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At least 163 records · Page 9

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DOE OSTI2023

Transcriptome architecture of the three main lineages of agrobacteria

ABSTRACT Agrobacteria are a diverse, polyphyletic group of prokaryotes with multipartite genomes capable of transferring DNA into the genomes of host plants, making them an essential tool in plant biotechnology. Despite their utility in plant transformation, genome-wide transcriptional regulation is not well understood across the three main lineages of agrobacteria. Transcription start sites (TSSs) are a necessary component of gene expression and regulation. In this study, we used differential RNA-seq and a TSS identification algorithm optimized on manually annotated TSS, then validated with existing TSS to identify thousands of TSS with nucleotide resolution for representatives of each lineage. We extend upon the 356 TSSs previously reported in Agrobacterium fabrum C58 by identifying 1,916 TSSs. In addition, we completed genomes and phenotyping of Rhizobium rhizogenes C16/80 and Allorhizobium vitis T60/94, identifying 2,650 and 2,432 TSSs, respectively. Parameter optimization was crucial for an accurate, high-resolution view of genome and transcriptional dynamics, highlighting the importance of algorithm optimization in genome-wide TSS identification and genomics at large. The optimized algorithm reduced the number of TSSs identified internal and antisense to the coding sequence on average by 90.5% and 91.9%, respectively. Comparison of TSS conservation between orthologs of the three lineages revealed differences in cell cycle regulation of ctrA as well as divergence of transcriptional regulation of chemotaxis-related genes when grown in conditions that simulate the plant environment. These results provide a framework to elucidate the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. IMPORTANCE Transcription start sites (TSSs) are fundamental for understanding gene expression and regulation. Agrobacteria, a group of prokaryotes with the ability to transfer DNA into the genomes of host plants, are widely used in plant biotechnology. However, the genome-wide transcriptional regulation of agrobacteria is not well understood, especially in less-studied lineages. Differential RNA-seq and an optimized algorithm enabled identification of thousands of TSSs with nucleotide resolution for representatives of each lineage. The results of this study provide a framework for elucidating the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The optimized algorithm also highlights the importance of parameter optimization in genome-wide TSS identification and genomics at large.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A process optimization framework for laser direct energy deposition: Densification, microstructure, and mechanical properties of an Fe-Cr alloy

Laser Direct Energy Deposition (DED) is a metal additive manufacturing technique with the ability to fabricate large and complex parts through deposition of metal powders. However, achieving high-density parts and targeted build heights using DED can be challenging due to the large number of highly sensitive process variables. This work proposes a robust fabrication parameter optimization framework to generate process maps for primary parameters in DED, including laser power, scan speed, mass flow rate, hatch spacing, and layer height. Simple single-track experiments were utilized to map out the parameter space, and a combination of geometric criteria for hatch spacing and layer height were proposed to determine parameter sets that achieve both targeted build heights and mitigate porosity formation. Using this framework, specimens with >99 % density and consistent mechanical properties were successfully fabricated over a wide range of process parameters for an Fe-9wt.%Cr (Fe9Cr) alloy, a surrogate for radiation damage-resistant reduced activation ferritic/martensitic (RAFM) steels. Processing these materials using DED is of particular interest in the development of plasma facing components for nuclear fusion applications. The microstructure and mechanical properties of as-printed Fe9Cr were characterized using optical and electron microscopy, X-ray diffraction, and uniaxial tensile tests. As-printed Fe9Cr displayed ~25 % elongation and ultimate tensile strengths of up to 475 MPa which is comparable to similar wrought alloys. Finally, the proposed framework will allow for accelerated DED parameter optimization for novel alloy systems, as well as open the possibility for local microstructure control while simultaneously mitigating defect formation.

42 ENGINEERING↗

DOE OSTI2025

Differentiable lagrangian shock hydrodynamics with application to stable shock acceleration of density interfaces

We develop a gradient based optimization approach for the equations of compressible, Lagrangian hydrodynamics and demonstrate how it can be employed to automatically uncover strategies to control hydrodynamic instabilities arising from shock acceleration of density interfaces. Strategies for controlling the Richtmyer-Meshkov instability (RMI) are of great benefit for inertial confinement fusion (ICF) where shock interactions with many small imperfections in the density interface lead to instabilities which rapidly grow over time. These instabilities lead to mixing which, in the case of laser driven ICF, quenches the runaway fusion process ruining the potential for positive energy return. Here, we demonstrate that control of these instabilities can be achieved by optimization of initial conditions with ( > 100) parameters. Optimizing over a large parameter space like this is not possible with gradient-free optimization strategies. This requires computation of the gradient of the outputs of a numerical solution to the equations of Lagrangian hydrodynamics with respect to the inputs. We show that the efficient computation of these gradients is made possible via a judicious application of (i) adjoint methods, the exact formal representation of sensitivities involving partial differential equations, and (ii) automatic differentiation (AD), the algorithmic calculation of derivatives of functions. Careful regularization of multiple operators including artificial viscosity and timestep control is required. We perform design optimization of > 100 parameter energy field driving the Richtmyer Meshkov instability showing significant suppression while simultaneously enhancing the acceleration of the interface relative to a nominal baseline case.

Hydrophysics↗

DOE OSTI2022

Machine Learning assisted optimization and parameter space exploration dataset of spin ice Hamiltonian

This repository contains both simulated and experimental structure factor data for the data challenge involving the inverse scattering problem. The simulated data were generated during a machine-learning-assisted optimization routine described in ref[1]. The experimental structure factor was measured on a rare-earth oxide, Dy2Ti2O7 using diffuse neutron scattering from time-of-flight techniques on the CORELLI instrument at the Spallation Neutron Source, Oak Ridge National Laboratory. A Metropolis Monte Carlo code implemented to run in a High-performance computing setting was used to calculated simulated structure factors for the spin-ice Hamiltonian at 680 mK, which is the same temperature as for the experimental data. The total size of all the files in this repository is 5.12 GB. A detailed description of the files is given below. ExperimentalData_630mK.dat â€“ A linearized version of 3-dimensional experimental data of size 61Ã—81Ã—21. This data was processed to remove an estimation of non-magnetic background, including nuclear scattering signal and instrumentation background. Parameters.dat â€“ 6700 samples were evaluated over the 4-dimensional parameter space (J_1, J_2, J_3 and J_(3^' )). There is an additional parameter, D in the spin Hamiltonian to mimic the dipolar interaction between magnetic ions. However, this parameter, D was fixed to a value determined by prior work. This file contains five columns for the parameters J_1, J_2, J_3, J_(3^' ) and D respectively. 3D_Simulation_Data.dat â€“ The simulated structure factor, S(Q) data are included in this file. Each raw contains a linearized array of 3D volumes of S(Q) calculated for the parameter set given in the corresponding row of the file Parameters.dat. The size of the volume data was matched to the experimental data. Qx(h,-h,0).dat, Qy(k,k,-2k).dat, Qz(l,l,l).dat â€“ These files contain the h, k, and l values along with the reciprocal vectors [h,-h,0], [k,k,-2k] and [l,l,l] respectively.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Practical guide to understanding goodness-of-fit metrics used in chemical state modeling of x-ray photoelectron spectroscopy data by synthetic line shapes using nylon as an example

Chemical state analysis of a sample surface through fitting bell-shaped curves to x-ray photoelectron spectroscopic polymer data is reviewed using nylon to introduce and discuss aspects of data analysis. Different strategies for modeling chemistry in nylon spectra are presented and in so doing, a case is made to include in published science the design logic and implementation in terms of line shapes and optimization parameter constraints between components in a peak model. Imperfections in line shape relative to the true shape for photoemission lines, when compensated for using constraints to optimization parameters, are shown to provide chemical state information about a sample that justify, for peak models constructed with these limitations, metrics for goodness-of-fit different from those expected for pulse-counted data.

Materials Science↗

NASA NTRS2022

Multi-Frequency Radiometer-Based Soil Moisture Retrieval and Algorithm Parameterization Using In Situ Sites

L-band brightness temperature (TB) has been shown to provide the best sensitivity to soil moisture (SM) although C- and X-band based products offer a longer time-series from satellite-based measurements. Currently, global coverage SM is routinely produced from spaceborne measurements using all three frequency bands, but despite continued validation efforts of the products, the relative characteristics and performance of these observations have not been fully established. Therefore, this study focused on the parametrization of SM retrieval algorithms at L-, C- and X-bands using TB observations from the L-band radiometer on NASA's SM Active Passive (SMAP) mission and the C- and X-band channels of JAXA's Advanced Microwave Scanning Radiometer 2 (AMSR2) onboard the GCOM-W satellite. These can be applied in global SM retrieval algorithms using either one of the frequencies or a combination of them. The reference in situ SM data was obtained from 12 core validation sites across various land cover types around the world. The investigation highlighted the known challenges of retrieving SM from C- and X-band data compared to the higher sensitivity of the L-band data. Even with a site-specific retrieval algorithm parameterization, the mean correlation of the C- and X-band retrievals for the core validation site SM measurement were much lower than that for L-band, being 0.52 (0.54) and 0.45 (0.47) for vertical (horizontal) polarization, respectively, while for the L-band retrieval the corresponding values were 0.81 (0.77). The parameterization exercise showed that matching the C- and X-band TB measurements with an emission model was not difficult; the problem was relating the observations to SM under the influence of large roughness and vegetation effects. As a result, parameter optimization produced values for some sites that were not realistic or did not allow any practical sensitivity to SM at C- and X-band. Considering the L-band observations, the parameter optimization resulted in superior bias performance as compared to the operational SMAP product parameterization, but the sensitivity to SM changes (R and unbiased root mean square difference) did not improve markedly, or in some cases degraded at the expense of a smaller bias.

passive microwave↗

DOE OSTI2024

Modulated Thermomechanical Analysis of Compression-Molded High-Density Polyethylene

Thermomechanical analysis (TMA) experiments conducted on high-density polyethylene (HDPE) show both reversible and irreversible dimensional changes. To further explore these reversible and irreversible processes, modulated thermomechanical analysis (MTMA) was used. Before reliable data on compression-molded HDPE was collected, a parameter optimization was performed to obtain a suitable MTMA method. Once a suitable method was obtained, several MTMA experiments were conducted on compression-molded HDPE. This work highlights the steps taken during the MTMA parameter optimization and the results obtained from MTMA experiments conducted on pristine compression-molded HDPE samples.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Gradient-informed Hamiltonian Monte Carlo for multicomponent CALPHAD model optimization and uncertainty quantification

CALPHAD model parameter optimization is inherently challenging due to non-smooth objective functions, high-dimensional parameter spaces, and the need for uncertainty quantification (UQ). Traditional weighted nonlinear least squares approaches are computationally efficient but local, whereas black-box global optimizers and ensemble Markov Chain Monte Carlo (MCMC) methods provide broader exploration at substantial computational cost. The objective of this work is to combine the global exploration capability of gradient-informed Hamiltonian Monte Carlo – specifically the No-U-Turn Sampler (NUTS) – with local deterministic refinement using BFGS to efficiently optimize multicomponent CALPHAD models with minimal manual intervention. Analytic gradients are computed via the Jansson derivative framework. The methodology is demonstrated on the Cr—Fe binary system and extended to the Cr—Fe—Ni ternary system with 32 degrees of freedom. For Cr—Fe, NUTS achieves comparable or superior optimality relative to ensemble MCMC while requiring over an order-of-magnitude fewer likelihood evaluations. Parameter uncertainties are quantified through NUTS sampling and propagated to thermodynamic observables using local expansion, demonstrating a novel modular approach that combines binary and ternary parameter subsets without requiring global relaxation. These results establish gradient-informed exploration as a scalable strategy for multicomponent CALPHAD optimization and provide a practical route towards efficient higher-order database development with quantified uncertainty.

36 MATERIALS SCIENCE↗

DOE OSTI2025

HPC for Optimizing Process Parameters to Control Material Evolution in Seamless Induction Hardening of Wind Turbine Main Shaft Bearings

Work proposed in this project focused on understanding the effect of martensitic transformation in the steel on the potential for cracking during seamless induction hardening (SIH) as a function of process conditions to allow the process to optimally scale up. Large-scale, three-dimensional phase-field simulations of martensitic transformation were performed using MEUMAPPS-SS (Microstructure Evolution Using Massively Parallel Phase-field Simulations – Solid State) code developed at Oak Ridge National Laboratory. The simulations were guided by location-specific thermal history generated by experimental measurements of time-temperature history generated at The Timken Company. The simulations were able to capture the morphological evolution of the martensite variants in an Fe-1.0C-1.5Cr steel based on the Nishiyama-Wasserman (NW) orientation relationship. The simulations were also able to quantify the stress-state at the interface between impinging martensite variants. The simulations indicated that the magnitude of the various stress and strain components were dependent on the sizes of the impinging plates with a reduction in these quantities with reduced plate size in agreement with experimental findings. The results obtained from the simulations will be used to guide the optimization of the alloy thermal conditions to eliminate quench cracking during SIH of bearing steels.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2025

HPC for optimizing process parameters to control material evolution in seamless induction hardening of wind turbine main shaft bearings

17 WIND ENERGY↗

NASA NTRS1981

Solar Power Satellite antenna phase control system hardware simulation, phase 4. Volume 2: Analytical simulation of SPS system performance

The pilot signal parameter optimization and power transponder analyses are presented. The SPS antenna phase control system is modeled and the hardware simulation study described. Ionospheric and system phase error effects and the effects of high power amplifier phase and amplitude jitters are considered. Parameter optimization of the spread spectrum receiver, consisting of the carrier tracking loop and the code tracking loop, is described.

Lindsey, W. C.↗

DOE OSTI2020

LCOE Design Optimization Using Genetic Algorithm with Improved Component Models for Medium-Voltage Transformerless PV Inverters

For real-world installations of photovoltaic and other renewable energy resources, the critical design metric is the levelized cost of energy (LCOE); however, many power electronics design optimizations are performed with efficiency and power density as the primary design goals. Recent work has shown that a new LCOE-focused optimization approach can yield improved system designs balancing cost and energy generation. This paper expands the LCOE optimization approach by considering comprehensive optimization parameters, adding new modeling of inductor cost, extending the semiconductor model to include effects of losses on housing cost, and implementing a genetic algorithm to improve computation efficiency.

41 EE - Solar Energy Technologies Office (EE-4S)↗

NASA NTRS1994

Heat transfer measurements for Stirling machine cylinders

The primary purpose of this study was to measure the effects of inflow-produced heat turbulence on heat transfer in Stirling machine cylinders. A secondary purpose was to provide new experimental information on heat transfer in gas springs without inflow. The apparatus for the experiment consisted of a varying-volume piston-cylinder space connected to a fixed volume space by an orifice. The orifice size could be varied to adjust the level of inflow-produced turbulence, or the orifice plate could be removed completely so as to merge the two spaces into a single gas spring space. Speed, cycle mean pressure, overall volume ratio, and varying volume space clearance ratio could also be adjusted. Volume, pressure in both spaces, and local heat flux at two locations were measured. The pressure and volume measurements were used to calculate area averaged heat flux, heat transfer hysteresis loss, and other heat transfer-related effects. Experiments in the one space arrangement extended the range of previous gas spring tests to lower volume ratio and higher nondimensional speed. The tests corroborated previous results and showed that analytic models for heat transfer and loss based on volume ratio approaching 1 were valid for volume ratios ranging from 1 to 2, a range covering most gas springs in Stirling machines. Data from experiments in the two space arrangement were first analyzed based on lumping the two spaces together and examining total loss and averaged heat transfer as a function of overall nondimensional parameter. Heat transfer and loss were found to be significantly increased by inflow-produced turbulence. These increases could be modeled by appropriate adjustment of empirical coefficients in an existing semi-analytic model. An attempt was made to use an inverse, parameter optimization procedure to find the heat transfer in each of the two spaces. This procedure was successful in retrieving this information from simulated pressure-volume data with artificially generated noise, but it failed with the actual experimental data. This is evidence that the models used in the parameter optimization procedure (and to generate the simulated data) were not correct. Data from the surface heat flux sensors indicated that the primary shortcoming of these models was that they assumed turbulence levels to be constant over the cycle. Sensor data in the varying volume space showed a large increase in heat flux, probably due to turbulence, during the expansion stroke.

Kornhauser, Alan A.↗

NASA NTRS2020

Designing Shading Schemes for Microphone Phased Arrays

A technique is proposed for designing sensor weightings, or array shading functions, for microphone phased arrays. The presented method attempts to maintain mathematical simplicity while maximizing array gain for a desired mainlobe beamwidth. It does so using the two-parameter optimization of a family of functions. The shading design process is described and applied to an array used recently in the NASA Langley Research Center 14- by 22-Foot Subsonic Tunnel. Several variants of the method are compared to an existing shading scheme for the array, along with a more general optimization formulation. Results are presented for both an idealized point source and experimental data from the wind tunnel test. The shading schemes are shown to improve the behavior of array operations, but have a stronger impact on visual interpretation of maps than on source level calculations. The study results show that the two-parameter optimization scheme provides favorable characteristics while maintaining implementation simplicity.

Christopher J Bahr↗

DOE OSTI2022

Membrane‐electrode assembly design parameters for optimal CO 2 reduction

Commercial-scale generation of carbon-containing chemicals and fuels by means of electrochemical CO 2 reduction (CO 2 R) requires electrolyzers operating at high current densities and product selectivities. Membrane-electrode assemblies (MEAs) have been shown to be suitable for this purpose. In such devices, the cathode catalyst layer controls both the rate of CO 2 R and the distribution of products. In this study, we investigate how the ionomer-to-catalyst ratio (I:Cat), catalyst loading, and catalyst-layer thickness influence the performance of a cathode catalyst layer containing Ag nanoparticles supported on carbon. In this paper, we explore how these parameters affect the cell performance and establish the role of the exchange solution (water vs. CsHCO 3 ) behind the anode catalyst layer in cell performance. We show that a high total current density is best achieved using an I:Cat ratio of 3 at a Ag loading of 0.01–0.1 mg Ag /cm 2 and with a 1.0 M solution of CsHCO 3 circulated behind the anode catalyst layer. For these conditions, the optimal CO partial current density depends on the voltage applied to the MEA. The work also reveals that the performance of the cathode catalyst layer is limited by a combination of the electrochemically active surface area and the degree to which mass transfer of CO 2 to the surface of the Ag nanoparticles and the transport of OH – anions away from it limit the overall catalyst activity. Hydration of the ionomer in the cathode catalyst layer is found not to be an issue when using an exchange solution. The insights gained allowed for a Ag CO 2 R MEA that operates between 200 mA/cm 2 and 1 A/cm 2 with CO faradaic efficiencies of 78–91%, and the findings and understanding gained herein should be applicable to a broad range of CO 2 R MEA-based devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1975

System design of a rudder coordination system

The application of the parameter optimization computer program to the design of a rudder coordination system for the F-8 airplane is summarized. The flight condition was Mach 0.56 at 20,000 feet altitude. The system configuration selected consisted of signal paths that fed yaw rate and aileron signals to the rudder. The two signal paths were summed and then modified by a high pass filter to eliminate any steady state bias signal. The input axis of the yaw gyro was perpendicular to the aircraft zero lift line and the trim angle of attack was 7.75 degrees. The parameter optimization was used to design the complete system first, and then a root locus analysis of the individual component effects was made. The results are presented.

Whitaker, H. P.↗

DOE OSTI2025

Directed energy deposition of functionally graded V-4Cr-4Ti to Fe-9Cr transition for fusion power systems

This study proposes a graded structure via additive manufacturing for divertor and first wall blanket applications in fusion reactors. Materials were selected based on thermodynamic calculations to operate from 1100 °C at the plasma-facing level to 550 °C at the structural steel level. Conventional joining methods often lead to failures due to discrete reaction layers with significant mechanical property differences. Using laser beam-directed energy deposition (LB-DED), this study demonstrates the fabrication of a VCrTi-Gr91 steel functionally graded component through a novel process parameter optimization framework. A systematic approach included powder characterization, single-track depositions, and construction of printability maps. Near full-density specimens of each interlayer were additively manufactured, and a transition from V-based alloys to reduced activation ferritic martensitic steels was achieved. Computational material selection of interlayer alloys and thermodynamic/diffusion kinetics simulations prevented most interface incompatibilities. A brittle intermetallic formed at one interface, causing cracking, which was not predicted by current thermodynamic models. Transition alloy design approach was updated with a more recent database and a mitigation strategy has been proposed to eliminate the formation of deleterious intermetallic phases. Ultimately, LB-DED has proven effective for producing multi-material graded systems for fusion applications, with the demonstrated process parameter optimization framework applicable to various materials.

Additive manufacturing↗

NASA NTRS1993

A time optimal Space Station reboost guidance strategy

A closed-loop guidance strategy for time and fuel optimal reboost of Space Station Freedom is discussed in this paper. The reboost maneuver is formulated as an optimal control problem rather than a parameter optimization problem, the parameters being the thrust switching times. In the present approach the thrust switching structure need not be prescribed a priori to solve the resulting two point boundary value problem. Non-optimality of singular control or intermediate thrust is proved by utilizing the second order Kelley condition or the Generalized Legendre-Clebsch condition. Only a few sets of initial co-states and time-to-go guess values need to be stored on-board for a wide range of reboost scenarios.

Kumar, Renjith R.↗