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At least 73 records · Page 4

Persistent minimal sequences of SARS-CoV-2

Abstract Motivation Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 14 million cases and more than half million deaths. Given the absence of implemented therapies, new analysis, diagnosis and therapeutics are of great importance. Results Analysis of SARS-CoV-2 genomes from the current outbreak reveals the presence of short persistent DNA/RNA sequences that are absent from the human genome and transcriptome (PmRAWs). For the PmRAWs with length 12, only four exist at the same location in all SARS-CoV-2. At the gene level, we found one PmRAW of size 13 at the Spike glycoprotein coding sequence. This protein is fundamental for binding in human ACE2 and further use as an entry receptor to invade target cells. Applying protein structural prediction, we localized this PmRAW at the surface of the Spike protein, providing a potential targeted vector for diagnostics and therapeutics. In addition, we show a new pattern of relative absent words (RAWs), characterized by the progressive increase of GC content (Guanine and Cytosine) according to the decrease of RAWs length, contrarily to the virus and host genome distributions. New analysis shows the same property during the Ebola virus outbreak. At a computational level, we improved the alignment-free method to identify pathogen-specific signatures in balance with GC measures and removed previous size limitations. Availability and implementation https://github.com/cobilab/eagle. Supplementary information Supplementary data are available at Bioinformatics online.

Pratas, Diogo↗

Polarized vector oscillons

Oscillons are spatially localized, time-periodic, and long-lived configurations that were primarily proposed in scalar field theories with attractive self-interactions. In this paper, we demonstrate that oscillons also exist in the low-energy effective theory of an interacting massive (real) vector field. We provide two types of vector oscillons with vanishing orbital angular momentum, and approximately spherically symmetric energy density, but not field configurations. These are: (1) “directional” oscillons (linearly polarized), with vanishing total intrinsic spin, and (2) “spinning” oscillons (circularly polarized) with a macroscopic intrinsic spin equal to ℏ× number of particles in the oscillon. In contrast to the case with only gravitational interactions, the two oscillons have different energy at a fixed particle number even in the nonrelativistic limit. By carrying out relativistic 3+1d simulations, we show that these oscillons can be long-lived (compared to the oscillation time for the fields), and can arise from a range of Gaussian initial spatial profiles. These considerations make vector oscillons potentially relevant during the early universe and in dark photon dark matter, with novel phenomenology related to their polarization.

79 ASTRONOMY AND ASTROPHYSICS↗

Characterizing Vulnerabilities Associated with Connected Lighting: Exploring Authorization Protocols

Cities are upgrading their infrastructure and converting traditional indoor and outdoor luminaires to Connected Lighting Systems equipped with sensors in an aggressive effort to reduce energy consumption, increase sustainability, and improve the quality of life. When you take something seemingly benign like a lighting system and connect it to the internet, if improperly secured a potential attack vector for hackers is created. Hackers could then access sensitive information, pivot into other networks, shut down services, or enslave devices to do their bidding. In attempt to close this attack vector and secure these systems, this paper extends previous work that investigated, compared and contrasted authentication vulnerabilities in Connected Lighting Systems that identified the need for additional testing and improved test method documentation. One additional authentication test and four new authorization tests were developed utilizing the Open Web Application Security Project (OWASP) as a test development and documentation guide. The new tests were integrated with the previous work to develop an updated test method with a focus on describing test procedures to make them easy to understand and repeat. In addition, a first Connected Lighting System use case was established to begin developing threat profiles that will aid in the identification of vulnerabilities whose focus areas extend beyond authentication and authorization. This use case describes the generation and flow of CLS data which assists in specifying methods to harden CLSs from outside interference and exploitation that can be implemented immediately on existing CLSs and as new products come to market.

97 MATHEMATICS AND COMPUTING↗

Ultrasound Interim cyber-physical research evaluation

Recent events have presented Medical Practitioners with concerns about safety and privacy implications associated with GE’s VScan MIot Ultrasound Device. Concerns relate to the devices potential risk to broadcast location data that can pose serious risks to device users and patients. This report was commission in collaboration with Augusta University to determine if device concerns pose real threat to operators and patients. In effort to ensure all potential threat vectors are targeted, the initial step was to analyze the supply chain. Here the devices are CT scanned to look for any hardware anomalies that could present threat vectors to users of these devices. (See SRNL-STI-2024-00225 for detailed analysis). No anomalies were found associated with the hardware utilized within the GE VScan Air.

42 ENGINEERING↗

Retrieval Augmented Generation for Robust Cyber Defense

In cybersecurity, the ability to efficiently analyze and respond to vulnerabilities, weaknesses, attack patterns, and threat tactics is critical for effective defense strategies. With the increasing complexity and volume of cybersecurity data, traditional methods of querying and retrieving information are often inadequate. To address this challenge, we implemented Retrieval-Augmented Generation (RAG) systems—CyRAG and GraphCyRAG—that integrate large language models (LLMs) with both structured data from relational databases and knowledge graphs such as Neo4j. CyRAG is designed to handle structured data, focusing on CVE (Common Vulnerabilities and Exposures) and CWE (Common Weakness Enumeration) entities to generate accurate and context-rich responses. In contrast, GraphCyRAG leverages Neo4j knowledge graphs to retrieve interconnected information from CVE, CWE, CAPEC (Common Attack Pattern Enumeration and Classification), and ATT&CK (Adversarial Tactics, Techniques, and Common Knowledge) datasets. By utilizing Neo4j’s graph-based framework, GraphCyRAG enables deeper traversal of relationships between vulnerabilities and attack patterns, providing cybersecurity analysts with more comprehensive insights into potential attack vectors and mitigation strategies. Our preliminary results demonstrate that integrating knowledge graphs with RAG significantly enhances both the accuracy and depth of threat analysis, allowing for the retrieval of dynamic, real-time data and the generation of contextually aware responses. This approach helps analysts uncover hidden relationships between cyber entities, predict exploit paths, and prioritize mitigation efforts effectively. The integration of RAG with cybersecurity knowledge graphs represents a significant advancement in cybersecurity threat intelligence, enabling more informed decision-making and stronger defense strategies.

97 MATHEMATICS AND COMPUTING↗

DEReliction: A Cybersecurity Vulnerability Assessment Methodology for Distributed Energy Resources

With the increasing integration of Distributed Energy Resources (DER) into the electric grid, maintaining grid reliability and resilience requires that these devices remain secure. This paper discusses a cybersecurity vulnerability assessment methodology that incorporates best practices from Sandia National Laboratories, SANS Institute, OWASP Foundation, and other web and Internet of Things (IoT) penetration testing (“pen testing”) programs, courses, and frameworks for assessing the security posture of devices. The methodology involves five sequential steps: (1) Collect Public Information, (2) Extract Hardware Details, (3) Inventory Software Components, (4) Identify Vulnerabilities, and (5) Test Vulnerabilities. Each step uncovers potential weaknesses in both hardware and software components of DER devices, considering adversary tactics, techniques, and procedures (TTPs), and potential attack vectors along the way. The results from the execution of this method on multiple residential- and small commercial-scale photovoltaic (PV) inverters reveled hardware and software vulnerabilities, which highlight the benefit of taking a methodical approach to discover vulnerabilities. While the specific vulnerability details are not shared here, a generalized overview of findings underscore the importance of robust security assessments for DER devices. Adoption of an assessment framework of this kind will identify and mitigate cybersecurity threats and bolster the resilience of DER-integrated electric grids.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DECOVALEX-2023: Task E Final Report

This is the Task E final report for DECOVALEX-2023. Task E is focused on understanding thermal, two-phase hydrological, and mechanical (TH2M) processes, especially related to predicting brine migration in the excavation damaged zone around a heated excavation in salt. Salt is attractive as a disposal medium for radioactive waste because it is self-healing and is essentially impermeable and essentially non-porous in the far field (away from excavations). Investigation of the short-term (days to years) near-field (centimeters to tens of meters) behavior of salt is important for radioactive waste disposal because this early period strongly controls the amount of brine in a salt repository. Brine leads to corrosion of waste forms and waste packages, and possible dissolution of radionuclides with brine transport being a potential transport vector to the accessible environment. The main test case used in Task E is the ongoing Brine Availability Test in Salt (BATS) heater test located underground at the Waste Isolation Pilot Plant (WIPP) near Carlsbad, New Mexico, USA. The Task was divided into a series of Steps. Step 0 was an introduction to processes in salt, that included matching historical unheated brine inflow data from boreholes at WIPP and matching temperature observations during BATS heater test 1a. Step 1 included validation of models against a thermo-poroelastic analytical solution relevant to heated boreholes in salt, and two-phase flow around an excavation in salt. Step 2 required all the individual components covered in steps 0 and 1 to come together to match observed brine inflow behavior during the BATS 1a heater test. There were a range of approaches from the teams, from mechanistic to prescriptive. Given the uncertainties in the problem, some teams used one- or two-dimensional models of the processes, while other teams included more geometrical complexity in three-dimensional models. The key learning points from Task E have been: • Heat conduction through salt typically requires non-linear thermal conductivity (as a function of temperature), but most models do a good job matching observations, given appropriate adjustments to the applied power and some thermocouple locations. • Thermal pressurization requires coupled thermal-hydrological-mechanical (THM) responses that consider the thermal expansion of the fluid and solid phases. • Initialization of two-phase flow models around a borehole or excavation in salt are more realistically represented as “wetting up”, rather than “drying down” (i.e., the initial state after excavation is mostly dry, rather than mostly wet). • The BATS 1a heater test includes a significant release of brine after the end of heating, which requires a large increase in permeability to recreate. Task E has been a great learning experience for all the teams involved, and feedback from the modeling teams has led to changes in the design of follow-on BATS experiments, which are now ongoing underground at WIPP. There was a balance throughout the task between freedom to model phenomena how each team saw fit, and prescriptiveness in problem design to bring the modeling teams closer together to allow attribution of smaller differences between models to different modeling choices. The modeling approaches seem to go through two phases: an early phase of discovery or testing, and a later phase of refinement and improvement. In future modeling efforts, different field data could be used (e.g., BATS 2) and more time should be included in the processes for teams to make multiple model refinement or even significant changes to their conceptual model or setup, based on lessons learned from the modeling exercise.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Visualizing a Vulnerability: Its Connections to Hardware and Software

All Hazards Analysis (AHA) is a framework developed by Idaho National Laboratory that provides capabilities to collect, store, analyze, and visualize critical infrastructure information. A core function of AHA is its ability to simulate faults or outages in networks of infrastructure originating from a plethora of causes, ranging from natural disasters to cyberattacks. AHA utilizes Hardware and Software Bills of Material (HBOM and SBOM, respectively) along with Known Exploited Vulnerabilities (KEVs) to document the potential attack vectors for each piece of infrastructure. The objective of this contribution to AHA was to create a visualization tool that could capture the small details held in each individual artifact as well as preserve the large-scale connections that link them together to aid threat modeling.

58 GEOSCIENCES↗

Circumnavigating collinear superspace

In this paper, we extend the collinear superspace formalism to include the full range of N = 1 supersymmetric interactions. Building on the effective field theory rules developed in a companion paper — Navigating Collinear Superspace — we construct collinear superspace Lagrangians for theories with non-trivial F- and D-term auxiliary fields. For (massless) Wess-Zumino models, the key ingredient is a novel type of Grassmann-valued supermultiplet whose lowest component is a (non-propagating) fermionic degree of freedom. For gauge theories coupled to charged chiral matter, the key ingredient is a novel type of vector superfield whose lowest component is a non-propagating gauge potential. This unique vector superfield is used to construct a gauge-covariant derivative; while such an object does not appear in the standard full superspace formalism, it is crucial for modeling gauge interactions when the theory is expres sed on a collinear slice. This brings us full circle, by showing that all types of N = 1 theories in four dimensions can beconstructed in collinear superspace from purely infrared considerations. We speculate that supersymmetric theories with N > 1 could also be implemented using similar collinear superspace constructions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Artificial Intelligence for Digital Security and Protections

Proper functioning of nuclear power plants relies on a mix of well-regulated human and machine-driven workflows. This regulation supports nuclear safety through a series of processes and many of the tasks that support these processes have a repetitive nature that make artificial intelligence (AI) informed by machine learning (ML) a potential aid in a variety of tasks. AI is being evaluated for activities that include inspections, fuel processing, monitoring, and other activities. The introduction of any new technology presents a potential new attack vector. In the case of AI/ML, there are many attacks that have already been discovered and over time the attacks can be expected to follow the growth pattern observed in cyber security. While future planning is necessary, current efforts need to be established now to predict the threat emergence over the next year 10 years and mitigate potential threats. Based on these observations, AI/ML will need to become trustworthy, which corresponds to techniques and procedures that emphasize AI explainability along with resilience techniques to data, algorithms, models, and systems. This kind of system robustness is the foundation for defenses against AI/ML-specific attacks. Attempting to look forward and take a broad view of capabilities provides input to research roadmaps and the ability to distill vulnerabilities into specific use cases may provide greater assistance in understanding the technology benefits while introducing new risks. The impact of current and future AI in three areas—capabilities, challenges, and recovery strategies—represents an initial attempt at balancing both.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Filling the gap: hunting for vector bosons at the MUonE experiment with displaced decay signature

The upcoming MUonE experiment aims to precisely measure the running of the fine structure constant via elastic muon-electron scattering, to shed light on the current tension in the muon’s anomalous magnetic moment. In addition to its primary function as a precision experiment, MUonE also offers a unique testing ground to probe long-lived vector bosons. Such vector bosons can be produced via μe → μeV or μN → μNV scattering and decay into an electron/positron pair a few centimeters away from the interaction point. With its high-resolution tracking system and unique geometric design, MUonE is well-suited to reconstruct displaced vertices close to the target, allowing it to probe parameter space previously unattainable at colliders and longer-baseline beam dump experiments. We present a comprehensive study of the discovery potential of BSM vector boson mediators at the MUonE experiment. We show that MUonE can fill the long-standing gap in the parameter space of vector boson mediators with masses up to around 100 MeV.

Models for Dark Matter↗

Multiple Sources of Riparian Wetland Suspended Solids during Episodic Rain Events: Influence on Uranium Transport

Suspended solids can be the primary vector for transporting contaminants in streams. The objective of this study was to determine whether changes in the properties of suspended solids during rain events impacted contaminant transport. Stream water was collected during five episodic events downstream from a U-contaminated wetland located in South Carolina, USA. The suspended particles were initially composed of Fe-flocs (particles formed in situ prior to the rain event) that had significantly greater Fe, Mn, organic-C, and U content than particles collected later during a sampling rain event. XANES and EXAFS revealed that U in the Fe-flocs was U(VI) and that it was not incorporated in a mineral structure but existed as inner- or outer-sphere adsorbed uranyl species associated with organic matter and Fe-oxides. The uranyl had an extraordinarily high affinity for the suspended solids, with solid to liquid U ratios of >72,000 (μg/kg)/(μg/L). After the initial flush of Fe-flocs, a greater fraction of the suspended solids had lower organic-C, Fe, Mn, and amorphous phases and were composed of more quartz, kaolinite, and gibbsite, resulting in lower U concentrations than those in the solids collected earlier in the rain event. This study highlights the importance of understanding suspended solids as transport vectors and their potential dynamic nature during rain events.

computer simulations↗

Physics-constrained 3D convolutional neural networks for electrodynamics

We present a physics-constrained neural network (PCNN) approach to solving Maxwell’s equations for the electromagnetic fields of intense relativistic charged particle beams. We create a 3D convolutional PCNN to map time-varying current and charge densities J(r, t) and ρ(r, t) to vector and scalar potentials A(r, t) and φ(r, t) from which we generate electromagnetic fields according to Maxwell’s equations: B = ∇ × A and E = −∇φ − ∂A/∂t. Our PCNNs satisfy hard constraints, such as ∇ · B = 0, by construction. Soft constraints push A and φ toward satisfying the Lorenz gauge.

97 MATHEMATICS AND COMPUTING↗

The role of vectors in reheating

We explore various aspects concerning the role of vector bosons during the reheating process. Generally, reheating occurs during the period of oscillations of the inflaton condensate and the evolution of the radiation bath depends on the inflaton equation of state. For oscillations about a quadratic minimum, the equation of state parameter, w = p/ρ = 0, and the evolution of the temperature, T(a) with respect to the scale factor is independent of the spin of the inflaton decay products. However, for cases when w > 0, there is a dependence on the spin, and here we consider the evolution when the inflaton decays or scatters to vector bosons. We also investigate the gravitational production of vector bosons as potential dark matter candidates. Gravitational production predominantly occurs through the longitudinal mode. We compare these results to the gravitational production of scalars.

79 ASTRONOMY AND ASTROPHYSICS↗

Superconducting pairing mechanism in CeCoIn 5 revisited

Spectroscopic-imaging scanning-tunneling microscopy (SI-STM) measurements have previously been applied to the study of the heavy-fermion system CeCoIn 5 to examine the superconducting gap structure and band dispersions via quasiparticle intereference. Here we directly measure the dispersing electron bands with angle-resolved-photoelectron spectroscopy (ARPES) and compare with first principles electronic structure calculations. By auto-correllating the ARPES-resolved bands with themselves we can measure the potential q-vectors and discern exactly which bands the STM is measuring. We find that the STM results are dominated by scattering associated with a cloverleaf shaped band centered at the zone corners. This same band is also a viable candidate to host the superconducting gap. Overall, the electronic structure calculations indicate that this region of the Fermi surface involves significant contributions from the Co d-electrons, an indication that the superconductivity in these materials is more 3-dimensional than that found in the related unconventional superconductors, the cuprates and the pnictides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Attack Surface of Wind Energy Technologies in the United States

Low cost, reliable electrical energy production from wind relies upon automation and control systems, arguably more so than traditional thermal generation. These same systems, however, can serve as the target of adversaries’ cyber-attacks. Idaho National Laboratory (INL), at the request of the Department of Energy’s (DOE’s) Office of Cybersecurity, Energy Security, and Emergency Response (CESER) and Energy Efficiency and Renewable Energy’s (EERE’s) Wind Energy Technologies Office (WETO), evaluated a generalized wind plant architecture to understand the classes of potential threat actors and the vectors that could enable a cyber-attack. This evaluation explores the attack surface of a representative wind plant, identifying potential methods and vectors that an adversary could leverage to conduct a cyber-attack. Included in this assessment are some recommended mitigations and approaches. Each recommendation requires a full security evaluation, cost/benefit analysis, and risk analysis by each owner and operator.

17 WIND ENERGY↗

Gene editing through microfluidic delivery

Gene editing can be performed by introducing gene-editing components into a cell by mechanical cell disruption. Related apparatus, systems, techniques, and articles are also described. The methods and systems of the invention solve the problem of intracellular delivery of gene editing components and gene editing complexes to target cells. The results described herein indicate that delivery of gene editing components, e.g., protein, ribonucleic acid (RNA), and deoxyribonucleic acid (DNA), by mechanical disruption of cell membranes leads to successful gene editing. Because intracellular delivery of gene editing materials is a current challenge, the methods provide a robust mechanism to engineer target cells without the use of potentially harmful viral vectors or electric fields.

Sharei, Armon R.↗

An Efficient Numerical Algorithm for Solving Coupled Time-Dependent Ginzburg-Landau Equation for Superconductivity and Elasticity

A decoupled finite element algorithm is developed for simulating the vortex dynamics on an elastic superconductor which couples the time-dependent Ginzburg- Landau equation with the complex-valued superconducting order parameter and the vector-valued magnetic potential, and the elasticity equation. We present an iterative algorithm for the decoupled system arising from the time and spatial discretization using a combination of preconditioner, algebraic multigrid method (AMG) and preconditioned conjugate gradient method (PCG). The iterative algorithm allows us to perform large-scale three-dimensional simulations of mesoscale pattern formation during superconducting phase transitions with arbitrary elastic boundary conditions. Here, the performance and efficiency of the algorithm are numerically verified by several benchmark problems, exhibiting up to two orders of magnitude improvement depending on the scale of discrete system compared to the exact solver.

Efficiency↗