 2.0.1 Report)

SimpleMass v2 is an updated GUI version of the SimpleMass Excel spreadsheet. It was developed using Python 3.7 and wxPython, a cross-platform GUI toolkit. The program was developed on Windows 10 and tested on macOS Catalina. In theory, the program should work on Linux based operating systems such as Ubuntu, but this has not been tested. Executable versions of the code were built using PyInstaller. The version described in this report is an alpha version that is still in development. It has only been tested by the developer.

97 MATHEMATICS AND COMPUTING↗

X-ray Source Characteristics from July 2020 SGEMP Experiments at the National Ignition Facility

This report details the measured x-ray characteristics radiating from laser targets on 7 shots at Lawrence Livermore National Laboratory's National Ignition Facility performed June 30 - July 2, 2020. Generally, the x-ray sources were designed to serve as meaningful drivers of a variety of Radiation Effects Sciences response experiments. Specifically, on these 7 shots, the measured x-ray output characteristics and the response experiments serve as a useful data set for validating performance and informing further development of Sandia National Laboratories' EMPIRE code. We present x-ray measurements and analyses relevant to simulating the System-Generated Electro Magnetic Pulse experiments that also occurred on these shots (described elsewhere). Sufficient detail is provided so that a motivated, but novice, x-ray source user could produce some of these analysis results from raw data on similar x-ray shots.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Atomistic theories and Simulations of Multiferroics

The goal of this award was to build a research program aimed at investigating puzzling complex phenomena in multiferroics, that are systems possessing electric and magnetic dipoles. We first emphasized the study of multiferroic nanostructures, that are 0D, 1D, 2D systems as well as superlattices and then also study multiferroics as a whole, i.e., bulks as well. In order to fully understand such complex systems, we also decided to study magnetic systems and ferroelectrics, both in their nanostructure and bulk forms. For that and in addition to use standard Density Functional Theory codes, we developed and used ab-initio tools that are able to model properties of large supercells (about a million atoms nowadays) at finite temperature and for any mechanical and boundary conditions. We also collaborated with experimentalists to fully understand the systems under study. The whole program resulted in 108 publications that are listed at the end of this report. In the following, I will put an emphasis on some publications before the last award period and also indicate a description of the last award period.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Human Liver Epithelial Cells (HuH7) Response to HCoV-229E Infection Epigenomics (ATAC-Seq) (ACS-DP4)

The purpose of this experiment was to evaluate how wild-type Human coronavirus strain 229E (HCoV-299E) infection alters chromatin accessibility in infected cells. Sample data was obtained from mock-infected cells, UV-inactivated virus treated cells, and replication competent HCoV-229E infected immortalized human liver cells (HuH7) at 24 hours post infection. Samples were processed using ATAC-seq methods for reported bar coded libraries. Sample data was acquired using an Illumina Hi-Seq 2500 sequencer system and further processed for ATAC-Seq expression analysis.

59 BASIC BIOLOGICAL SCIENCES↗

Advancing 1D thermo-hydraulic tools for large cryogenic facilities

The Cryogenic Division at Fermilab develops large-scale cryogenic systems for particle accelerators and superconducting test facilities. To support design and diagnostics, a Python-based code was created to calculate pressure drops in components such as valves and pipes. This paper presents recent enhancements to the code, including new heat transfer functions that improve the accuracy of thermal and hydraulic predictions. The first application models pressure and temperature changes in PIP-II relief pipes, aiding pipe sizing and protecting relief valves. The second example analyzes heat load evolution in a pipe carrying sub-atmospheric helium, helping interpret temperature sensor data and understand gas return behavior to cold compressors. These improvements significantly expand the tool’s capabilities, offering a practical resource for designing and troubleshooting cryogenic systems under dynamic thermal and flow conditions.

Beckwith, Rosalyn [Fermilab]↗

Development of a Reference Model for Molten-Salt-Cooled Pebble-Bed Reactor Using SAM

To support the development and utilization of the SAM code for fluoride-salt-cooled high-temperature pebble-bed reactor (PB-FHR) safety analysis and licensing, an effort was devoted to developing reference models for PB-FHR primary loop and the reactor cavity cooling system (RCCS). A reference standard problem of a prototypical reactor design is foundational to NRC and industry to verify the adequacy of computer codes and evaluation models for a specific reactor type. The SAM code was enhanced for the reference PB-FHR model development, including a 1D-3D flow coupling scheme and conjugate heat transfer between porous media and solid structures. The reference FHR primary loop model was developed based on the UC Berkeley Mk1 FHR design with additional design features from the Kairos Power’s KP-FHR core. The PB-FHR core is modeled by a two-dimensional porous medium while the rest of the primary loop is represented by a SAM one-dimensional model. A SAM one-dimensional primary loop model was also developed for comparison using a single channel approach for the reactor core. Furthermore, the water-based NSTF cavity was modeled using SAM multi-dimensional flow module, to assist in evaluating SAM capabilities of modeling the emergency heat removal systems relying on RCCS concepts.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Disrupting EV Charging Sessions and Gaining Remote Code Execution with DoS, MITM, and Code Injection Exploits using OCPP 1.6

Open Charge Point Protocol (OCPP) 1.6 is widely used in the electric vehicle (EV) charging industry to communicate between Charging System Management Services (CSMSs) and Electric Vehicle Supply Equipment (EVSE). Unlike OCPP 2.0.1, OCPP 1.6 uses unencrypted websocket communications to exchange information between EVSE devices and an onpremise or cloud-based CSMS. In this work, we demonstrate two machine-in-the-middle (MITM) attacks on OCPP sessions to terminate charging sessions and gain root access to the EVSE equipment via remote code execution (RCE). Second, we demonstrate a malicious firmware update with a code injection payload to compromise an EVSE. Lastly, we demonstrate two methods to prevent availability of the EVSE or CSMS. One of these, originally reported by SaiFlow, prevents traffic to legitimate EVSE equipment using a DoS-like attack on CSMSs by repeatedly connecting and authenticating several CPs with the same identities as the legitimate CP. These vulnerabilities were demonstrated with proof-of-concept exploits in a virtualized Cyber Range at Wright State University and/or with a 350 kW Direct Current Fast Charger (DCFC) at Idaho National Laboratory. The team found that OCPP 1.6 could be protected from these attacks by adding secure shell (SSH) tunnels to the protocol, if upgrading to OCPP 2.0.1 was not an option. Index Terms—Electric vehicle charging, cybersecurity, OCPP, cyberattack, cyber-resilience. INSPEC Accession Number: 23981565

99 GENERAL AND MISCELLANEOUS↗

Fox Trails

1. This software utilizes python pandas to pull data from P6 databases or XER files. The software transforms the datasets into multiple main tables by joining, filtering, iteratively flattening hierarchical structured data, and pivoting datasets to give simple flat output tables. The activity table includes all of the information related to an activity including activity codes, global, EPS, and project codes, UDFs, and WBS information as separate columns. This includes the code id, code value and sequence number for all levels in hierarchical codes. The resource table is similar to the activity table and includes all of the information related to resources on activities including UPFs and resource codes. The resource time phased table takes the resource information and time phases it for the budget, forecast, late, and actual dates/units/costs that closely matches P6's user interface's values as it implements the resource curve and calendars. The wbs table contains the WBS structure broken out by levels and includes UDFs, codes, and notebook topics. The final P6 data table is the relationships table which simply contains the relationships. 2. When a user updates the tool with data (via giving it P6 project names with database username/password information or XER files) the system creates the data in #1, then creates a networkx graph with the activity data imbedded in the node data and the relationships added as edges. Each edge also has it's float calculated (working time distance between the predecessor and successor) and attached to the edge. Activities are also tagged as a potential start of a path based on their constraints, constraint dates, remaining start date, and activity status. When a user enters an activity ID into the UI, it runs a shortest path calculation on the network graph between each node tagged as potential start to the entered activity id based on the float tagged on the edge. Each path returned by the algorithm contains all of the nodes on the path in order, as well as the total float of the edges that make the path. This data is then collected and returned to the user in the form of a gantt chart with groupings for each path that includes the total float for each group. 3. Similar to 2, if the user passes through a reference dataset each activity set in the path is checked to see if it had a path in the reference dataset, if that path was the primary path between the start and end activities, and what has changed regarding logic and durations. These changes are color coded and summarized before sent to the user to be displayed by the UI for simple discovery. 4. Utilizing the data from #1, the user can submit desired grouping code(s) and filters to the system. The system will then pull the activities, resources, and relationships and create a gantt chart based on the groupings sent and filtered based on the filters sent. 5. The system will produce a gantt chart in a similar method to #4, but allows interactivity with the data. As the user interacts with the gantt chart, the software captures the changes and stores it with the user making the change so that project controls and implement those changes in P6.

Fox, Ben↗

Domesticating a food spoilage yeast into an organic acid–tolerant metabolic engineering host: Lactic acid production by engineered Zygosaccharomyces bailii

Lactic acid represents an important class of commodity chemicals, which can be produced by microbial cell factories. However, due to the toxicity of lactic acid at lower pH, microbial production requires the usage of neutralizing agents to maintain neutral pH. Zygosaccharomyces bailii, a food spoilage yeast, can grow under the presence of organic acids used as food preservatives. This unique trait of the yeast might be useful for producing lactic acid. With the goal of domesticating the organic acid!tolerant yeast as a metabolic engineering host, seven Z. bailii strains were screened in a minimal medium with 10 g/L of acetic, or 60 g/L of lactic acid at pH 3. The Z. bailii NRRL Y7239 strain was selected as the most robust strain to be en- gineered for lactic acid production. By applying a PAN!ARS!based CRISPR!Cas9 system consisting of a transfer RNA promoter and NAT selection, we demonstrated the targeted deletion of ADE2 and site!specific integration of Rhizopus oryzae ldhA coding for lactate dehydrogenase into the PDC1 locus. The resulting pdc1::ldhA strain produced 35 g/L of lactic acid without ethanol production. Here, this study de- monstrates the feasibility of the CRISPR!Cas9 system in Z. bailii, which can be applied for a fundamental study of the species.

59 BASIC BIOLOGICAL SCIENCES↗

Progress in the HTTF Benchmark and RELAP5-3D Gas-Cooled Reactor Validation

This slide set presents results of analysis done in the first year after the kickoff of the HTTF benchmark. This work includes the development of a new RELAP5-3D model of the facility and collection and presentation of results from one of the exercises in the benchmark. Highlights include good agreement between the new and legacy models for full-power steady state and similar predictions of maximum block temperature during a pressurized conduction cooldown. Additionally, code-to-code comparisons of a full-power steady state and depressurized conduction cooldown (DCC) from full-power steady state as part of Problem 2 Exercises 1A and 1B show good agreement on temperatures predicted in the core but considerable spread in central reflector temperatures. During the DCC, temperature behavior is similar across all models, but cooldown rates are dictated by the performance of the reactor cavity cooling system

22 GENERAL STUDIES OF NUCLEAR REACTORS↗