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Results for “model fine-tuning”

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.

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333 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Efficient Modeling of Structural, Electronic, and Optical Properties of Silver and Gold Metal Nanoclusters and Alloys Using Optimized SCC-DFTB Parameters

Computation of optical properties using conventional time-dependent density functional theory (TD-DFT) is time-consuming and memory-intensive. In this study, we investigate the accuracy and efficiency of the density functional tight binding (DFTB) framework with newly optimized Slater–Koster (SK) parameters for modeling the structural, electronic properties, and absorption spectra of silver and gold nanoclusters and their alloys. Our investigation of the ground state (GS) properties demonstrates that the newly developed GS-SK parameters enable DFTB to closely approximate DFT-calculated bond lengths for octahedron, tetrahedron, icosahedra, and truncated octahedron with sizes Ag n /Au n (n = 19, 20, 38, 55), nanoclusters and Ag 20 /Au 20 nanoalloys, with a maximum deviation of approximately 0.15 Å. Formation energy results indicate that the GS-SK parameters can closely estimate changes in formation energies with alloy composition, and the comparison of electronic structures for Ag 20 , Au 20 , and AgAu alloy nanoclusters using the DFTB approximation reveals good agreement in the projected density of states (DOS) profiles and energy levels. A second set of SK parameters, ES-SK, has been developed to describe excited state (ES) properties, including the absorption spectra of silver octahedron Ag 19 , tetrahedral Ag n (n = 20, 56, 84), truncated octahedron Ag 38 , and icosahedra Ag 55 closed-shell clusters and their gold and alloy counterparts over a broad range of alloy compositions. This parametrization uses TD-DFTB calculations and fine-tunes the d and p eigenvalues by comparing them to reference absorption spectra from first-principles TD-DFT. This enables the generation of absorption spectra that closely match the reference spectra when plasmon excitation is dominant, as demonstrated by studying the plasmonic properties of icosahedral Ag n and Au n (n = 309 and 561) nanoparticles. This includes the rapid loss in plasmon quality when Au partially replaces Ag in alloy clusters. Furthermore, these results provide a foundation for addressing computational bottlenecks in plasmonics and with new prospects for applications in the quantum plasmonics for bimetallic alloys.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon

Nitrogen (N) fixation in cereals by root-associated bacteria is a promising solution for reducing use of chemical N fertilizers in agriculture. However, plant and bacterial responses are unpredictable across environments. We hypothesized that cereal responses to N-fixing bacteria are dynamic, depending on N supply and time. To quantify the dynamics, a gnotobiotic, fabricated ecosystem (EcoFAB) was adapted to analyse N mass balance, to image shoot and root growth, and to measure gene expression of Brachypodium distachyon inoculated with the N-fixing bacterium Herbaspirillum seropedicae. Phenotyping throughput of EcoFAB-N was 25–30 plants h -1 with open software and imaging systems. Herbaspirillum seropedicae inoculation of B. distachyon shifted root and shoot growth, nitrate versus ammonium uptake, and gene expression with time; directions and magnitude depended on N availability. Primary roots were longer and root hairs shorter regardless of N, with stronger changes at low N. At higher N, H. seropedicae provided 11% of the total plant N that came from sources other than the seed or the nutrient solution. The time-resolved phenotypic and molecular data point to distinct modes of action: at 5 mM NH 4 NO 3 the benefit appears through N fixation, while at 0.5 mM NH 4 NO 3 the mechanism appears to be plant physiological, with H. seropedicae promoting uptake of N from the root medium.Future work could fine-tune plant and root-associated microorganisms to growth and nutrient dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Engineered reduction of S-adenosylmethionine alters lignin in sorghum

Abstract Background Lignin is an aromatic polymer deposited in secondary cell walls of higher plants to provide strength, rigidity, and hydrophobicity to vascular tissues. Due to its interconnections with cell wall polysaccharides, lignin plays important roles during plant growth and defense, but also has a negative impact on industrial processes aimed at obtaining monosaccharides from plant biomass. Engineering lignin offers a solution to this issue. For example, previous work showed that heterologous expression of a coliphage S -adenosylmethionine hydrolase (AdoMetase) was an effective approach to reduce lignin in the model plant Arabidopsis. The efficacy of this engineering strategy remains to be evaluated in bioenergy crops. Results We studied the impact of expressing AdoMetase on lignin synthesis in sorghum ( Sorghum bicolor L. Moench). Lignin content, monomer composition, and size, as well as biomass saccharification efficiency were determined in transgenic sorghum lines. The transcriptome and metabolome were analyzed in stems at three developmental stages. Plant growth and biomass composition was further evaluated under field conditions. Results evidenced that lignin was reduced by 18% in the best transgenic line, presumably due to reduced activity of the S -adenosylmethionine-dependent O -methyltransferases involved in lignin synthesis. The modified sorghum features altered lignin monomer composition and increased lignin molecular weights. The degree of methylation of glucuronic acid on xylan was reduced. These changes enabled a ~20% increase in glucose yield after biomass pretreatment and saccharification compared to wild type. RNA-seq and untargeted metabolomic analyses evidenced some pleiotropic effects associated with AdoMetase expression. The transgenic sorghum showed developmental delay and reduced biomass yields at harvest, especially under field growing conditions. Conclusions The expression of AdoMetase represents an effective lignin engineering approach in sorghum. However, considering that this strategy potentially impacts multiple S -adenosylmethionine-dependent methyltransferases, adequate promoters for fine-tuning AdoMetase expression will be needed to mitigate yield penalty.

Tian, Yang↗
DOE OSTI2021

Progress on Optimizing Wind Farms and Rotor Designs Using Adjoints

Modern wind plants are increasingly tasked with multiple performance objectives. In addition to designing plants that maximize power output and minimize the levelized cost of energy (LCOE), the design and operation of wind plants is increasingly influenced by challenges regarding grid integration of variable generation renewables. This places a growing emphasis on making wind plants more controllable and predictable. WindSE is a Reynolds-averaged Navier-Stokes (RANS) model designed around analytical gradient and adjoint methods, with the ability to capture terrain-induced effects, as shown in Figure 1. The recent addition of an unsteady solver with an actuator line method (ALM) and ongoing work to enable massively parallel optimizations gives it a unique niche to explore coupled plant-level controls and design problems. This code is an open source python package built on the FEniCS framework that utilizes fast, parallel PETSc solvers to model fluid flow throughout wind-farm scale domains. Two recent studies performed using WindSE demonstrate the capability to optimize under a wide variety of flow conditions and objective functions. In the first, we present an optimization focused on modifying the layout of a wind farm with a fixed number of turbines for maximum total power output [1]. This study highlights the ability to quickly perform simulations using the steady Navier-Stokes solver combined with rotors represented as actuator disks while also stressing the importance of capturing terrain-induced effects. Gradient-based optimization using the RANS equations is viable due to the inclusion of efficiently computed adjoint derivatives. We interpret the physical results of the optimal layout and also discuss the computational cost of scaling to larger problems. In the second study, we present the capabilities of the unsteady Navier-Stokes solver, where rotor-blade profiles represented by actuator lines are optimized to enhance wake steering effects and overall power production [2]. We quantify the wind plant performance gains obtained from this type of simultaneous control co-design optimization as compared to optimizing the blade design and yaw independently. Figure 2 shows the differences between a baseline two-turbine system and an optimized system where we fine-tune the blade chord profile. Results and challenges from each study are quickly summarized and used to motivate the current development efforts within WindSE. Current and future work is focused on enabling higher-resolution studies with more degrees of freedom through parallelization of both the simulation and optimization algorithms. We present benchmarking results to show that WindSE performs well in both weak- and strong-scaling tests and further demonstrate that the optimizer obtains the same convergence rates in both shared- and distributed-memory environments. Using larger wind farms, we can study deep-array effects within an optimization context, allowing the use of objective functions that have been previously unstudied. As an example, we present ongoing work on a blockage metric which characterizes the loss of available kinetic energy due to wake effects from multiple upstream turbines.

adjoint optimization↗
DOE OSTI2022

Computational studies of structural, energetic, and electronic properties of pure Pt and Mo and mixed Pt/Mo clusters: Comparative analysis of characteristics and trends

The added technological potential of bimetallic clusters and nanoparticles, as compared to their pure (i.e., one-component) counterparts, stems from the ability to further fine-tune their properties and, consequently, functionalities through a simultaneous use of the “knobs” of size and composition. The practical realization of this potential can be greatly advanced by the knowledge of the correlations and relationships between the various characteristics of bimetallic nanosystems on the one hand and those of their pure counterparts as well as pure constituent components on the other hand. Here, in this study, we present results of a density functional theory based study of pure Pt n and Mo n clusters aimed at revisiting and exploring further their structural, electronic, and energetic properties. These are then used as a basis for analysis and characterization of the results of calculations on two-component Pt n-m Mo m clusters. The analysis also includes establishing relationships between the properties of the Pt n-m Mo m clusters and those of their Pt n-m and Mo m components. One of the particularly intriguing findings suggested by the calculated data is a linear dependence of the average binding energy per atom in sets of Pt n-m Mo m clusters that have the same fixed number m of Mo atoms and different number n-m of Pt atoms on the fractional content (n-m)/n of Pt atoms. We derive an analytical model that establishes the fundamental basis for this linearity and expresses its parameters—the m-dependent slope and intercept—in terms of characteristic properties of the constituent components, such as the average binding energy per atom of Mo m and the average per-atom adsorption energy of the Pt atoms on Mo m . The conditions of validity and degree of robustness of this model and of the linear relationship predicted by it are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

The Beam Dump eXperiment

Hadronic matter makes about 14% of the known universe. The remaining 86% is Dark Matter (DM). Since it does not interact with the ordinary matter via electromagnetic force, DM is not visible and, to date, it escaped detection. The search for Dark Matter (DM) is one of the hottest topic in modern physics. Despite the increasing number of astrophysical and cosmological observations proving the existence, so far no particle physics experiment has detected DM yet. Up to now, most of the experimental efforts have been focused on the so called WIMP (Weakly Interacting Massive Particle) paradigm, which predicts heavy DM (10 GeV-10 TeV mass range) interacting with Standard Model (SM) particles via the weak force mediators (W or Z bosons). More recently, due to the lack of clear evidence of WIMPs, other models of DM gained the interest of the physics community. These models consider Light DM particles (LDM), in MeV-GeV mass range. Among LDM theories, the Dark Photon theory predicts the existence of a Dark Sector interacting with SM particles via a new massive vector boson (Dark Photon, Heavy Photon or A0), mediator of a new force. This scenario, despite being theoretically well motivated, is remarkably experimentally unexplored. The Beam Dump eXperiment (BDX), is an approved experiment at Jefferson Lab (JLab), aiming to discover the DM predicted witihn the Dark Photon theory. The experiment uses the CEBAF (Continuous Electron Beam Accelerator Facility) 11 GeV electron beam, impinging on the JLab Hall-A beam-dump, to produce a beam of DM particles, detected by a ~ 1 m3 detector made of thallium doped cesium iodide (CsI(Tl)) crystals located ~ 20 m downstream. In order to achieve excellent background rejection, the experimental setup includes active vetos and passive shielding surrounding CsI(Tl) crystals. Given the weakness of the DM-SM interaction, the scattering of a DM particle in the BDX detector is a rare event. Therefore, the characterization of the expected background is a critical aspect of the experiment. Both cosmogenic and penetrating SM particles produced by the beam interaction in the dump contribute to the background of the experiment. While the cosmogenic contribution can be measured during the experiment when the beam is off, beam-related background can only be estimated via Monte Carlo (MC) simulations. Therefore, a careful assessment of possible systematics introduced by the MC is needed. The beam-correlated background characterization was made by measuring the muon flux produced by the interaction of the CEBAF beam with Hall-A dump in a dedicated experimental campaign in spring 2018 [1]. The comparison to the ?ux predicted by MC allowed us to validate the BDX simulation framework. The reach of BDX, i.e. the region that the experiment can probe in the LDM theory parameter space, depends critically on the background rejection capability and signal detection effciency. For this reason, the detector setup was fine-tuned through a dedicated study. The response to LDM and background events was evaluated for different setups and selection cuts. As a result of this procedure, the configuration resulting in the best sensitivity was selected [2]. The reach calculation was performed taking into account the different LDM production mechanisms, including the contribution of secondary particles produced in the beam-dump. In particular, the effect of the secondary positrons annihilation was found to be extremely significant. In the majority of the sensitivity studies, this contribution is neglected, but recent results [3] [4] demonstrated that this process significantly enhances the sensitivity of lepton beam-dump experiments. Currently, the BDX collaboration is focused on the deployment and operation of a small detector, called BDX-MINI, built to perform a preliminary physics measurement searching for LDM at JLab. This test will pave the way to the realization of the full BDX experiment. The measurement is currently ongoing but results are expected by the end of this year. During my PhD I was involved in all aspects of the BDX experiment: design, simulation, prototyping and data analysis. The main results of my work are reported in this thesis. This manuscript is organized as follows: the first Chapter provides an introduction to the theory of LDM, with particular attention to the Dark Photon paradigm; the second Chapter illustrates the BDX experimental setup, the LDM production and detection mechanisms and the expected backgrounds; Chapter 3 and 4 describe, respectively, the BDX-HODO measurement, with a detailed description of the simulations, and the BDX experimental setup and analysis cuts optimization. Chapter 5 reports about BDXMINI detector characterization, calibration and sensitivity estimate. Finally, Chapter 6 describes in detail the calculation of the secondary positron annihilation contribution to the sensitivity of BDX and other electron-beam thick-target experiment.

Marsicano, Luca↗
DOE OSTI2026

Thiol post-translational modifications modulate allosteric regulation of the OpcA–G6PDH complex through conformational gate control

In cyanobacteria, the redox-sensitive protein OpcA acts as a metabolic switch for G6PDH, enabling rapid adjustment of reducing power generation from glycogen catabolism and thereby precisely regulating carbon flux between anabolic and catabolic pathways. Although redox-sensitive cysteines in OpcA are known to regulate G6PDH, the mechanisms by which redox post-translational modifications (PTMs) on OpcA control G6PDH structure and activity remain unclear. Here, we combine computational modeling with experimental redox proteomics in Synechococcus elongatus PCC 7942 to dissect this mechanism. Experimentally, redox proteome analysis revealed differential redox PTM patterns, particularly on cysteines within the G6PDH-binding site of OpcA. These environmentally sensitive PTM changes at the interface suggest that thiol modifications in this region form a key regulatory node. More broadly, redox proteomics identified site-specific cysteine modifications under light/dark transitions and circadian cycling, linking distinct redox regimes to discrete PTM states. We employed PTM-Psi simulations to show that thiol PTMs near the OpcA–G6PDH interface are critical for allosteric regulation of G6PDH. The thiol PTMs on OpcA affect a putative gate region in G6PDH for substrate ingress and product egress as well as key hydrogen-bond networks within the active site. We infer that PTMs on OpcA tune the conformational landscapes of individual G6PDH subunits toward functionally relevant configurations according to environmental gradients, biasing the enzyme toward catalytically favorable states. Together, our results reveal a molecular mechanism in which thiol PTMs on OpcA modulate G6PDH structure and function through PTM-induced reorganization of conformational dynamics and allosteric communication. These findings demonstrate that PTM-level regulation provides a critical control layer from genotypes to phenotypes that enables cyanobacteria to rapidly adapt to environmental fluctuations through precise metabolic fine-tuning.

Allosteric regulation↗
DOE OSTI2025

The influence of cooling rates on strain phase diagrams and domain structures of ferroelectric thin films: A case study of PbTiO 3

Strain engineering has been established as an effective approach to control phase equilibria, domain configurations, and functional properties of ferroelectric thin films. Temperature-strain phase diagrams have been used as powerful tools for providing insights into strain engineering. However, almost all existing phase diagrams established using the phase-field approach assume quenching conditions without considering actual cooling rates during the post-deposition annealing process of ferroelectric thin films. Within this work, we systematically investigate the influence of cooling rates on domain structures and the strain-phase diagram of ferroelectric thin films using phase-field simulations, taking PbTiO 3 thin films as a model system. We found that both the position of phase boundaries in the strain phase diagrams and the domain morphology are significantly influenced by the cooling rates. It is revealed that while the paraelectric-ferroelectric phase boundary remains invariant, the phase boundaries between single-phase and multi-phase regions tend to shift toward the corresponding multi-phase region as the cool rate reduces. Slow cooling generally leads to more ordered domain structures with increased domain size. Using the obtained equilibrium domain structures, we calculated effective thermal conductivities and found significant variations that can be tuned by the cooling rates. In conclusion, this work reveals an underexplored yet critical impact of cooling rates on phase equilibria and domain structures in ferroelectric thin films, which may inspire further fine-tuning of domains and domain walls in low-dimensional ferroelectrics for multifunctional applications.

Domain structures↗
DOE OSTI2025

Studying the Power Sources behind Type Ic Supernovae

Astrophysical transients can be powered by a broad range of energy sources, including shock heating (internal and external shocks), decay of radioactive isotopes, and long-lived central engines (magnetar and fallback). The dominant energy source for astrophysical transients depends on the nature of the explosive engine and its progenitor. To model all transients, light-curve codes must include all of these energy sources. Here, we present a supernova light-curve code implementing analytic source models to compare the role of different energy sources in these transients. To demonstrate the utility of this code, we conduct an extensive study of Type Ic broad-line (Ic-BL) supernovae. A diverse set of energy sources have been linked to Ic-BL supernovae, making them an excellent candidate for this light-curve code. In this paper, we explore which features of the explosion (mass, velocity, etc.) affect the Type Ic supernovae light curves, focusing on shock-interaction and radioactive-decay energy sources. Although the explosion properties under both energy sources can be tuned to match the peak emission, matching the light-curve evolution in many Ic-BL supernovae requires fine-tuned conditions. We find that shock interactions in the stellar wind are likely to be the dominant energy source at peak for these supernovae.

79 ASTRONOMY AND ASTROPHYSICS↗