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Here we continue our exploration of novel genomes discovered in module 1. We will explore different approaches for examining the genome sequence and annotation data, investigating the best approaches for answering our question: Do benthic microbes have functioning circadian clocks?
Ionizing radiation (IR) is lethal to most organisms at high doses, damaging every cellular macromolecule via induction of reactive oxygen species (ROS). Utilizing experimental evolution and continuing previous work, we have generated the most IR-resistant Escherichia coli populations developed to date. After 100 cycles of selection, the dose required to kill 99% the four replicate populations (IR9-100, IR10-100, IR11-100, and IR12-100) has increased from 750 Gy to approximately 3,000 Gy. Fitness trade-offs, specialization, and clonal interference are evident. Long-lived competing sub-populations are present in three of the four lineages. In IR9, one lineage accumulates the heme precursor, porphyrin, leading to generation of yellow-brown colonies. Major genomic alterations are present. IR9 and IR10 exhibit major deletions and/or duplications proximal to the chromosome replication terminus. Contributions to IR resistance have expanded beyond the alterations in DNA repair systems documented previously. Variants of proteins involved in ATP synthesis (AtpA), iron-sulfur cluster biogenesis (SufD) and cadaverine synthesis (CadA) each contribute to IR resistance in IR9-100. Major genomic and physiological changes are emerging. An isolate from IR10 exhibits protein protection from ROS similar to the extremely radiation resistant bacterium Deinococcus radiodurans, without evident changes in cellular metal homeostasis. Selection is continuing with no limit to IR resistance in evidence as our E. coli populations approach levels of IR resistance typical of D. radiodurans.
Problem Statement: There is a pervasive talent deficit in the cybersecurity industry that prevents employers from being able to fill their open positions efficiently. A holistic approach to security is required to ensure organizations have adequate prevention and response capabilities in case of a cyberattack. Specifically, industrial control systems (ICS’s) and their operational technology (OT) components have become a constant target for cyberattacks. Research Questions: It is proposed that the NICE Framework should be extended in the following areas: 1) Include guidance regarding the job roles and competencies for both IT and OT professionals. 2) Offer step-by-step solutions, based on the work role mappings from the NICE Framework, to increase cybersecurity through employee training and education. 3) Provide a streamlined, lifecycle approach to building a cybersecurity program. Contribution: The CYBER security – Competency Health and Maturity Progression (CYBER-CHAMP©) model provides a customized solution for businesses to understand their education gaps in organizational security and target areas for improvement. Rationale: The Framework for Improving Critical Infrastructure Cybersecurity v1.1 addresses ICS but does not offer a measurement of cybersecurity maturity or clear methods to ascertain an organization’s current risk profile. In Phases 1 and 5 of the model, measurements are provided to help an organization build their current and target risk profiles. The NICE framework provides a structure for planning an IT cybersecurity workforce, but the OT aspects of cybersecurity are only briefly discussed. The model uses Phases 2-3 to examine the competencies of an organization’s workforce, which includes both IT and OT roles. Current frameworks do not offer next steps to increase an organization’s cybersecurity. During Phase 4, employees’ roles are mapped to training, education, and/or certifications from common vendors. Investigative Approach: The model provides measurements and metrics for both an organization’s status and continual improvement. This improvement methodology includes guidance for creating an overall strategic plan for security improvement via products designed to increase an organization’s operational readiness through workforce competency health. Lessons Learned: Depending on who was participating, there were contradicting answers given in Phase 1 due to different security cultures in the organization. This revelation has influenced the steps listed in the User’s Guide, where Phase 1’s first recommended step is to assemble a team that champions the facilitation and implementation of the model in the organization. During Phase 2, the discovery was made that organizations may be missing roles that are necessary to perform critical cybersecurity functions. By understanding the functional roles and competencies needed, they can contract or hire cybersecurity help to fill these gaps. Implications: Using the model, organizations can discuss quantitative measures for improvement as a business case for advancing their security program. Future research can validate and extend the present theory and model to a variety of environments. It is of interest to investigate additional security roles and knowledge domains that are used to build standardized cybersecurity curriculum.
Abstract One of the major challenges in large‐domain hydrological modeling efforts lies in the estimation of spatially distributed hydrological parameters while simultaneously accounting for their associated uncertainties. Addressing this challenge is particularly difficult in ungauged locations. With growing societal demands for large‐scale streamflow projections to inform water resource management and long‐term planning, evaluating and constraining hydrological parameter uncertainty is increasingly vital. This study introduces a hybrid regionalization approach to enhance hydrological predictions of the Community Land Model version 5 (CLM5) across the Continental United States (CONUS), with a total of 50,629 1/8° grid cells. This hybrid method combines the strengths of two existing techniques: parameter regionalization and streamflow signature regionalization. It identifies ensemble behavioral parameters for each 1/8° grid cell across the CONUS domain, tailored to three distinct streamflow signatures focused on low flows, high flows, and annual water balance. Evaluating this hybrid method for 464 CAMELS (Catchment Attributes and Meteorology for Large‐sample Studies) basins demonstrates a significant improvement in CLM5 hydrological predictions, even in challenging arid regions. In CONUS applications, the derived spatially distributed parameter sets capture both spatial continuity and variation of parameters, highlighting their heterogeneous nature within specific regions. Overall, this hybrid regionalization approach offers a promising solution to the complex task of improving hydrological modeling over large domains for important hydrological applications.
In this work, we investigate the applicability and relative merit of discrete and continuous versions of physics-informed neural network (PINN) methods for learning unknown governing equations or constitutive relations in a nonlinear dynamical system. In the case of unknown dynamics, entire right-hand-side (RHS) equations of the ordinary differential equations are unknown. In the case of unknown constitutive relations, however, the RHS equations are known up to the specification of constitutive relations (that may depend on the state of the system). We use a deep neural network to model unknown governing equations or constitutive relations. The discrete PINN approach combines classical multistep discretization methods for dynamical systems with neural-network-based machine learning methods. On the other hand, the continuous versions utilize deep neural networks to minimize the residual function for the continuous governing equations. We use the case of a fedbatch bioreactor system to study the effectiveness of these approaches and discuss conditions for their applicability. Our results indicate that the accuracy of the trained neural network models is much higher for the cases where we only have to learn a constitutive relation instead of all dynamics. This finding corroborates the well-known fact from scientific computing that building as much structural information as is available into an algorithm can enhance its efficiency and/or accuracy.
This work presents the development of a multistaged stabilized continuation for the three-dimensional unpowered hypersonic trajectory planning problem using indirect optimal control methods. The stabilized continuation method is noniterative and guaranteed to terminate within a finite number of floating point operations, thereby making it well suited for onboard autonomous implementations. Here, we present a multistage formulation of the stabilized continuation scheme that involves starting with a “loose” integration tolerance during the first stage and ramping up toward a “strict” integration tolerance through subsequent stages. An important benefit of this approach is that even when the solution to the underlying optimal control problem is numerically unstable, such as with the hypersonic vehicle footprint generation problem, the stabilized continuation algorithm is shown to be successful in finding a solution while providing some additional insights into the underlying cause of the numerical instability.
Hard-x-ray photoelectron spectroscopy (HAXPES) is a valuable source of information on band-edge profiles deep inside semiconductor thin films and heterojunctions. However, extracting this information requires robust and physically meaningful decomposition of spectra into contributions from individual atomic planes. We present an approach that utilizes the physical requirements of a monotonic dependence of the built-in electrostatic potential on depth and continuity of the potential function and its derivatives. These constraints enable efficient extraction of band-edge profiles and allow one to capture details of the electronic structure, including determination of the signs and magnitudes of the band bending as well as the valence band offsets. The utility of this approach to generate quantitative insight into the electronic structure of complex materials is illustrated for epitaxial SrTiO 3 on intrinsic Si(001).
Radiation portal monitors (RPMs) are widely used at border security checkpoints to detect the presence of radioactive materials in people, vehicles, and cargo. Typically, RPM detection systems consist of two pillars equipped with gamma and neutron detectors. To improve detection efficiency, RPMs employ techniques such as a limited energy window, dynamic alarm thresholds, and lead shielding. However, without continuous monitoring of background radiation, signal interpretation can be compromised, because environmental factors and mechanical failures can cause fluctuations. Here, we introduce a daily file format that logs gamma background and neutron background radiation levels continuously over a 24 h period; this format is different from traditional formats that record data only when the RPM is active or occupied. The approach enables RPM operators and analysts to (1) identify and diagnose malfunctioning components, (2) adjust system settings to account for dynamic environmental factors, and (3) use the recorded data to characterize outer space phenomena. Continuous background reporting is essential for identifying issues such as faulty connections, voltage divider failures, and errors in background updates. Continuous background reporting also enables the detection of external influences, including nearby X-ray scanners, temperature fluctuations, rainfall, cosmic radiation, and lunar phase changes. These data files are designed to be easily evaluated and parsed using common tools, and a quick review by an expert is often sufficient for problem diagnosis. We anticipate that continuous background radiation monitoring and these new strategies will significantly improve the accuracy and reliability of RPM systems, reducing the rate of false alarms and enhancing overall system performance.
In the Central Plateau at the U.S. Department of Energy Hanford Site, a large inventory of contaminants resides in unsaturated sediments within the approximately 100-meter-thick vadose zone, posing a potential continuing risk to groundwater. Vadose zone remedies used to address these contaminants will require performance monitoring to provide feedback during implementation and for long-term verification that remedial action objectives have been met. Passive approaches may also need long-term monitoring to demonstrate that the flux of contaminants from the vadose zone to the groundwater are below thresholds established to meet groundwater protection goals. Collection of physical (e.g., groundwater or sediment) samples is a common method for identifying contaminant concentration distributions, but this approach is limited by the number of locations and the frequency with which data can be collected. In situ vadose zone measurements have evolved over the past few years to include key measurements of water content, soil water pressure, temperature, and chemical concentration. However, the current generation of sensors is designed for relatively short-term use in near-surface soils or sediments. Geophysical methods have been evolving but are also limited in that they have not been designed for the specific long-term vadose zone monitoring needs at the Hanford Site. Overall, monitoring under unsaturated conditions can be difficult due to the need to install and maintain instrumentation over a large area and depth and the need to identify preferential flow pathways due to geologic and chemical heterogeneities over long periods. Thus, a vadose zone monitoring test bed was initiated to address these challenges and identify cost-effective approaches for implementation and postclosure monitoring of the deep vadose zone. The monitoring test bed is expected to provide valuable field-scale information for the design of vadose zone monitoring systems. (authors)
Recent global interest in pyroprocessing and molten salt reactors has brought salt sampling methods and techniques back to the forefront of nuclear safeguards concerns. Issues with uranium supplies have also encouraged various countries to pursue advanced nuclear fuel cycles. Tracking nuclear material in molten salt has proven to be a challenge and updating molten salt sampling will greatly help in this endeavor. Molten salt is problematic to sample due to salt stratification, lack of homogeneity, solids, and difficulty with hot cell adaptations. Various salt sampling techniques have been used since before the 1960s including surface, spoon/spatula, and bar solidification. Since then, new types of sampling techniques have been developed to improve sampling results. These include rod/dip, pipet, suction, filtered sampling along with devices such as the Valve Core Sampler and the Multi-Level Sampler. These different approaches are being analyzed and improved upon along with developing requirements for an improved salt sampling device. Work continues to develop salt samplers that are more robust, easier to segment, collect at a specific depth, can work with filters, and can collect fines. Sampling parameters are also being narrowed in terms of stirring, settling time, filtration, depth, etc. In the future, we hope to address deficiencies for process control and nuclear material accountancy control by determining the best way to collect samples that minimizes contaminants and is representative. A compilation of salt sampling approaches, analyses techniques, and an evaluation of findings will be presented.
Continuous manufacturing (CM) has been used to produce several immediate release drug products. No extended-release (ER) product manufactured employing CM technology has been approved yet. Herein this study investigated the critical aspects of switching from the batch mode of high shear granulation to the continuous operation of twin-screw granulation for extended-release tablets. Metoprolol succinate ER tablets was used as a model ER formulation for this purpose. A central composite design (CCD) was employed to determine the effects of high shear granulator (HSG) parameters, namely impeller speed, granulation time, and binder liquid feeding rate, on the critical granulation characteristics important for product performance. These critical granulation characteristics served as a guide for switching from the batch processing to the continuous operation for achieving the same breaking strength and dissolution for this ER metoprolol tablets. The granulation time was the most critical factor affecting the bulk properties of granules which contributed to tablet dissolution. The higher density and lower compressibility of granules were attained at the longest granulation time of 5.4 min with the fastest liquid feeding rate of 75 g/min. The granules’ density was the primary factor negatively affecting the dissolution of metoprolol tablets. However, the breaking strength of tablets confounded the effect of granules density on metoprolol dissolution. Switching the processing parameters of high shear granulation to twin-screw granulation achieved similar dissolution profiles (F2 greater than 50). The screw speed was not found to affect bulk properties of granules. The root cause of granulation failures in twin-screw granulation, such as premature consolidation, excessive swelling, poor cohesion, inconsistent shearing effects, and formation of deformed agglomerates, were identified. In conclusion, the use of critical granulation characteristics through a performance-based approach of ER tablets facilitated the switching of manufacturing of an ER formulation form batch to continuous operation.
Solar-driven photocatalytic generation of H 2 O 2 over metal-free catalysts is a sustainable approach for value-added chemical production. Here, we synthesized chlorine-doped graphitic carbon nitride (Cl-doped g-C 3 N 4 ) through a solvothermal method to effectively produce H 2 O 2 with a rate of 1.19 ± 0.06 µM min –1 under visible light irradiation, which was improved by 104 times compared to pristine g-C 3 N 4 . Continuous net production of H 2 O 2 was realized at a rate of 2.78 ± 0.10 µM min –1 up to 54 h with isopropanol as the hole scavenger, whereas H 2 O 2 production was only sustained for ~ 6 h without scavengers. Both molecular simulations and advanced spectroscopic characterizations elucidated that the Cl dopant increased the charge transfer rate, decreased the bandgap, and reduced the activation energy of the rate-limiting step of O 2 reduction, all of which favored H 2 O 2 production. Furthermore, this work implemented a novel metal-free photocatalyst for sustainable H 2 O 2 production and elucidated the mechanism for promoting H 2 O 2 production that can guide future photoreactive nanomaterial design.
Background: The nuclear shell model is a powerful framework for predicting nuclear structure observables, but relies on interaction matrix elements fit to experimental data as its inputs. Extending the shell model's applicability, particularly toward dripline nuclei, requires efficient fitting methods and credible uncertainty quantification. Traditional approaches face computational challenges and may underestimate uncertainties. Purpose: We develop and test a framework combining eigenvector continuation and Markov chain Monte Carlo to efficiently fit shell model interaction matrix elements and quantify their uncertainties. Methods: Eigenvector continuation is used to emulate shell model calculations, reducing computational costs. The emulator enables Markov chain Monte Carlo sampling to optimize interaction matrix elements and rigorously assess parametric uncertainties. Here, the framework is benchmarked using the USDB interaction in the 𝑠𝑑 shell. Results: The emulator reproduces the USDB interaction with negligible error, validating its use in shell model fitting applications. However, we find that to obtain credible predictive intervals, the model defect of the shell model itself, rather than experimental or emulator error, must be taken into account in order to obtain credible uncertainties. Conclusions: The proposed framework provides an efficient and rigorous approach for fitting shell model interactions and quantifying uncertainties. Further, the normality assumption used in the past appears sufficient to describe the distribution of interaction matrix elements. However, it is crucial to account for model correlations to avoid underestimating uncertainties.
Microelectronics are the cornerstone of the modern world, enhancing our daily lives by providing services such as communications and datacenters. These resources are accessible thanks to the continual pursuit of a deeper understanding of the chemical and physical phenomena underlying the materials synthesis approaches and fabrication processes used to create microelectronic components and subsequently the components' responses to electrical, optical, and other stimuli that are utilized within microelectronic systems. Today, further development of microelectronics requires multidisciplinary expertise across scientific disciplines and fields of study—synthesis, materials characterization, nanoscale fabrication, and performance characterization—with focus placed on comprehending the nanoscale forms and features of microelectronic components. The Nanoscale Science Research Centers (NSRCs) are Department of Energy, Office of Science user facilities that support the international scientific community in advancing nanoscale science and technology. As a key component of the U.S. Government's National Nanotechnology Initiative, the NSRCs enable transformative discoveries by providing world-class facilities, expertise, and collaborative opportunities. Here, in this perspective, we showcase a non-exhaustive cross-section of the capabilities housed at and developed by the NSRCs and their user communities to address fundamental synthesis, metrology, fabrication, and performance considerations toward advancing the development of new microelectronics. Finally, we provide a timely outlook on the next major areas of necessary development in nanoscale sciences to continue the innovation of microelectronics into the next generation.
Abstract COVID‐19, caused by SARS‐CoV‐2 infection, continues to be a major public health crisis around the globe. Development of vaccines and the first cluster of antiviral drugs has brought promise and hope for prevention and treatment of severe coronavirus disease. However, continued development of newer, safer, and more effective antiviral drugs are critically important to combat COVID‐19 and counter the looming pathogenic variants. Studies of the coronavirus life cycle revealed several important biochemical targets for drug development. In the present review, we focus on recent drug design and medicinal chemistry efforts in small molecule drug discovery, including the development of nirmatrelvir that targets viral protein synthesis and remdesivir and molnupiravir that target viral RdRp. These are recent FDA approved drugs for the treatment of COVID‐19.
With the goal of maximizing plant reliability and availability, complex systems such as nuclear power plants continuously monitor and record the performance and the health status of many components, assets, and systems. Such data may take the form of online monitoring data, condition reports, and maintenance reports and it carries the potential to provide system engineers with insights into anomalous behaviors or degradation trends as well as the possible causes behind them and to predict their direct consequences. The analysis of such data poses however few challenges. While some of these challenges are technical in nature (i.e., data are often distributed over several physical servers or databases), others are conceptual in nature (i.e., data elements come in different formats, numeric or textual), and measured values have different scales (e.g., vibration spectra and oil temperature). This paper directly tackles these challenges, and it focuses on the integration of all these data elements in order to assist plant system engineers in analyzing component, assets, and systems performances and optimize maintenance activities. This is performed by 1) extracting knowledge from textual data via technical language processing methods, and 2) quantifying system, asset, and component health from numeric condition-based data. We rely on model-based system engineering (MBSE) models of systems and assets to identify their architecture and functional (i.e., cause and effect) relations. Numeric and textual data elements are then associated with an MBSE graph element, based on their nature. This bonding of MBSE models and data elements constitutes a first-of-its-kind knowledge graph of a nuclear power plants system, with data elements being organized in a structured manner that enables system engineers to identify cause-effect trends in data elements and carry out appropriate actions in response.
Since hydride microstructure can significantly influence Zr alloy nuclear fuel cladding’s ductility, a new metric has been developed to quantify hydride microstructure in 2D micrographs and relate it to crack propagation. As cladding failure usually results from a hoop stress, this new metric, called the Radial Hydride Continuous Path (RHCP), is based on quantifying the continuity of brittle hydride particles along the radial direction of the cladding tube. Compared to previous metrics, this approach more closely relates to the propensity of a crack to propagate radially through the cladding tube thickness. The RHCP takes into account hydride length, orientation, and connectivity to choose the optimal path for crack propagation through the cladding thickness. The RHCP can therefore be more closely linked to hydride embrittlement of the Zr alloy material, thus creating a relationship between material structure, properties, and performance. The new definition, along with previously proposed metrics such as the Radial Hydride Fraction (RHF), the Hydride Continuity Coefficient (HCC), and the Radial Hydride Continuity Factor (RHCF), have been implemented and automated in MATLAB. These codes are made available with this publication as supplementary materials. These metrics were verified by comparing their predictions of hydride morphology against expected values in simple cases, and the implementation of the new metric was validated by comparing its predictions with manual measurements of hydride microstructure performed on ImageJ. The RHCP was also validated against experimental measurements of fracture behavior and it was shown to correlate with cladding failure better than previous metrics. The information provided by these metrics will help accurately assess cladding integrity during operation, transportation, and storage.
Cold spray deposition of Inconel nickel alloys has emerged as a promising strategy for mitigating cavitation erosion in hydropower facilities. Most prior developments employ helium (He) as the carrier gas because it enables high particle velocities and the formation of dense coatings. However, He is nearly two orders of magnitude more expensive than nitrogen (N2), which limits its widespread adoption in the hydropower sector. Although He-based cold spray can be justified for high value repairs, the lower cost and broad availability of N2 make it an attractive alternative. This study assesses the feasibility of N2-based cold spray of Inconel 625 powders for hydropower applications. Cavitation erosion testing shows that He-based coating exhibits cavitation resistance of ~398% relative to the 304L stainless steel (SS304L) substrate. In contrast, N2-based coating shows substantially lower cavitation resistance, reaching only ~69% of the SS304L substrate, even when higher carrier gas temperature and pressure are applied. When the Inconel 625 powder size is reduced from 44 to 22 µm under N2-based cold spray conditions, cavitation resistance increases significantly to ~148% of the SS304L substrate. Additional improvement can be obtained by incorporating fine chromium carbide powders into the feedstock, resulting in cavitation resistance of ~172% of the SS304L substrate. Overall, with optimized feedstock design, N2-based cold spray offers a practical and cost-effective approach for producing cavitation resistant coatings on hydropower components, although He-based cold spray continues to deliver higher cavitation resistance.