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At least 1,513 records · Page 84

Thermodynamically consistent Cahn–Hilliard–Navier–Stokes equations using the metriplectic dynamics formalism

Cahn–Hilliard–Navier–Stokes (CHNS) systems describe flows with two-phases, e.g., a liquid with bubbles. Obtaining constitutive relations for general dissipative processes for such systems, which are thermodynamically consistent, can be a challenge. We show how the metriplectic 4-bracket formalism (Morrison and Updike, 2024) achieves this in a straightforward, in fact algorithmic, manner. First, from the noncanonical Hamiltonian formulation for the ideal part of a CHNS system we obtain an appropriate Casimir to serve as the entropy in the metriplectic formalism that describes the dissipation (e.g. viscosity, heat conductivity and diffusion effects). General thermodynamics with the concentration variable and its thermodynamics conjugate, the chemical potential, are included. Having expressions for the Hamiltonian (energy), entropy, and Poisson bracket, we describe a procedure for obtaining a metriplectic 4-bracket that describes thermodynamically consistent dissipative effects. The 4-bracket formalism leads naturally to a general CHNS system that allows for anisotropic surface energy effects. Furthermore, this general CHNS system reduces to cases in the literature, to which we can compare.

Cahn–Hilliard↗

Logic-based analysis of gene expression data predicts association between TNF, TGFB1 and EGF pathways in basal-like breast cancer

For breast cancer, clinically important subtypes are well characterized at the molecular level in terms of gene expression profiles. In addition, signaling pathways in breast cancer have been extensively studied as therapeutic targets due to their roles in tumor growth and metastasis. However, it is challenging to put signaling pathways and gene expression profiles together to characterize biological mechanisms of breast cancer subtypes since many signaling events result from post-translational modifications, rather than gene expression differences. We designed a logic-based computational framework to explain the differences in gene expression profiles among breast cancer subtypes using Pathway Logic and transcriptional network information. Pathway Logic is a rewriting-logic-based formal system for modeling biological pathways including post-translational modifications. Our method demonstrated its utility by constructing subtype-specific path from key receptors (TNFR, TGFBR1 and EGFR) to key transcription factor (TF) regulators (RELA, ATF2, SMAD3 and ELK1) and identifying potential association between pathways via TFs in basal-specific paths, which could provide a novel insight on aggressive breast cancer subtypes. Lastly, codes and results are available at http://epigenomics.snu.ac.kr/PL/.

59 BASIC BIOLOGICAL SCIENCES↗

Expression of the high capacity calcium-binding domain of calreticulin increases bioavailable calcium stores in plants

Modulation of cytosolic calcium levels in both plants and animals is achieved by a system of Ca2+-transport and storage pathways that include Ca2+ buffering proteins in the lumen of intracellular compartments. To date, most research has focused on the role of transporters in regulating cytosolic calcium. We used a reverse genetics approach to modulate calcium stores in the lumen of the endoplasmic reticulum. Our goals were two-fold: to use the low affinity, high capacity Ca2+ binding characteristics of the C-domain of calreticulin to selectively increase Ca2+ storage in the endoplasmic reticulum, and to determine if those alterations affected plant physiological responses to stress. The C-domain of calreticulin is a highly acidic region that binds 20-50 moles of Ca2+ per mole of protein and has been shown to be the major site of Ca2+ storage within the endoplasmic reticulum of plant cells. A 377-bp fragment encoding the C-domain and ER retention signal from the maize calreticulin gene was fused to a gene for the green fluorescent protein and expressed in Arabidopsis under the control of a heat shock promoter. Following induction on normal medium, the C-domain transformants showed delayed loss of chlorophyll after transfer to calcium depleted medium when compared to seedlings transformed with green fluorescent protein alone. Total calcium measurements showed a 9-35% increase for induced C-domain transformants compared to controls. The data suggest that ectopic expression of the calreticulin C-domain increases Ca2+ stores, and that this Ca2+ reserve can be used by the plant in times of stress.

NASA Discipline Plant Biology↗

Nonlinear beam kinematics by decomposition of the rotation tensor

A simple matrix expression is obtained for the strain components of a beam in which the displacements and rotations are large. The only restrictions are on the magnitudes of the strain and of the local rotation, a newly-identified kinematical quantity. The local rotation is defined as the change of orientation of material elements relative to the change of orientation of the beam reference triad. The vectors and tensors in the theory are resolved along orthogonal triads of base vectors centered along the undeformed and deformed beam reference axes, so Cartesian tensor notation is used. Although a curvilinear coordinate system is natural to the beam problem, the complications usually associated with its use are circumvented. Local rotations appear explicitly in the resulting strain expressions, facilitating the treatment of beams with both open and closed cross sections in applications of the theory. The theory is used to obtain the kinematical relations for coupled bending, torsion, extension, shear deformation, and warping of an initially curved and twisted beam.

Danielson, D. A.↗

Nonlinear Beam Kinematics by Decomposition of the Rotation Tensor

A simple matrix expression is obtained for the strain components of a beam in which the displacements and rotations are large. The only restrictions are on the magnitudes of the strain and of the local rotation, a newly-identified kinematical quantity. The local rotation is defined as the change of orientation of material elements relative to the change of orientation of the beam reference triad. The vectors and tensors in the theory are resolved along orthogonal triads of base vectors centered along the undeformed and deformed beam reference axes, so Cartesian tensor notation is used. Although a curvilinear coordinate system is natural to the beam problem, the complications usually associated with its use are circumvented. Local rotations appear explicitly in the resulting strain expressions, facilitating the treatment of beams with both open and closed cross sections in applications of the theory. The theory is used to obtain the kinematical relations for coupled bending, torsion extension, shear deformation, and warping of an initially curved and twisted beam.

Danielson, D. A.↗

A Statistics-Based Threshold for the RMS-Energy Oscillation Detector

System operators and reliability coordinators currently rely on extensive baselining studies to set thresholds for their oscillation detectors. The resulting thresholds are based largely on engineering judgment and may vary significantly between organizations. In this paper, statistical distribution theory is used to derive a detection threshold for the widely deployed root-mean-square (RMS)-energy detector. This expression provides a theoretical basis for the detector's configuration, simplifies the process of selecting the threshold, and enables improved consistency among organizations that need to coordinate during system-wide events. Three methods for calculating the threshold using synchrophasor measurements are also proposed. These methods ensure that the threshold can be calculated reliably for various applications. Tests with simulated and field-measured data demonstrate that the statistics-based threshold provides consistent detection of grid disturbances while maintaining a low probability of false alarm.

Follum, James D.↗

Effects of Simulated Microgravity on a Host-Pathogen System

While it has been shown that decades of astronauts and cosmonauts suffer from immune disorders both during and after spaceflight, the underlying causes are still poorly understood, due in part to the fact that there are so many variables to consider when investigating the human immune system in a complex environment. Invertebrates have become popular models for studying human disease because they are cheap, highly amenable to experimental manipulation, and have innate immune systems with a high genetic similarity to humans. Fruit flies (Drosophila melanogaster) have been shown to experience a dramatic shift in immune gene expression following spaceflight, but are still able to fight off infections when exposed to bacteria. Furthermore, a recent spaceflight mission showed that flies are more susceptible to infection following exposure to microgravity conditions, compared to ground-reared flies from the same population. Additionally, the common bacterial pathogen Serratia marcescens was shown to become more lethal to fruit flies (both space- and ground-reared) after being cultured in space, suggesting that not only do we need to consider host changes in susceptibility, but also changes in the pathogen itself after spaceflight conditions. Being able to simulate spaceflight conditions in a controlled environment on the ground gives us the ability to not only evaluate the effects of microgravity on the host immune system, but also how the microorganisms that cause immune disorders are being affected by these drastic environmental shifts. In this study, I use both spaceflight and ground-based (simulated microgravity) environments to examine the genetic changes associated with increased S. marcescens virulence in order to understand how microgravity is affecting this pathogen, as well as to evaluate how these genetic changes influence and interact with the host immune system. This study will provide us with more directed approaches to studying the effects of spaceflight on human beings, with the ultimate goal of being able to ameliorate human immune dysfunction in future space exploration.

Immunology↗

A mathematical representation of an advanced helicopter for piloted simulator investigations of control system and display variations

A mathematical model of an advanced helicopter is described. The model is suitable for use in control/display research involving piloted simulation. The general design approach for the six degree of freedom equations of motion is to use the full set of nonlinear gravitational and inertial terms of the equations and to express the aerodynamic forces and moments as the reference values and first order terms of a Taylor series expansion about a reference trajectory defined as a function of longitudinal airspeed. Provisions for several different specific and generic flight control systems are included in the model. The logic required to drive various flight control and weapon delivery symbols on a pilot's electronic display is also provided. Finally, the model includes a simplified representation of low altitude wind and turbulence effects. This model was used in a piloted simulator investigation of the effects of control system and display variations for an attack helicopter mission.

Aiken, E. W.↗

Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation

Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.

54 ENVIRONMENTAL SCIENCES↗

Origin of Chirality Induced Spin Selectivity in Photoinduced Electron Transfer

Here we propose a mechanism by which spin-polarization can be generated dynamically in chiral molecular systems undergoing photoinduced electron transfer. The proposed mechanism explains how spin-polarization emerges in systems where charge transport is dominated by incoherent hopping, mediated by spin-orbit and electronic exchange couplings through an intermediate charge transfer state. We derive a simple expression for the spin-polarization that predicts a nonmonotonic temperature dependence, consistent with recent experiments, and a maximum spin-polarization that is independent of the magnitude of the spin-orbit coupling. We validate this theory using approximate quantum master equations and the numerically exact hierarchical equations of motion. The proposed mechanism of chirality induced spin selectivity should apply to many chiral systems, and the ideas presented here have implications for the study of spin transport at temperatures relevant to biology and provide simple principles for the molecular control of spins in fluctuating environments.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

A Kinetic Monte Carlo Approach for Simulating Cascading Transmission Line Failure

In this work, cascading transmission line failures are studied through a dynamical model of the power system operating under fixed conditions. The power grid is modeled as a stochastic dynamical system where first-principles electromechanical dynamics are excited by small Gaussian disturbances in demand and generation around a specified operating point. In this context, a single line failure is interpreted in a large deviation context as a first escape event across a surface in phase space defined by line security constraints. The resulting system of stochastic differential equations admits a transverse decomposition of the drift, which leads to considerable simplification in evaluating the quasipotential (rate function) and, consequently, computation of exit rates. Tractable expressions for the rate of transmission line failure in a restricted network are derived from large deviation theory arguments and validated against numerical simulations. Extensions to realistic settings are considered, and individual line failure models are aggregated into a Markov model of cascading failure inspired by chemical kinetics. Cascades are generated by traversing a graph composed of weighted edges representing transitions to degraded network topologies. Numerical results indicate that the Markov model can produce cascades with qualitative power-law properties similar to those observed in empirical cascades.

Kinetic Monte Carlo, rare events, Cascading Failur↗

H2@Airports (Workshop Summary Report)

This report serves as the proceedings of the H2@Airports Workshop held virtually by the U.S. Department of Energy (DOE) in collaboration with the U.S. Department of Transportation (DOT) and Department of Defense (DOD), November 4-6, 2020. Presentations from the workshop can be found at H2@Airports Workshop: https://www.energy.gov/eere/fuelcells/h2airports-workshop. The workshop was held to assess the state of the art for electric aircraft and airport applications specifically using hydrogen fuel cells, to discuss operational requirements and lessons learned on early fuel cell aviation and airport projects, to understand current technology gaps, to identify collaborative research and development (R&D) opportunities, to highlight codes, standards, safety, and regulatory challenges, and to identify potential actions that address them. Experts and stakeholders from industry, government, and academia met to discuss the current state of the art of hydrogen and fuel cell technologies and the requirements for using these technologies in aviation applications and land-based applications at airports. This report summarizes the discussions and diverse opinions expressed at the workshop.

08 HYDROGEN↗

Defining A Modelling Language to Support Functional Hazard Assessment

Functional Hazard Assessment (FHA) is a key early-stage engineering process that supports the incorporation of safety in design by identifying the high-level functional hazards the system may encounter. While many FHA-like methodologies have been proposed in the design engineering literature, many of these methodologies have had difficulty becoming accepted industry practice. Industry standards, on the other hand, either provide too little recommendation on how to represent the function of the system to perform FHA, or rely on existing design artefacts which insufficiently support the goals of the process. This paper presents some of the problems with current modeling languages (both proposed and used) for FHA which limit the scope, expressiveness, flexibility, and precision of the analysis. It then outlines desirable principles an FHA-supporting analysis language should embody, and introduces the Functional Reasoning Design Language (FRDL), a formal modeling language for describing the functional elements of a system and their interactions, which aims to satisfy these principles. To demonstrate the use of this language, the modeling and hazard analysis of a disaster response drone is presented. While this case study is limited in scope, it highlights how FRDL can represent system function while reducing the ambiguity present in typical FHA-supporting functional modeling languages

Hazard Assessment↗

Kuiper Express: A Sciencecraft

The Kuiper Express is a mission to achieve the first reconnaissance of one of the primitive objects in the Kuiper Belt. The Kuiper Express is a sciencecraft mission. It will be launched using a Delta vehicle and will use solar electric propulsion to shape its trajectory in the inner Solar System, while executing two Earth gravity-assist flybys.

Kuiper↗

HAT m:N Activity Overview

Since 2020, researchers from the Human Autonomy Teaming (HAT) Laboratory at NASA Ames Research Center have conducted human-in-the-loop (HITL) simulation research to study a new control paradigm for operations involving multiple remotely piloted aircraft systems (RPAS). Colloquially referred to as "m:N," this paradigm is characterized by multiple operators collaboratively controlling multiple vehicles between them. The m:N name expresses a ratio whereby m is the number of operators and N is the number of vehicles shared between them. In this presentation, HAT Lab researchers provide a high-level overview of the m:N studies that have been performed to-date. These include a study of the m:N concept of operations (CONOPS) and the attending roles and responsibilities ("ConOps/R&R Sim"), a study focused on contingency management involving dynamic, inter-operator transfers of vehicles ("Handoff Sim"), and a study examining the effects of pilot-ATC communication systems on workload ("UAM Comms Sim"). A selection of key results are provided. The presentation concludes with a brief discussion of planned research into m:N operations.

m:N↗

SpaceVPX Interoperability Assessment

The existing VMEbus (VersaModular Eurocard bus) International Trade Association (VITA)-78 industry standard, also known as SpaceVPX, is an avionics board- and chassis-level standard derived from the OpenVPX standard as defined in VITA-65. While VITA-65 defines backplane and board-level profiles from COTS vendors to ensure interoperability of products used in developing systems and subsystems, the VITA-78 standard defines SpaceVPX to incorporate fault tolerance features that are required by many spaceflight systems. However, VITA-78 allows so much flexibility that interoperability between modules cannot be assured. This assessment provides guidelines on the use of, and extensions to, the VITA-78 standard to enable avionics interoperability for future NASA missions. The assessment team was comprised of subject matter experts (SMEs) from Goddard Space Flight Center (GSFC), the Jet Propulsion Laboratory (JPL), Johnson Space Center (JSC), and Langley Research Center (LaRC). The team included valuable external consulting support from a SME who was a key participant in the development of the VITA-78 standard. The team had extensive collaboration with the NASA Space Technology Mission Directorate (STMD) High Performance Spaceflight Computing (HPSC) project, specifically in the development of SpaceVPX interconnect findings, observations, and NESC recommendations. To provide an understanding of the breadth of implementations that SpaceVPX must accommodate, multiple NASA use cases were analyzed to assess the requirements for SpaceVPX implementations across a wide range of NASA missions (Appendix C). Applications included crewed missions, science missions, and orbital and surface robotic systems. Product surveys were conducted to assess the level of industry support for SpaceVPX, applications, and the variations in their implementations (Appendix D). In-depth analysis was conducted in the areas of: (a) power management and distribution, (b) form factors and daughtercards, (c) interconnect, and (d) fault tolerance. Leveraging the use cases, product surveys, and SMEs from multiple NASA Centers, these areas were analyzed to determine the range of implementations permitted by the VITA-78 standard and potential interoperability issues. Applicable findings and NESC recommendations were provided for each area. During this assessment, there were multiple opportunities to engage with other agencies to learn about their interest in SpaceVPX, their strategies for implementing SpaceVPX-based systems, and their internal development efforts. These engagements also generated findings and NESC recommendations. Based on this assessment analysis, NESC recommendations were made regarding the feature set and module profiles to support NASA SpaceVPX implementations. This feature set includes restrictions on features in VITA-78, and extensions to the standard. Key recommendations in this area include the use of 10 Gigabit Ethernet and Peripheral Component Interconnect Express (PCIe) as high bandwidth interconnect on the backplane, the retention of SpaceWire interconnect for control functions, and support for 3U (unit) and 6U, form factors for NASA systems. Restrictions were proposed on the usage of user-defined signals to promote interoperability, and specific power managements and distribution schemes for 3U systems. Beyond the technical implementation of SpaceVPX, recommendations were made on areas that warrant further investigation. Primary among these is the recommendation for NASA to collaborate with other space-going agencies and industry to incorporate recommendations into a future ‘dot spec’ of VITA-78. This would ensure wide adoption and availability of the modules that comply with the specification. The assessment includes appendices with candidate module profiles that can be considered as a starting point for this activity, and example systems based on the recommendations. Follow-on studies are recommended for architectures beyond SpaceVPX to address potential enhancements including condensed set of interconnect, software required to implement protocol layers on the interconnect (and other features), alternative power architectures, and system-level testability.

SpaceVPX↗

Elastic cross section is entanglement entropy

We present universal relations between entanglement entropy, which quantifies the quantum correlation between subsystems, and the cross section, which is the primary observable for high-energy particle scattering, by employing a careful formulation of wave packets for the incoming particles. For 2-to-2 elastic scattering with no initial entanglement and subdividing the system along particle labels, we show that both the Rényi and Tsallis entropies in the final states are directly proportional to the elastic cross section in units of the transverse size for the initial wave packets, which is then interpreted as the elastic scattering probability. The relations do not depend on the underlying dynamics of the quantum field theory and are valid to all orders in coupling strengths. Furthermore, computing quantum correlations between momentum and nonkinematic data leads to entanglement entropies expressed as various semi-inclusive elastic cross sections. Our result gives rise to a novel “area law” for entanglement entropy in a two-body system. Published by the American Physical Society 2025

Low, Ian (ORCID:0000000275709597)↗

Dual-Phase Malicious User Detection Scheme for IM-OFDMA Systems Using IQ Imbalance

Physical-layer security techniques have contributed to the achievement of various security objectives in an efficient and lightweight manner. Thus, these techniques have been widely considered for limited-resource networks such as Internet of Things networks. Among the different security objectives, malicious user detection by exploiting physical-layer parameters has demonstrated efficient performance. In this work, malicious user detection in the recently proposed index modulation-based orthogonal frequency division multiple access (IM-OFDMA) is addressed. The proposed malicious user detection scheme exploits the hardware impairments, especially the in-phase and quadrature imbalance parameters, for both legitimate and malicious users to design a dual-phase efficient detection scheme. The proposed scheme accounts for the special characteristics of IM-OFDMA transmission that are different from other multiple-access techniques. The performance of the proposed scheme was evaluated considering detection probability and false alarm probability performance metrics. Moreover, closed-form expressions of these metrics were derived for both phases and were validated by Monte Carlo simulation results under different configurations of IM-OFDMA systems.

Alaca, Ozgur [ORNL] (ORCID:0000000153713758)↗