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At least 343 records · Page 19

Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning

Abstract mRNA degradation is a central process that affects all gene expression levels, though it remains challenging to predict the stability of a mRNA from its sequence, due to the many coupled interactions that control degradation rate. Here, we carried out massively parallel kinetic decay measurements on over 50,000 bacterial mRNAs, using a learn-by-design approach to develop and validate a predictive sequence-to-function model of mRNA stability. mRNAs were designed to systematically vary translation rates, secondary structures, sequence compositions, G-quadruplexes, i-motifs, and RppH activity, resulting in mRNA half-lives from about 20 seconds to 20 minutes. We combined biophysical models and machine learning to develop steady-state and kinetic decay models of mRNA stability with high accuracy and generalizability, utilizing transcription rate models to identify mRNA isoforms and translation rate models to calculate ribosome protection. Overall, the developed model quantifies the key interactions that collectively control mRNA stability in bacterial operons and predicts how changing mRNA sequence alters mRNA stability, which is important when studying and engineering bacterial genetic systems.

Cetnar, Daniel P.↗

Recent Developments and Challenges Implementing New and Improved Stress Intensity Factor (K) Solutions in NASGRO for Damage Tolerance Analyses

Fatigue crack growth analysis software has been available to damage tolerance analysts for many years in either commercial products or via proprietary in-house codes. The NASGRO software has been publicly available since the mid-80s (known as NASA/FLAGRO up to 1999) and since 2000 has been sustained and further developed by a collaborative effort between Southwest Research Institute® (SwRI®), the NASA Johnson Space Center (JSC), and the members of the NASGRO Industrial Consortium. Since the stress intensity factor (K) is the foundation of fracture mechanics and damage tolerance analysis of aircraft structures, a significant focus of development efforts in the past fifteen years has been geared towards enhancing legacy K solutions and developing new and efficient numerical K solutions that can handle the complicated stress gradients computed by today’s analysts using detailed finite element models of fatigue critical locations. This paper provides an overview of K solutions that have been recently implemented or improved for the analysis of geometries such as two unequal through cracks at a hole and two unequal corner cracks at a hole, as well as state-of-the-art weight function models capable of computing K in the presence of univariant and/or bivariant stress gradients and complicated residual stress distributions. Some historical background is provided to review how common K solutions have evolved over the years, including selective examples from the literature and from new research. Challenges and progress in rectifying discrepancies between older legacy solutions and newer models are reviewed as well as approaches and challenges for verification and validation of K solutions. Finally, a summary of current challenges and future research and development needs is presented. A key theme throughout the presentation of this paper will be how members of the aerospace industry have collaborated with software developers to develop a practical analysis tool that is used world-wide to support new design as well as the ongoing sustainment and airworthiness of commercial and military aircraft.

Cardinal, Joseph W.↗

Capabilities of multivariate Bayesian inference toward seismic hazard assessment

Multivariate Bayesian analysis can bring significant benefits to seismic hazard analysis: Its multivariate feature enables computing scalar and vector hazard without making any approximations; Correlations between intensity measures are implicitly modeled, permitting direct simulation of ground motion selection tools such as the conditional mean spectrum and the generalized conditioning intensity measure; and Its updating feature enables a seamless integration of new ground motion data into the hazard results. Here, we first develop a multivariate Bayesian ground motion model through the NGA-West2 database. The model functional form considers fault-type, magnitude, and distance dependencies, and also the linear and the rock intensity dependent site response. We use a hybrid Markov Chain Monte Carlo sampling to perform Bayesian inference consisting of Gibbs step and a multilevel Metropolis-Hastings step. We then perform several checks on the model and note that its performance is satisfactory. Finally, we illustrate the merits of this multivariate Bayesian analysis, which include: ground motion model updating with ground motion data recorded in the last four years not part of the NGA-West2 database; computation of scalar and vector seismic hazard using the un-updated and updated ground motion models for Los Angeles, CA; and simulation of the conditional mean spectrum under scalar and vector IM conditioning while accounting for different sources of aleatoric and epistemic uncertainties.

58 GEOSCIENCES↗

Computational and Experimental Study for the Denitrification of Biomass-Derived Hydrothermal Liquefaction Oil

Hydrothermal liquefaction (HTL) is a promising method for processing wet biomass and waste feedstock to produce biofuels. During the HTL process, proteins and other biomolecules in certain feedstock get converted into nitrogenous compounds in produced biocrude, which represents a major challenge to further upgrading them into fuels. One promising approach is to separate nitrogenous compounds from the biocrude using polymeric resins. In this study, experiments were conducted to down-select sorbent and resin systems using a nitrogen-compound-containing surrogate biocrude. We model the binding interactions between an Amberlyst polymeric resin with various compounds present in the biocrude mixture such as nitrogenous compounds like pyrrole, pyridine, hexanamide, and representative co-existing compounds like phenol and dodecanoic acid. To ascertain the efficiency of various resins in the denitrogenation process, we have developed a quantitative structure–function model for the interacting components in the mixture. Our results suggest that the Amberlyst resin is a viable candidate for efficient removal of target nitrogen-containing compounds (such as pyridine) from the biocrude as a result of favorable interactions. The computational studies provide some insight into how and why the identified resin (Amberlyst) works in selective extraction of nitrogenous compound(s).

09 BIOMASS FUELS↗

Off-shell pion properties: Electromagnetic form factors and light-front wave functions

The off-shell pion electromagnetic form factors are explored with corresponding off-shell light-front wave functions modeled by constituent quark and antiquark. We apply the Mandelstam approach for the microscopic computation of the form factors relating the model parameters with the pion decay constant and charge radius. Analyzing the existing data on the cross sections for the Sullivan process, 1 H(e,e',π + )⁢n, Charged pion form factor between Q 2 = 0.60, and 2.45 GeV 2 . I. Measurements of the cross section for the 1 H⁡(e,e'⁢π + )⁢n reaction, we extract the off-shell pion form factor using the relation derived from the generalized Ward-Takahashi identity for the pion electromagnetic current. They are compared with our previous results from exactly solvable manifestly covariant model of a (3+1)-dimensional fermion field theory. We find that the adopted constituent quark model reproduces the extracted off-shell form factor F 1 ⁡(Q 2 ,t) from the experimental data within a few percent difference and matches well with our previous theoretical simulation which exhibits a variation of about 10% for the extracted off-shell pion form factor g(Q 2 ,t). We also identify the pion valence parton distribution function (PDF) and transverse momentum distribution (TMD) in terms of the light-front wave function and discuss their off-shell properties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Intelligent Command and Control Systems for Satellite Ground Operations

This grant, Intelligent Command and Control Systems for Satellite Ground Operations, funded by NASA Goddard Space Flight Center, has spanned almost a decade. During this time, it has supported a broad range of research addressing the changing needs of NASA operations. It is important to note that many of NASA's evolving needs, for example, use of automation to drastically reduce (e.g., 70%) operations costs, are similar requirements in both government and private sectors. Initially the research addressed the appropriate use of emerging and inexpensive computational technologies, such as X Windows, graphics, and color, together with COTS (commercial-off-the-shelf) hardware and software such as standard Unix workstations to re-engineer satellite operations centers. The first phase of research supported by this grant explored the development of principled design methodologies to make effective use of emerging and inexpensive technologies. The ultimate performance measures for new designs were whether or not they increased system effectiveness while decreasing costs. GT-MOCA (The Georgia Tech Mission Operations Cooperative Associate) and GT-VITA (Georgia Tech Visual and Inspectable Tutor and Assistant), whose latter stages were supported by this research, explored model-based design of collaborative operations teams and the design of intelligent tutoring systems, respectively. Implemented in proof-of-concept form for satellite operations, empirical evaluations of both, using satellite operators for the former and personnel involved in satellite control operations for the latter, demonstrated unequivocally the feasibility and effectiveness of the proposed modeling and design strategy underlying both research efforts. The proof-of-concept implementation of GT-MOCA showed that the methodology could specify software requirements that enabled a human-computer operations team to perform without any significant performance differences from the standard two-person satellite operations team. GT-VITA, using the same underlying methodology, the operator function model (OFM), and its computational implementation, OFMspert, successfully taught satellite control knowledge required by flight operations team members. The tutor structured knowledge in three ways: declarative knowledge (e.g., What is this? What does it do?), procedural knowledge, and operational skill. Operational skill is essential in real-time operations. It combines the two former knowledge types, assisting a student to use them effectively in a dynamic, multi-tasking, real-time operations environment. A high-fidelity simulator of the operator interface to the ground control system, including an almost full replication of both the human-computer interface and human interaction with the dynamic system, was used in the GT-MOCA and GT-VITA evaluations. The GT-VITA empirical evaluation, conducted with a range of'novices' that included GSFC operations management, GSFC operations software developers, and new flight operations team members, demonstrated that GT-VITA effectively taught a wide range of knowledge in a succinct and engaging manner.

Mitchell, Christine M.↗

SPOT 4 space magnetic recorder mechanisms

The design of the SPOT 4 satellite will be quite different from the previous ones. The design of the new magnetic tape recorder, which was derived from industrial knowledge and mission requirements; the main technical characteristics of the recorder; and the mechanical subsystems of the recorder and their locations and contributions to the final performance are all discussed. The philosophy of the development program, required to achieve the desired performance and reliability for each flight model, is described, and information on the schedule and current development is presented. The components of the tape plate system, (the transmission belts, tape rollers of the recorders, and reel hub ball bearings) which are subjected to heavy mechanical operation, fatigue, and wear in the thermal environment of the mission, are discussed. For each of the components, a description of its function in the recorder is given, as well as the mechanical stress imposed during the various operational phases. The quality testing program, which was used to verify the design safety margins, is described. Finally, the first test results of a functioning model of the flight system are presented.

Borrien, A.↗

Mutual coupling effects in antenna arrays, volume 1

Mutual coupling between rectangular apertures in a finite antenna array, in an infinite ground plane, is analyzed using the vector potential approach. The method of moments is used to solve the equations that result from setting the tangential magnetic fields across each aperture equal. The approximation uses a set of vector potential model functions to solve for equivalent magnetic currents. A computer program was written to carry out this analysis and the resulting currents were used to determine the co- and cross-polarized far zone radiation patterns. Numerical results for various arrays using several modes in the approximation are presented. Results for one and two aperture arrays are compared against published data to check on the agreement of this model with previous work. Computer derived results are also compared against experimental results to test the accuracy of the model. These tests of the accuracy of the program showed that it yields valid data.

Collin, R. E.↗

Joint U.S./Japan Conference on Adaptive Structures, 1st, Maui, HI, Nov. 13-15, 1990, Proceedings

The present volume of adaptive structures discusses the development of control laws for an orbiting tethered antenna/reflector system test scale model, the sizing of active piezoelectric struts for vibration suppression on a space-based interferometer, the control design of a space station mobile transporter with multiple constraints, and optimum configuration control of an intelligent truss structure. Attention is given to the formulation of full state feedback for infinite order structural systems, robustness issues in the design of smart structures, passive piezoelectric vibration damping, shape control experiments with a functional model for large optical reflectors, and a mathematical basis for the design optimization of adaptive trusses in precision control. Topics addressed include approaches to the optimal adaptive geometries of intelligent truss structures, the design of an automated manufacturing system for tubular smart structures, the Sandia structural control experiments, and the zero-gravity dynamics of space structures in parabolic aircraft flight.

Wada, Ben K.↗

Frequency-Domain Identification of XV-15 Tilt-Rotor Aircraft Dynamics in Hovering Flight

Frequency-domain methods are used to identify the open-loop dynamics of the XV-15 tilt-rotor aircraft from flight tests. Piloting and data analysis techniques are presented to determine frequency response plots and equivalent transfer function models. The open-loop pitch and roll dynamics for the hover flight condition exhibit unstable low-frequency oscillations, whereas the dynamics in the remaining degrees of freedom are lightly damped and generally decoupled. Comparisons of XV-15 flight-test and simulator data are more favorable for high-frequency inputs (omega greater than 1.0 rad/sec) than low-frequency inputs. Time-domain comparisons of the extracted transfer functions with step response flight data are very favorable, even for large amplitude motions. The results presented in this paper demonstrate the utility of the frequency-domain techniques for dynamics identification and simulator fidelity studies.

Tischler, Mark B.↗

Impact of Wide-Area Oscillation Damping Control using Measurement-Driven Approach on System Separation - Saudi Grid Case Study

In any interconnected power grid, low-frequency oscillations is a major problem that can limit the power transfer capability and deteriorate power system security due to potential low-damped or even undamped oscillations. Synchronized measurements provided by PMUs enable the design and development of wide-area oscillation damping controllers (WADC) based on measurement-driven model to overcome the limitations of traditional controllers. This work focuses on the impact of a W ADC based on a measurement-driven approach on system separation for the Saudi Electricity Company (SEC) grid. A grid model is provided by SEC for this study. Modal analysis is performed to identify the oscillation mode of interest for which the controller is designed. Damping the dominant oscillation mode helps slightly to improve transient stability of the system. Considering bus frequency at different locations in SEC's system as the candidate observation signals, the optimal observation signal is chosen for the W ADC by using the FFT method. The system transfer function model is constructed by utilizing probing measurements. Then, the W ADC parameters are calculated based on the identified model. The performance of the designed W ADC is tested under different contingencies.

Altarjami, Ibrahim↗

Model-based real-time surface heat flux and temperature estimation for the DIII-D tokamak

A control-oriented model for monitoring of wall power flux densities on the DIII-D tokamak has been successfully implemented and validated experimentally. Future reactors will have to withstand severe steady state high heat flux loads on plasma-facing components (PFCs). Due to the difficulty of directly-measuring local heat fluxes on these components, monitoring and protection of PFCs during the plasma discharge can benefit from simplified physics-based real-time (RT) functional models to estimate and guide heat load control. As a first step into the development, a control-oriented model for monitoring of wall power flux densities and temperatures on DIII-D tokamak has been successfully implemented. The paper discusses the experimental demonstration and comparison of the 2-D model-based wall heat flux algorithm on the DIII-Dinner wall limiter (IWL) against infra-red camera heat flux measurements for limited plasma configurations. The paper also reports on the benchmarking of the field line tracing environment, SMITER, developed at ITER organization on DIII-D tokamak against experimental IR diagnostic data and the derivation of the component shaping weighting factors for the 2-D model-based approach. Here, the extension of the model-based approach for surface temperature estimation on the DIII-D IWL is also presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Diagnostic calculations of the circulation in the Martian atmosphere

The circulation of the Martian atmosphere during late southern summer is derived from atmospheric temperature and dust distributions retrieved from a subset of the Mariner 9 infrared interferometer spectrometer (IRIS) thermal emission spectra (LS = 343-348 deg) (Santee and Crisp, 1933). Zonal-mean zonal winds are calculated by assuming gradient wind balance and zero surface zonal wind. Both hemispheres have intense midlatitude westerly jets with velocities of 80-90 m/s near 50 km; in the southern tropics the winds are easterly with velocities of 40 m/s near 50 km. The net effect of the zonal-mean meridional circulation and large-scale waves can be approximated by the diabatic ciculation, which is defined from the atmospheric thermal structure and net radiative heating rates. The radiative transfer model described by Crisp (1990) and Santee (1993) is used to compute solar heating and thermal cooling rates from diurnal averages of the retrieved IRIS temperature and dust distributions. At pressures below 4 mbar, there are large net radiative heating rates (up to 5 K/d) in the equatorial region and large net radiative cooling rates (up to 12 K/d) in the polar regions. These net radiative heating rates are used in a diagnostic stream function model which solves for the meridonal and vertical components of the diabatic circulation simultaneously. We find a two cell circulation, with rising motion over the equator, poleward flow in both hemispheres, sinking motion over both polar regions, and return flow in the lowest atmospheric levels. The maximum poleward velocity is 3 m/s in the tropics at approximately 55 km altitude, and the maximum vertical velocity is 2.5 cm/s downward over the north pole at approximately 60 km altitude. If these large transport rates are sustained for an entire season, the Martian atmosphere above the 1-mbar level is overturned in about 38 days. This diabatic circulation is qualitatively similar to the terrestial diabatic circulation at the comparable season, but is more vigorous.

Santee, Michelle L.↗

Diagnostic calculations of the circulation in the Martian atmosphere

The circulation of the Martian atmosphere during late southern summer is derived from atmospheric temperature and dust distributions retrieved from a subset of the Mariner 9 infrared interferometer spectrometer (IRIS) thermal emission spectra (L(sub s) = 343-348 deg). Zonal-mean zonal winds are calculated by assuming gradient wind balance and zero surface zonal wind. Both hemispheres have intense midlatitude westerly jets with velocities of 80-90 m/s near 50 km; in the southern tropics the winds are easterly with velocities of 40 m/s near 50 km. The net effect of the zonal mean meridional circulation and large-scale waves can be approximated by the diabatic circulation, which is defined from the atmospheric thermal structure and net radiative heating rates. The radiative transfer model described by Crisp (1990) and Santee (1993) is used to compute solar heating and thermal cooling rates from diurnal averages of the retrieved IRIS temperature and dust distributions. At pressures below 4 mbar, there are large net radiative heating rates (up to 5 K/d) in the equatorial region and large net radiative cooling rates (up to 12 K/d) in the polar regions. These net radiative heating rates are used in a diagnostic stream function model which solves for the meridional and vertical components of the diabatic circulation simultaneously. We find a two-cell circulation, with rising motion over the equator, poleward flow in both hemispheres, sinking motion over both polar regions, and return flow in the lowest atmospheric levels. The maximum poleward velocity is 3 m/s in the tropics at approx. 55 km altitude, and the maximum vertical velocity is 2.5 cm/s downward over the north pole at approx. 60 km altitude. If these large transport rates are sustained for an entire season, the Martian atmosphere above the 1-mbar level is overturned in about 38 days. This diabatic circulation is qualitatively similar to the terrestrial diabatic circulation at the comparable season, but is more vigorous.

Santee, Michelle L.↗

Challenges of Sustaining the International Space Station Through 2020 and Beyond: Reassessing Confidence Targets for System Availability

The International Space Station (ISS) was originally designed to operate until 2015 with a plan for deorbiting the ISS in 2016. Currently, the international partnership has agreed to extend the operations until 2020 and discussions are underway to extend the life even further to 2028. Each partner is responsible for the sustaining engineering, sparing, and maintenance of their own segments. National Aeronautics and Space Administration's (NASA's) challenge is to purchase the needed number of spares to maintain the functional availability of the ISS systems necessary for the United States On-Orbit Segment s contribution. This presentation introduces an analytical approach to assessing uncertainty in ISS hardware necessary to extend the life of the vehicle. Some key areas for consideration are: establishing what confidence targets are required to ensure science can be continuously carried out on the ISS, defining what confidence targets are reasonable to ensure vehicle survivability, considering what is required to determine if the confidence targets are too high, and whether sufficient number of spares are purchased. The results of the analysis will provide a methodological basis for reassessing vehicle subsystem confidence targets. This analysis compares the probability of existing spares exceeding the total expected unit demand of the Orbital Replacement Unit (ORU) in functional hierarchies approximating the vehicle subsystems. In cases where the functional hierarchies' availability does not meet subsystem confidence targets, the analysis will further identify which ORUs may require additional spares to extend the life of the ISS. The resulting probability is dependent upon hardware reliability estimates. However, the ISS hardware fleet carries considerable epistemic uncertainty which must be factored into the development and execution of sparing risk postures. In addition, it is also recognized that uncertainty in the assessment is due to disconnects between modeled functions and actual subsystem operations. Perhaps most importantly, it is acknowledged that conservative confidence targets per subsystem are currently accepted. This presentation will also discuss how subsystem confidence targets may be relaxed based on calculating the level of uncertainty for each corresponding ORU-function. The presentation will conclude with the various strengths and limitations for implementing the analytical approach in sustaining the ISS through end of life; 2020 and beyond.

Lutomski, Michael G.↗

The Artificial Intelligence Ontology: LLM-Assisted Construction of AI Concept Hierarchies

The Artificial Intelligence Ontology (AIO) is a systematization of artificial intelligence (AI) concepts, methodologies, and their interrelations. Developed via manual curation, with the additional assistance of large language models (LLMs), AIO aims to address the rapidly evolving landscape of AI by providing a comprehensive framework that encompasses both technical and ethical aspects of AI technologies. The primary audience for AIO includes AI researchers, developers, and educators seeking standardized terminology and concepts within the AI domain. We use the term “branches” for classes, and their subclasses, in our ontology that are subclasses of owl:Thing. AIO contains eight branches: Bias, Layer, Machine Learning Task, Mathematical Function, Model, Network, Preprocessing, and Training Strategy, each designed to support the modular composition of AI methods and facilitate a deeper understanding of deep learning architectures and ethical considerations in AI. AIO uses the Ontology Development Kit (ODK) for its creation and maintenance, with its content being more easily updated through AI-driven curation support. This approach not only ensures the ontology's relevance amidst the fast-paced advancements in AI but also significantly enhances its utility for researchers, developers, and educators by simplifying the integration of new AI concepts and methodologies. The ontology's utility is demonstrated through the annotation of AI methods data in a catalog of AI research publications and the integration into the BioPortal ontology resource, highlighting its potential for cross-disciplinary research. The AIO ontology is open source and is available on GitHub ( https://w3id.org/aio/ ) and BioPortal ( https://bioportal.bioontology.org/ontologies/AIO ).

Joachimiak, Marcin P. [Biosystems Data Science Dep↗

Inter-Domain Fusion for Enhanced Intrusion Detection in Power Systems: An Evidence Theoretic and Meta-Heuristic Approach

False alerts due to misconfigured or compromised intrusion detection systems (IDS) in industrial control system (ICS) networks can lead to severe economic and operational damage. However, research using deep learning to reduce false alerts often requires the physical and cyber sensor data to be trustworthy. Implicit trust is a major problem for artificial intelligence or machine learning (AI/ML) in cyber-physical system (CPS) security, because when these solutions are most urgently needed is also when they are most at risk (e.g., during an attack). To address this, the Inter-Domain Evidence theoretic Approach for Inference (IDEA-I) is proposed that reframes the detection problem as how to make good decisions given uncertainty. Specifically, an evidence theoretic approach leveraging Dempster–Shafer (DS) combination rules and their variants is proposed for reducing false alerts. A multi-hypothesis mass function model is designed that leverages probability scores obtained from supervised-learning classifiers. Using this model, a location-cum-domain-based fusion framework is proposed to evaluate the detector’s performance using disjunctive, conjunctive, and cautious conjunctive rules. The approach is demonstrated in a cyber-physical power system testbed, and the classifiers are trained with datasets from Man-In-The-Middle attack emulation in a large-scale synthetic electric grid. For evaluating the performance, we consider plausibility, belief, pignistic, and general Bayesian theorem-based metrics as decision functions. To improve the performance, a multi-objective-based genetic algorithm is proposed for feature selection considering the decision metrics as the fitness function. Finally, we present a software application to evaluate the DS fusion approaches with different parameters and architectures.

42 ENGINEERING↗