Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “time sequence analysis”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Shadow energy functionals and potentials in Born–Oppenheimer molecular dynamics

In Born–Oppenheimer molecular dynamics (BOMD) simulations based on the density functional theory (DFT), the potential energy and the interatomic forces are calculated from an electronic ground state density that is determined by an iterative self-consistent field optimization procedure, which, in practice, never is fully converged. The calculated energies and forces are, therefore, only approximate, which may lead to an unphysical energy drift and instabilities. Here, we discuss an alternative shadow BOMD approach that is based on backward error analysis. Instead of calculating approximate solutions for an underlying exact regular Born–Oppenheimer potential, we do the opposite. Instead, we calculate the exact electron density, energies, and forces, but for an underlying approximate shadow Born–Oppenheimer potential energy surface. In this way, the calculated forces are conservative with respect to the approximate shadow potential and generate accurate molecular trajectories with long-term energy stabilities. We show how such shadow Born–Oppenheimer potentials can be constructed at different levels of accuracy as a function of the integration time step, δt, from the constrained minimization of a sequence of systematically improvable, but approximate, shadow energy density functionals. For each energy functional, there is a corresponding ground state Born–Oppenheimer potential. These pairs of shadow energy functionals and potentials are higher-level generalizations of the original “zeroth-level” shadow energy functionals and potentials used in extended Lagrangian BOMD. The proposed shadow energy functionals and potentials are useful only within this extended dynamical framework, where also the electronic degrees of freedom are propagated as dynamical field variables together with the atomic positions and velocities. The theory is quite general and can be applied to MD simulations using approximate DFT, Hartree–Fock, or semi-empirical methods, as well as to coarse-grained flexible charge models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1986

Tether crawler system

A crawler system is designed to move a low-g/variable-g laboratory module along a tether between the Space Station and an attached space platform. An analysis is made of the effects of control law parameter change on the displacement, velocity, and acceleration of the crawler system. The control law is then modified by the addition of a constant-velocity section and the values of distance traveled, velocity, and acceleration are analyzed as a function of time. The power and torque equations are derived for a crawler system moving along a tether in orbit and numerical values of power and torque required for each prescribed movement are calculated versus time for four different cases using the control laws. A two-step control sequence is selected to permit initial location along the tether by distance traveled, followed by a vernier movement to reach the final desired constant net acceleration level. The components for the control system are identified and arranged in a block disgram configuration. The support subsystems are also identified. The sections were integrated to develop a procedure for the determination of crawler system performance requirements and the initial design of tether crawler systems.

Swanson, Frank R.↗
NASA NTRS1988

Extended period of K/T boundary mass extinction in the marine realm

The Cretaceous/Tertiary (K/T) boundary mass extinction has been widely recognized as a nearly instantaneous catastrophy among marine plankton such as foraminifera. However, the suddenness of this extinction event may have been overemphasized because most pelagic K/T boundary sequences are stratigraphically incomplete and generally lack the earliest Tertiary (Zones P0 and P1a) either due to carbonate dissolution and/or non-deposition. Stratigraphically complete sections appear to be restricted to continental shelf regions with high sedimentation rates and deposition well above the CCD. Such sections have been recovered from El Kef, Tunisia (1) and Brazos River, Texas. Quantitative foraminiferal analysis of these sections indicate an extinction pattern beginning below the K/T boundary and ending above the boundary. These data imply that the mass extinction event was not geologically instantaneous, but occurred over an extended period of time. Evidence supporting this conclusion is discussed.

Keller, G.↗
NASA NTRS2009

Alternative Representations of Convective Processes in the NASA GEOS-5 AGCM

The gap in explicit resolution of phenomena between global climate models and cloud resolving models is shrinking at a steady pace with global integrations of several km in resolution now practical for at least some time scales. In moving toward finer resolution the long standing problem of convective parameterization is being examined along with the assumption of convective quasi-equilibrium and how this can be reconciled with the stochastic and intermittent nature of convection. In this context we examine the nature of parameterized convection in the NASA Goddard Earth Observing System (GEOS-5) Atmospheric General Circulation Model. Our analysis uses both coarse (2.5 degree) and fine scale 0.25 degree spatial resolution integrations. Two basic formulations are compared: the default option is the Relaxed Arakawa-Schubert (RAS) scheme which invokes a sequence of linearly entraining plumes and quasi-equilibrium closure. An optional modification of this method (the "Stochastic Tokioka" constraint) places a random lower limit on plume entrainment. An alternative representation is the Kain-Fritsch parameterization which was originally developed for mesoscale numerical modeling strategies. Here entrainment is determined by a crude buoyancy sorting approach that allows the plume spectrum to be more responsive to ambient vertical stratification of moisture. Diagnostics of the model behavior are referenced to recent observational evidence of continuous phase transition behavior. In particular we examine the relationship between column water vapor and probablility of convective presence and intensity. Sensitivity of the statistics of convective behavior to parcel mixing/entrainment formulations and parcel initial thermodynamics are considered. Observational statistics from A-Train and TRMM sensors provide validation of the model integrations.

Robertson, Franklin↗
NASA NTRS1993

Towards a generalized computational fluid dynamics technique for all Mach numbers

Currently there exists no single unified approach for efficiently and accurately solving computational fluid dynamics (CFD) problems across the Mach number regime, from truly low speed incompressible flows to hypersonic speeds. There are several CFD codes that have evolved into sophisticated prediction tools with a wide variety of features including multiblock capabilities, generalized chemistry and thermodynamics models among other features. However, as these codes evolve, the demand placed on the end user also increases simply because of the myriad of features that are incorporated into these codes. In order for a user to be able to solve a wide range of problems, several codes may be needed requiring the user to be familiar with the intricacies of each code and their rather complicated input files. Moreover, the cost of training users and maintaining several codes becomes prohibitive. The objective of the current work is to extend the compressible, characteristic-based, thermochemical nonequilibrium Navier-Stokes code GASP to very low speed flows and simultaneously improve convergence at all speeds. Before this work began, the practical speed range of GASP was Mach numbers on the order of 0.1 and higher. In addition, a number of new techniques have been developed for more accurate physical and numerical modeling. The primary focus has been on the development of optimal preconditioning techniques for the Euler and the Navier-Stokes equations with general finite-rate chemistry models and both equilibrium and nonequilibrium thermodynamics models. We began with the work of Van Leer, Lee, and Roe for inviscid, one-dimensional perfect gases and extended their approach to include three-dimensional reacting flows. The basic steps required to accomplish this task were a transformation to stream-aligned coordinates, the formulation of the preconditioning matrix, incorporation into both explicit and implicit temporal integration schemes, and modification of the numerical flux formulae. In addition, we improved the convergence rate of the implicit time integration schemes in GASP through the use of inner iteration strategies and the use of the GMRES (General Minimized Resisual) which belongs to the class of algorithms referred to as Krylov subspace iteration. Finally, we significantly improved the practical utility of GASP through the addition of mesh sequencing, a technique in which computations begin on a coarse grid and get interpolated onto successively finer grids. The fluid dynamic problems of interest to the propulsion community involve complex flow physics spanning different velocity regimes and possibly involving chemical reactions. This class of problems results in widely disparate time scales causing numerical stiffness. Even in the absence of chemical reactions, eigenvalue stiffness manifests itself at transonic and very low speed flows which can be quantified by the large condition number of the system and evidenced by slow convergence rates. This results in the need for thorough numerical analysis and subsequent implementation of sophisticated numerical techniques for these difficult yet practical problems. As a result of this work, we have been able to extend the range of applicability of compressible codes to very low speed inviscid flows (M = .001) and reacting flows.

Walters, R. W.↗
DOE OSTI2023

COMPUTATIONAL MODELING OF IGNITION AND PREMIXED FLAME PROPAGATION INITIATED BY A PRE-CHAMBER TURBULENT JET

Addressing the pressing need for reduced carbon emissions, Turbulent Jet Ignition (TJI) emerges as a promising technology for ultra-lean combustion, offering enhanced thermal efficiencies and minimized cyclic variability in spark-ignited engines. To facilitate rapid testing and integration of this technology, a robust computational modeling framework is crucial. This study delves into the predictive capabilities of computational models for main-chamber ignition and premixed flame propagation using a single-cycle TJI rig measured by Biswas et al. (Applied Thermal Engineering, vol 106, 2016). Employing an open-source compressible flow simulation solver with Large Eddy Simulation (LES) for turbulence modeling, the investigation integrates the conventional Laminar Finite Rate Chemistry (LFRC) model alongside the transported Probability Density Method (PDF) for turbulence-chemistry interaction. A fully-consistent Eulerian Monte-Carlo Fields (EMCF) method is utilized to approximate the transported PDF, while Interaction by Exchange with Mean is employed to close micro-mixing terms in stochastic differential equations. A reduced chemical reaction mechanism with 21 species and 84 reactions (DRM-19) is used for solving chemical kinetics, and a double Gaussian energy deposition model is used to approximate the spark ignition in the pre-chamber. An unstructured O-grid mesh with 0.3 million cells in the prechamber and 1 million cells in the main chamber is employed. Results are divided into two phases: pre-chamber initialization and full TJI simulations. Validation of the predicted pre-chamber flame propagation and the lean ignition in the main-chamber is carried out by using available experimental data. Under quiescent conditions, both the LFRC and transported PDF methods largely underestimate the flame speed and subsequent pressure growth in the pre-chamber. A linear momentum forcing technique is applied to investigate the impact of initial turbulence in the pre-chamber, demonstrating a notable influence on flame propagation. Fine-tuning of the forcing coefficient reproduces the sudden pressure growth observed in the experiment. The experimentally validated pre-chamber simulation serves as the initial condition for the full TJI simulations. It is found that the LFRC model fails to predict lean-ignition in the main-chamber, resulting in a misfiring event. Incorporation of turbulence-chemistry interaction using the transported PDF method substantially improves the prediction of the ignition event in the main-chamber, achieving fair qualitative agreement and quantitative validation of combustion parameters within ±10% of the reported experimental data. The rich simulation results consisting of a full set of statistical description of the thermo-chemical states enable us to gain deep insights into the ignition mechanisms in the main chamber, which is limited when done experimentally. A novel dual ignition phenomenon is revealed in the TJI rig for the first time. Initially, a primary ignition kernel is formed at a downstream location which eventually detaches from the main jet. As the jet momentum decreases, a secondary ignition event follows, this time at a more upstream location which eventually combines with the primary ignition kernel to form a single connected flame front. Investigation of these ignition sequences in chemical composition space reveal distinct differences between the two. The primary ignition event in the main-chamber is followed by a large concentration of active radicals from the pre-chamber jet, accelerating the chain-branching steps, characterizing what has been referred to as flame ignition. In contrast, the secondary ignition occurs in the absence of active radicals in the pre-chamber jet, hence characterized as jet ignition. Further analysis of the effect of pre-chamber jet characteristics on lean ignition in the main-chamber is conducted by setting up cases with different initial pressure ratios (por) between the two chambers, a non-dimensional parameter, ranging from 1.2 to 3.2. As the initial pressure ratio increases, jet momentum increases, with dual ignition observed in cases above por= 2.2. Case with por= 3.2 lead to misfiring. The effect of ignition sequence on global combustion characteristics of TJI is analyzed. Dual ignition events lead to non-monotonicity in combustion characteristics such as global reaction progress variable, flame penetration, and global heat release rate. In dual ignition events, although the rate of fuel consumption and global heat release rate is initially lower, the secondary ignition leads to a sudden increase in flame surface area, resulting in a sudden jump and promoting the overall performance of the TJI system.

42 ENGINEERING↗
NASA NTRS2012

Calibration and Sequence Development Status for the Sample Analysis at Mars Investigation on the Mars Science Laboratory

The measurement goals of the Sample Analysis at Mars (SAM) instrument suite on the "Curiosity" Rover of the Mars Science Laboratory (MSL) include chemical and isotopic analysis of organic and inorganic volatiles for both atmospheric and solid samples [1,2]. SAM directly supports the ambitious goals of the MSL mission to provide a quantitative assessment of habitability and preservation in Gale crater by means of a range of chemical and geological measurements [3]. The SAM FM combined calibration and environmental testing took place primarily in 2010 with a limited set of tests implemented after integration into the rover in January 2011. The scope of SAM FM testing was limited both to preserve SAM consumables such as life time of its electromechanical elements and to minimize the level of terrestrial contamination in the SAM instrument. A more comprehensive calibration of a SAM-like suite of instruments will be implemented in 2012 with calibration runs planned for the SAM testbed. The SAM Testbed is nearly identical to the SAM FM and operates in a ambient pressure chamber. The SAM Instrument Suite: SAM's instruments are a Quadrupole Mass Spectrometer (QMS), a 6-column Gas Chromatograph (GC), and a 2-channel Tunable Laser Spectrometer (TLS). Gas Chromatography Mass Spectrometry is designed for identification of even trace organic compounds. The TLS [5] secures the C, H, and O isotopic composition in carbon dioxide, water, and methane. Sieved materials are delivered from the MSL sample acquisition and processing system to one of68 cups of the Sample Manipulation System (SMS). 59 of these cups are fabricated from inert quartz. After sample delivery, a cup is inserted into one of 2 ovens for evolved gas analysis (EGA ambient to >9500C) by the QMS and TLS. A portion of the gas released can be trapped and subsequently analyzed by GCMS. Nine sealed cups contain liquid solvents and chemical derivatization or thermochemolysis agents to extract and transform polar molecules such as amino acids, nucleobases, and carboxylic acids into compounds that are sufficiently volatile to transmit through the GC columns. The remaining 6 cups contain calibrants. SAM FM Calibration Overview: The SAM FM calibration in the Mars chamber employed a variety of pure gases, gas mixtures, and solid materials. Isotope calibration runs for the TLS utilized 13C enriched C02 standards and 0 enriched CH4. A variety of fluorocarbon compounds that spanned the entire mass range of the QMS as well as C3-C6 hydrocarbons were utilized for calibration of the GCMS. Solid samples consisting of a mixture of calcite, melanterite, and inert silica glass either doped or not with fluorocarbons were introduced into the SAM FM cups through the SAM inlet funnel/tube system.

Mahaffy, Paul R.↗
NASA NTRS1987

Fluvial valleys on Martian volcanoes

Channels and valleys were known on the Martian volcanoes since their discovery by the Mariner 9 mission. Their analysis has generally centered on interpretation of possible origins by fluvial, lava, or viscous flows. The possible fluvial dissection of Martian volcanoes has received scant attention in comparison to that afforded outflow, runoff, and fretted channels. Photointerpretative, mapping, and morphometric studies of three Martian volcanoes were initiated: Ceraunius Tholus, Hecate Tholus, and Alba Patera. Preliminary morphometric results indicate that, for these three volcanoes, valley junction angles increase with decreasing slope. Drainage densities are quite variable, apparently reflecting complex interactions in the landscape-forming factors described. Ages of the Martian volcanoes were recently reinterpreted. This refined dating provides a time sequence in which to evaluate the degradational forms. An anomaly has appeared from the initial study: fluvial valleys seem to be present on some Martian volcanoes, but not on others of the same age. Volcanic surfaces characterized only by high permeability lava flows may have persisted without fluvial dissection.

Baker, Victor R.↗
DOE OSTI2023

Causal interaction in high frequency turbulence at the biosphere–atmosphere interface: Structure–function coupling

At the biosphere–atmosphere interface, nonlinear interdependencies among components of an ecohydrological complex system can be inferred using multivariate high frequency time series observations. Information flow among these interacting variables allows us to represent the causal dependencies in the form of a directed acyclic graph (DAG). Here, we use high frequency multivariate data at 10 Hz from an eddy covariance instrument located at 25 m above agricultural land in the Midwestern US to quantify the evolutionary dynamics of this complex system using a sequence of DAGs by examining the structural dependency of information flow and the associated functional response. We investigate whether functional differences correspond to structural differences or if there are no functional variations despite the structural differences. We base our analysis on the hypothesis that causal dependencies are instigated through information flow, and the resulting interactions sustain the dynamics and its functionality. To test our hypothesis, we build upon causal structure analysis in the companion paper to characterize the information flow in similarly clustered DAGs from 3-min non-overlapping contiguous windows in the observational data. We characterize functionality as the nature of interactions as discerned through redundant, unique, and synergistic components of information flow. Through this analysis, we find that in turbulence at the biosphere–atmosphere interface, the variables that control the dynamic character of the atmosphere as well as the thermodynamics are driven by non-local conditions, while the scalar transport associated with CO and H 2 O is mainly driven by short-term local conditions.

58 GEOSCIENCES↗
DOE OSTI2022

A Census of the 32 Ori Association with Gaia*

I have used high-precision photometry and astrometry from the third data release of Gaia (DR3) to identify candidate members of the 32 Ori association. Spectral types and radial velocities have been measured for subsets of the candidates using new and archival spectra. For the candidates that have radial velocity measurements, I have used UVW velocities to further constrain their membership, arriving at a final catalog of 169 candidates. I estimate that the completeness of the survey is ~90% for spectral types of ≲M7 (≳0.06 M ⊙ ). The histogram of spectral types for the 32 Ori candidates exhibits a maximum at M5 (~0.15 M ⊙ ), resembling the distributions measured for other young clusters and associations in the solar neighborhood. The available UVW velocities indicate that the association is expanding, but they do not produce a well-defined kinematic age. Based on their sequences of low-mass stars in color–magnitude diagrams, the 32 Ori association and Upper Centaurus-Lupus/Lower Centaurus-Crux (UCL/LCC) are coeval to within ±1.2 Myr, and they are younger than the β Pic moving group by ~3 Myr, which agrees with results from previous analysis based on the second data release of Gaia. Finally, I have used mid-IR photometry from the Wide-field Infrared Survey Explorer to check for excess emission from circumstellar disks among the 32 Ori candidates. Disks are detected for 18 candidates, half of which are reported for the first time in this work. The fraction of candidates at ≤M6 that have full, transitional, or evolved disks is 10/149 = 0.07$^{+0.03}_{-0.02'}$ which is consistent with the value for UCL/LCC.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2007

Solar and Interplanetary Sources of Major Geomagnetic Storms (Dst less than or equal to -100 nT) During 1996 - 2005

We present the results of an investigation of the sequence of events from the Sun to the Earth that ultimately led to the 88 major geomagnetic storms (defined by minimum Dst less than or equal to -100 nT) that occurred during 1996 - 2005. The results are achieved through cooperative efforts that originated at the Living with a Star (LWS) Coordinated Data- Analysis Workshop (CDAW) held at George Mason University in March 2005. Based on careful examination of the complete array of solar and in-situ solar wind observations, we have identified and characterized, for each major geomagnetic storm, the overall solar-interplanetary (solar-IP) source type, the time, velocity and angular width of the source coronal mass ejection (CME), the type and heliographic location of the solar source region, the structure of the transient solar wind flow with the storm-driving component specified, the arrival time of shock/disturbance, and the start and ending times of the corresponding IP CME (ICME). The storm-driving component, which possesses a prolonged and enhanced southward magnetic field (B(sub s)) may be an ICME, the sheath of shocked plasma (SH) upstream of an ICME, a corotating interaction region (CIR), or a combination of these structures. We classify the Solar-IP sources into three broad types: (1) S-type, in which the storm is associated with a single ICME and a single CME at the Sun; (2) M-type, in which the storm is associated with a complex solar wind flow produced by multiple interacting ICMEs arising from multiple halo CMEs launched from the Sun in a short period; (3) C-type, in which the storm is associated with a CIR formed at the leading edge of a high speed stream originating from a solar coronal hole (CH). For the 88 major storms, the S-type, M-type and C-type events number 53 (60%): 24 (27%) and 11 (13%), respectively. For the 85 events for which the surface source regions could be investigated, 54 (63%) of the storms originated in solar active regions, 10 (12%) in quiet Sun regions associated with quiescent filaments or filament channels, and 11 (13%) were associated with coronal holes. Remarkably, 10 (12%) CME-driven events showed no sign of eruptive features on the surface (e.g., no flare, no coronal dimming, and no loop arcade, etc), even though all the available solar observation in a suitable time period were carefully examined. Thus, while it is generally true that a major geomagnetic storm is more likely to be driven by a front-side fast halo CME associated with a major flare, our study indicates a broad distribution of source properties. The implications of the results for space weather forecasting are briefly discussed.

Zhang, J.↗
NASA NTRS2008

FootFall: A Ground Based Operations Toolset Enabling Walking for the ATHLETE Rover

The ATHLETE (All-Terrain Hex-Limbed Extra-Terrestrial Explorer) vehicle consists of six identical, six degree of freedom limbs. FootFall is a ground tool for ATHLETE intended to provide an operator with integrated situational awareness, terrain reconstruction, stability and safety analysis, motion planning, and decision support capabilities to enable the efficient generation of flight software command sequences for walking. FootFall has been under development at NASA Ames for the last year, and having accomplished the initial integration, it is being used to generate command sequences for single footfalls. In this paper, the architecture of FootFall in its current state will be presented, results from the recent Human Robotic Systems Project?s Integrated Field Test (Moses Lake, Washington, June, 2008) will be discussed, and future plans for extending the capabilities of FootFall to enable ATHLETE to walk across a boulder field in real time will be described.

SunSpiral, Vytas↗
DOE OSTI2020

Genome-Wide Analysis of RNA Decay in the Cyanobacterium Synechococcus sp. Strain PCC 7002

ABSTRACT RNA degradation is an important process that influences the ultimate concentration of individual proteins inside cells. While the main enzymes that facilitate this process have been identified, global maps of RNA turnover are available for only a few species. Even in these cases, there are few sequence elements that are known to enhance or destabilize a native transcript; even fewer confer the same effect when added to a heterologous transcript. To address this knowledge gap, we assayed genome-wide RNA degradation in the cyanobacterium Synechococcus sp. strain PCC 7002 by collecting total RNA samples after stopping nascent transcription with rifampin. We quantified the abundance of each position in the transcriptome as a function of time using RNA-sequencing data and later analyzed the global mRNA decay map using machine learning principles. Half-lives, calculated on a per-ORF (open reading frame) basis, were extremely short, with a median half-life of only 0.97 min. Despite extremely rapid turnover of most mRNA, transcripts encoding proteins involved in photosynthesis were both highly expressed and highly stable. Upon inspection of these stable transcripts, we identified an enriched motif in the 3′ untranslated region (UTR) that had similarity to Rho-independent terminators. We built statistical models for half-life prediction and used them to systematically identify sequence motifs in both 5′ and 3′ UTRs that correlate with stabilized transcripts. We found that transcripts linked to a terminator containing a poly(U) tract had a longer half-life than both those without a poly(U) tract and those without a terminator. IMPORTANCE RNA degradation is an important process that affects the final concentration of individual mRNAs, affecting protein expression and cellular physiology. Studies of how RNA is degraded increase our knowledge of this fundamental process as well as enable the creation of genetic tools to manipulate RNA stability. By studying global transcript turnover, we searched for sequence elements that correlated with transcript (in)stability and used these sequences to guide tool design. This study probes global RNA turnover in a cyanobacterium, Synechococcus sp. strain PCC 7002, that both has a unique array of RNases that facilitate RNA degradation and is an industrially relevant strain that could be used to convert CO 2 and sunlight into useful products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Turbo‐charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond

Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and de novo domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene‐free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High‐throughput sequencing technologies, including long‐read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements—often missed by standard genotyping—when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user‐friendly, synthetic biology‐compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue‐specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next‐generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Uncertainty quantification and sensitivity analysis of a nuclear thermal propulsion reactor startup sequence

The research presented in this article describes progress in applying stochastic methods, uncertainty quantification, parametric studies, and variance-based sensitivity analysis (also known as Sobol sensitivity analysis) to a full-core model of a nuclear thermal propulsion (NTP) system simulated via the radiation transport code Griffin to simulate neutronics. Our goal is to develop a reduced-order (surrogate) model that can be rapidly sampled with perturbations to multiple input parameters. In this NTP system, reactivity and power feedback affect the rotation of control drums (CDs), which is itself controlled by a hybrid proportional-integral-derivative (PID) controller actuated by the power demand and reactivity feedback from the numerical model. This model uses reactor kinetic feedback (mean generation time [Λ] and effective delayed neutron fraction [ β eff ] from a transient Griffin simulation executed via Griffin’s improved quasi-static solver to provide the kinetic parameters) as inputs to functions that control the CD rotation angle. By investigating numerous stochastic approaches, we developed a dual-purpose surrogate model of the NTP system, using polynomial regression in the Multiphysics Object-Oriented Simulation Environment (MOOSE) Stochastic Tools Module (STM). The trained model can be rapidly sampled while simultaneously perturbing various input parameters, such as coefficients on the PID control or temperature (directly affecting the neutron cross section). The surrogate model delivers accurate (within 5%) results at speeds orders of magnitude faster (minutes, not days of computational time) than the base model. Once the surrogate model has been trained, distributions of the uncertain parameters can be changed at will to investigate the effects of perturbing multiple inputs as well as the effects of these inputs on the model output. For example, coefficients used in the PID control system may vary due to some type of physical interference, or uncertainty may exist in the temperature of the neutron cross sections in various regions of the reactor. A distribution can be placed on these parameters, and operational boundaries can be determined. The goal of this work is to support development of an advanced control system for operating CDs in a functioning NTP system. This work is a scoping study of the MOOSE STM.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗
DOE OSTI2021

Reoptimization of Quantum Circuits via Hierarchical Synthesis

The current phase of quantum computing is in the Noisy Intermediate-Scale Quantum (NISQ) era. On NISQ devices, two-qubit gates such as CNOTs are much noisier than single-qubit gates, so it is essential to minimize their count. Quantum circuit synthesis is a process of decomposing an arbitrary unitary into a sequence of quantum gates, and can be used as an optimization tool to produce shorter circuits to improve overall circuit fidelity. However, the time-to-solution of synthesis grows exponentially with the number of qubits. As a result, synthesis is intractable for circuits on a large qubit scale. In this paper, we propose a hierarchical, block-by-block opti-mization framework, QGo, for quantum circuit optimization. Our approach allows an exponential cost optimization to scale to large circuits. QGo uses a combination of partitioning and synthesis: 1) partition the circuit into a sequence of independent circuit blocks; 2) re-generate and optimize each block using quantum synthesis; and 3) re-compose the final circuit by stitching all the blocks together. We perform our analysis and show the fidelity improvements in three different regimes: small-size circuits on real devices, medium-size circuits on noisy simulations, and large-size circuits on analytical models. Our technique can be applied after existing optimizations to achieve higher circuit fidelity. Further, using a set of NISQ benchmarks, we show that QGo can reduce the number of CNOT gates by 29.9% on average and up to 50% when compared with industrial compiler optimizations such as t|ket). When executed on the IBM Athens system, shorter depth leads to higher circuit fidelity. We also demonstrate the scalability of our QGo technique to optimize circuits of 60+ qubits, Our technique is the first demonstration of successfully employing and scaling synthesis in the compilation tool chain for large circuits. Overall, our approach is robust for direct incorporation in production compiler toolchains to further improve the circuit fidelity.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Identification Uncertainty in Inverse Material Model Parameter Determination: A Sensitivity‐Based Decision Process for Load Path Selection

This research proposes a sensitivity-based framework for selecting the optimal prescribed loading path for a biaxial cruciform specimen. Optimality here is determined by the direction and magnitude of the prescribed displacement that minimizes the influence of random noise on the material model parameter identification. Using simulated experimental data based on finite element simulation, in this work, we identify the material model parameters of a Ludwik hardening model and plane stress implementation of the Hill-48 yield criterion using finite element model updating (FEMU). Our analysis reveals that the identification (or estimator) uncertainty of model parameters depends on the displacement boundary conditions (i.e., loading sequence) and the ground-truth value of the individual parameters. Optimal experimental design (OED) criteria based on the Fisher information matrix were investigated to mitigate indecision in the choice of optimal load path when the identification uncertainty of different material model parameters optimized at different load paths. The determinant of the Fisher information matrix was chosen here as the more useful metric due to its ability to capture uncertainty of the most influential material model parameters. The proposed framework demonstrates potential for real-time automated load step selection using scalar criteria derived prior to mechanical loading. The framework can be generalized to other geometries, boundary conditions and material models, allowing this procedure to be utilized for different experimental configurations and materials.

Fayad, Samuel S. [University of Illinois at Urbana↗
DOE OSTI2024

The direct and indirect drivers shaping RNA viral communities in grassland soils

ABSTRACT Recent studies have revealed diverse RNA viral communities in soils. Yet, how environmental factors influence soil RNA viruses remains largely unknown. Here, we recovered RNA viral communities from bulk metatranscriptomes sequenced from grassland soils managed for 5 years under multiple environmental conditions including water content, plant presence, cultivar type, and soil depth. More than half of the unique RNA viral contigs (64.6%) were assigned with putative hosts. About 74.7% of these classified RNA viral contigs are known as eukaryotic RNA viruses suggesting eukaryotic RNA viruses may outnumber prokaryotic RNA viruses by nearly three times in this grassland. Of the identified eukaryotic RNA viruses and the associated eukaryotic species, the most dominant taxa were Mitoviridae with an average relative abundance of 72.4%, and their natural hosts, Fungi with an average relative abundance of 56.6%. Network analysis and structural equation modeling support that soil water content, plant presence, and type of cultivar individually demonstrate a significant positive impact on eukaryotic RNA viral richness directly as well as indirectly on eukaryotic RNA viral abundance via influencing the co-existing eukaryotic members. A significant negative influence of soil depth on soil eukaryotic richness and abundance indirectly impacts soil eukaryotic RNA viral communities. These results provide new insights into the collective influence of multiple environmental and community factors that shape soil RNA viral communities and offer a structured perspective of how RNA virus diversity and ecology respond to environmental changes. IMPORTANCE Climate change has been reshaping the soil environment as well as the residing microbiome. This study provides field-relevant information on how environmental and community factors collectively shape soil RNA communities and contribute to ecological understanding of RNA viral survival under various environmental conditions and virus-host interactions in soil. This knowledge is critical for predicting the viral responses to climate change and the potential emergence of biothreats.

59 BASIC BIOLOGICAL SCIENCES↗