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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Evaluation of Force Fields for Molecular Dynamics Simulations of Platinum in Bulk and Nanoparticle Forms

Here, understanding the size- and shape-dependent properties of platinum nanoparticles is critical for enabling the design of nanoparticle-based applications with optimal and potentially tunable functionality. Toward this goal, we evaluated nine different empirical potentials with the purpose of accurately modeling faceted platinum nanoparticles using molecular dynamics simulation. First, the potentials were evaluated by computing bulk and surface properties - surface energy, lattice constant, stiffness constants, and the equation of state - and comparing these to prior experimental measurements and quantum mechanics calculations. Then, the potentials were assessed in terms of the stability of cubic and icosahedral nanoparticles with faces in the {100} and {111} planes, respectively. Although none of the force fields predicts all the evaluated properties with perfect accuracy, one potential - the embedded atom method formalism with a specific parameter set - was identified as best able to model platinum in both bulk and nanoparticle forms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A transfer learning approach to energy-efficient control of small and medium-sized commercial buildings

Model-free reinforcement learning (RL) provides a data-driven and adaptive approach to optimize building energy use while satisfying occupant comfort. This powerful tool does not need any prior knowledge about the environment and system it is optimizing and can adapt its policy based on the changes in captures. Like any other data-driven tool, it faces high training costs due to the extensive agent-environment interactions required to capture long-term building dynamics and user comfort. Transfer learning, particularly policy distillation, offers a promising way to accelerate training by leveraging pretrained RL agents in different building and system types. Here, this study investigates online student distillation, in which the student model updates its neural network weights using outputs from teacher models. The work introduces a student distillation strategy designed for efficient knowledge transfer, along with a teacher selection method that ensures high-quality guidance. The approach is validated using a highly calibrated whole building energy model for a small/medium commercial building test facility. Results show substantial reductions in training time and data requirements while surpassing the performance of ASHRAE Guideline 36, an advanced rule-based control strategy. The distilled RL model required 45% less data and achieved 20% higher cumulative rewards than a state-of-the-art RL model, with faster convergence and lower energy consumption. These outcomes demonstrate that effective transfer learning enables a scalable and data-efficient energy management solution for commercial buildings.

ASHRAE guideline 36↗
DOE OSTI2025

The approximate second order coupled-cluster method based on a size-consistent Brillouin–Wigner partitioning

We present a variant of the approximate second order coupled-cluster method (CC2) with a two-parameter size-consistent Brillouin–Wigner (BW-s) partitioning instead of a Møller–Plesset (MP) partitioning for the unperturbed Hamiltonian, which we refer to as BWs-CC2. The computational complexity of this model scales identically to CC2 with molecular size. Conventional CC2 and its regularized BWs-CC2 variants, as well as conventional MP2 and two of its regularized BW-s2 variants, were assessed on a 535 element database spanning thermochemistry, non-covalent interactions, barrier heights, and isomerization energies. To ensure a well-defined model chemistry, the assessment was performed using internally stable spin-polarized Hartree–Fock (HF) orbitals in the finite aug-cc-pVQZ basis without counterpoise corrections. As a result of using stable orbitals, contrary to conventional wisdom, we find that CC2 substantially outperforms MP2 on molecules with significantly spin contaminated reference orbitals without a significant increase in error on systems with a spin-pure reference, showing the value of its single substitutions. While no single choice of regularization parameters can be optimal for all datasets, we find that BWs-CC2 generally outperforms both CC2 and BW-s2 with a single judicious parameter choice. Additional tests on dipole moments and bond lengths of diatomics provide further support for the utility of this choice. Furthermore, the main outliers and poorest performing cases are associated with large amounts of spin-contamination in the HF reference, which is indicative of systems with either strong correlation or extensive artificial symmetry breaking. Overall, these findings argue that the perception of the quality of the CC2 ground state should be reevaluated and that it can be further improved upon by the soundly based BWs-CC2 variant with the recommended parameter choice.

Correlation energy↗
DOE OSTI2015

Time-resolved fast-neutron radiography of air-water two-phase flows in a rectangular channel by an improved detection system

In a previous work, we have demonstrated the feasibility of high-frame-rate, fast-neutron radiography of generic air-water two-phase flows in a 1.5 cm thick, rectangular flow channel. The experiments have been carried out at the high-intensity, white-beam facility of the Physikalisch-Technische Bundesanstalt, Germany, using an multi-frame, time-resolved detector developed for fast neutron resonance radiography. The results were however not fully optimal and therefore we have decided to modify the detector and optimize it for the given application, which is described in the present work. Furthermore, we managed to improve the image post-processing methodology and the noise suppression. Using the tailored detector and the improved post-processing, significant increase in the image quality and an order of magnitude lower exposure times, down to 3.33 ms, have been achieved with minimized motion artifacts. Similar to the previous study, different two-phase flow regimes such as bubbly slug and churn flows have been examined. The enhanced imaging quality enables an improved prediction of two-phase flow parameters like the instantaneous volumetric gas fraction, bubble size, and bubble velocities. Instantaneous velocity fields around the gas enclosures can also be more robustly predicted using optical flow methods as previously.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Planarization of Isolated Defects on ICF Target Capsule Surfaces by Pulsed Laser Ablation

Demanding surface quality requirements for inertial confinement fusion (ICF) capsules motivated the development of a pulsed laser ablation method to reduce or eliminate undesirable surface defects. The pulsed laser ablation technique takes advantage of a full surface (4π) capsule manipulation system working in combination with an optical profiling (confocal) microscope. Based on the defect topography, the material removal rate, the laser pulse energy and its beam profile, a customized laser raster pattern is derived to remove the defect. The pattern is a table of coordinates and number of pulses that dictate how the defect will be vaporized until its height is level with the capsule surface. This paper explains how the raster patterns are optimized to minimize surface roughness and how surface roughness after laser ablation is simulated. The simulated surfaces are compared with actual ablated surfaces. Large defects are reduced to a size regime where a tumble finishing process produces very high quality surfaces devoid of high mode defects. The combined polishing processes of laser ablation and tumble finishing have become routine fabrication steps for National Ignition Facility capsule production.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Next-Generation Materials Design: Quantum Mechanics and Data-Driven Modeling

The future of materials design is rapidly advancing through the combination of quantum mechanics and data-driven modeling. These approaches integrate quantum principles with advanced data analysis, enabling precise insights into material behavior. This talk will highlight recent progress in using these methods for computational design, particularly in high-entropy alloy catalysts, emphasizing the role of hierarchical machine-learning architectures for accurate predictions. Additionally, I will discuss our work on developing machine learning interatomic potentials (MLPs) for single-element metals, metal oxides, and alloys under extreme conditions, focusing on melting behavior and phase properties at high temperatures and pressures. We have also refined our MLP models to capture dynamic surface interactions, such as CO2 and CO adsorption on MgO, using both static and molecular dynamics simulations. These models maintain high accuracy while significantly reducing computational costs compared to first-principles calculations. By enabling efficient and accurate simulations, this work supports broader community adoption, optimizes datasets for materials discovery, and extends the accessible time, size, and environmental conditions beyond the limits of experiments and traditional simulations.

machine learning↗
DOE OSTI2024

Learning with Adaptive Conservativeness for Distributionally Robust Optimization: Incentive Design for Voltage Regulation: Preprint

Information asymmetry between the Distribution System Operator (DSO) and Distributed Energy Resource Aggregators (DERAs) obstructs designing effective incentives for voltage regulation. To capture this effect, we employ a Stackelberg game-theoretic framework, where the DSO seeks to overcome the information asymmetry and refine its incentive strategies by learning from DERA behavior over multiple iterations. We introduce a model-based online learning algorithm for the DSO, aimed at inferring the relationship between incentives and DERA responses. Given the uncertain nature of these responses, we also propose a distributionally robust incentive design model to control the probability of voltage regulation failure and then reformulate it into a convex problem. This model allows the DSO to periodically revise distribution assumptions on uncertain parameters in the decision model of the DERA. Finally, we present a gradient-based method that permits the DSO to adaptively modify its conservativeness level, measured by the size of a Wasserstein metric-based ambiguity set, according to historical voltage regulation performance. The effectiveness of our proposed method is demonstrated through numerical experiments.

distribution system operator↗
DOE OSTI2017

Correlation consistent basis sets for actinides. II. The atoms Ac and Np–Lr

New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th–U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac–Lr have been calculated using the Feller-Peterson-Dixon (FPD) composite approach, primarily with the multireference configuration interaction (MRCI) method. Excellent convergence towards the respective complete basis set (CBS) limits is achieved with the new sets, leading to good agreement with experiment, where these exist, after accurately accounting for spin-orbit effects using the 4-component Dirac-Hartree-Fock method. For a molecular test, the IP and atomization energy (AE) of PuO 2 have been calculated also using the FPD method but using a coupled cluster approach with spin-orbit coupling accounted for using the 4-component MRCI. The present calculations yield an IP 0 for PuO 2 of 159.8 kcal/mol, which is in excellent agreement with the experimental electron transfer bracketing value of 162 ± 3 kcal/mol. Likewise, the calculated 0 K AE of 305.6 kcal/mol is in very good agreement with the currently accepted experimental value of 303.1 ± 5 kcal/mol. The ground state of PuO 2 is predicted to be the 5 Σ$+\atop{0g}$ state.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Structured illumination with thermal imaging (SI-TI): A dynamically reconfigurable metrology for parallelized thermal transport characterization

The recent push for the “materials by design” paradigm requires synergistic integration of scalable computation, synthesis, and characterization. Among these, techniques for efficient measurement of thermal transport can be a bottleneck limiting the experimental database size, especially for diverse materials with a range of roughness, porosity, and anisotropy. Traditional contact thermal measurements have challenges with throughput and the lack of spatially resolvable property mapping, while non-contact pump-probe laser methods generally need mirror smooth sample surfaces and also require serial raster scanning to achieve property mapping. Here, we present structured illumination with thermal imaging (SI-TI), a new thermal characterization tool based on parallelized all-optical heating and thermometry. Experiments on representative dense and porous bulk materials as well as a 3D printed thermoelectric thick film (~50 μm) demonstrate that SI-TI (1) enables paralleled measurement of multiple regions and samples without raster scanning; (2) can dynamically adjust the heating pattern purely in software, to optimize the measurement sensitivity in different directions for anisotropic materials; and (3) can tolerate rough (~3 μm) and scratched sample surfaces. Here, this work highlights a new avenue in adaptivity and throughput for thermal characterization of diverse materials.

42 ENGINEERING↗
DOE OSTI2026

Accelerating Bilevel Optimization With Hierarchical Many-Threaded Parallel Differential Evolution

Bilevel optimization is encountered in many relevant real-world applications. The main feature of this type of problem is that an upper-level optimization problem is constrained by a nested lower-level optimization problem. Because of this nested structure, bilevel problems (BLPs) are usually computationally expensive to solve. Differential evolution (DE) has demonstrated promising results in solving BLPs of relatively small scales. As the problem scale increases, the decision space becomes intrinsically larger, requiring a growing number of function evaluations for the method to work properly. In this context, heavy parallelization and high-performance computing techniques are indispensable to enable the resolution of more complex and challenging optimization problems. Hence, we propose a hierarchical many-threaded parallel DE approach for BLPs, where both levels are parallelized. The computational experiments demonstrate that the parallel implementation achieved runtime speeds ranging from 44 to 2559 times faster than the sequential version on a well-known scalable SMD benchmark test problem when executed on an NVIDIA A100 GPU. The findings indicate that the algorithm’s convergence is strongly influenced by the number of both upper- and lower-level generations. Moreover, the success of experiments with large-scale problems is closely linked to the choice of small population sizes.

Dufek, Amanda S↗
DOE OSTI2015

SU-E-I-09: The Impact of X-Ray Scattering On Image Noise for Dedicated Breast CT

Purpose: To quantify the impact of detected x-ray scatter on image noise in flat panel based dedicated breast CT systems and to determine the optimal scanning geometry given practical trade-offs between radiation dose and scatter reduction. Methods: Four different uniform polyethylene cylinders (104, 131, 156, and 184 mm in diameter) were scanned as the phantoms on a dedicated breast CT scanner developed in our laboratory. Both stationary projection imaging and rotational cone-beam CT imaging was performed. For each acquisition type, three different x-ray beam collimations were used (12, 24, and 109 mm measured at isocenter). The aim was to quantify image noise properties (pixel variance, SNR, and image NPS) under different levels of x-ray scatter, in order to optimize the scanning geometry. For both projection images and reconstructed CT images, individual pixel variance and NPS were determined and compared. Noise measurement from the CT images were also performed with different detector binning modes and reconstruction matrix sizes. Noise propagation was also tracked throughout the intermediate steps of cone-beam CT reconstruction, including the inverse-logarithmic process, Fourier-filtering before backprojection. Results: Image noise was lower in the presence of higher scatter levels. For the 184 mm polyethylene phantom, the image noise (measured in pixel variance) was ∼30% lower with full cone-beam acquisition compared to a narrow (12 mm) fan-beam acquisition. This trend is consistent across all phantom sizes and throughout all steps of CT image reconstruction. Conclusion: From purely a noise perspective, the cone-beam geometry (i.e. the full cone-angle acquisition) produces lower image noise compared to the lower-scatter fan-beam acquisition for breast CT. While these results are relevant in homogeneous phantoms, the full impact of scatter on noise in bCT should involve contrast-to-noise-ratio measurements in heterogeneous phantoms if the goal is to optimize the scanning geometry for dedicated breast CT. This work was supported by a grant from the National Institute for Biomedical Imaging and Bioengineering (R01 EB002138)

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Data for Comparison of Genotyping Assays for Detection of Targeted CRISPR/Cas Mutagenesis in Highly Polyploid Sugarcane

Sugarcane ( Saccharum spp.) is an important biofuel feedstock and a leading source of global table sugar. Saccharum hybrid cultivars are highly polyploid (2n = 100–130), containing large numbers of functionally redundant hom(e)ologs in their genomes. Genome editing with sequence-specific nucleases holds tremendous promise for sugarcane breeding. However, identification of plants with the desired level of co-editing within a pool of primary transformants can be difficult. While DNA sequencing provides direct evidence of targeted mutagenesis, it is cost-prohibitive as a primary screening method in sugarcane and most other methods of identifying mutant lines have not been optimized for use in highly polyploid species. In this study, non-sequencing methods of mutant screening, including capillary electrophoresis (CE), Cas9 RNP assay, and high-resolution melt analysis (HRMA), were compared to assess their potential for CRISPR/Cas9-mediated mutant screening in sugarcane. These assays were used to analyze sugarcane lines containing mutations at one or more of six sgRNA target sites. All three methods distinguished edited lines from wild type, with co-mutation frequencies ranging from 2% to 100%. Cas9 RNP assays were able to identify mutant sugarcane lines with as low as 3.2% co-mutation frequency, and samples could be scored based on undigested band intensity. CE was highlighted as the most comprehensive assay, delivering precise information on both mutagenesis frequency and indel size to a 1 bp resolution across all six targets. This represents an economical and comprehensive alternative to sequencing-based genotyping methods which could be applied in other polyploid species.

Genomics↗
DOE OSTI2015

Scalable Parallel Methods for Analyzing Metagenomics Data at Extreme Scale

The field of bioinformatics and computational biology is currently experiencing a data revolution. The exciting prospect of making fundamental biological discoveries is fueling the rapid development and deployment of numerous cost-effective, high-throughput next-generation sequencing technologies. The result is that the DNA and protein sequence repositories are being bombarded with new sequence information. Databases are continuing to report a Moore’s law-like growth trajectory in their database sizes, roughly doubling every 18 months. In what seems to be a paradigm-shift, individual projects are now capable of generating billions of raw sequence data that need to be analyzed in the presence of already annotated sequence information. While it is clear that data-driven methods, such as sequencing homology detection, are becoming the mainstay in the field of computational life sciences, the algorithmic advancements essential for implementing complex data analytics at scale have mostly lagged behind. Sequence homology detection is central to a number of bioinformatics applications including genome sequencing and protein family characterization. Given millions of sequences, the goal is to identify all pairs of sequences that are highly similar (or “homologous”) on the basis of alignment criteria. While there are optimal alignment algorithms to compute pairwise homology, their deployment for large-scale is currently not feasible; instead, heuristic methods are used at the expense of quality. In this dissertation, we present the design and evaluation of a parallel implementation for conducting optimal homology detection on distributed memory supercomputers. Our approach uses a combination of techniques from asynchronous load balancing (viz. work stealing, dynamic task counters), data replication, and exact-matching filters to achieve homology detection at scale. Results for a collection of 2.56M sequences show parallel efficiencies of ~75-100% on up to 8K cores, representing a time-to-solution of 33 seconds. We extend this work with a detailed analysis of single-node sequence alignment performance using the latest CPU vector instruction set extensions. Preliminary results reveal that current sequence alignment algorithms are unable to fully utilize widening vector registers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Using ARM Measurements to Understand and Reduce the Double ITCZ Biases in the Community Atmospheric Model

1. Understanding of the observed variability of ITCZ in the equatorial eastern Pacific. The annual mean precipitation in the eastern Pacific has a maximum zonal band north of the equator in the ITCZ where the maximum SST is located. During the boreal spring (referring to February, March, and April throughout the present paper), because of the accumulated solar radiation heating and oceanic heat transport, a secondary maximum of SST exists in the southeastern equatorial Pacific. Associated with this warm SST is also a seasonal transitional maximum of precipitation in the same region in boreal spring, exhibited as a weak double ITCZ pattern in the equatorial eastern Pacific. This climatological seasonal variation, however, varies greatly from year to year: double ITCZ in the boreal spring occurs in some years but not in other years; when there a single ITCZ, it can appear either north, south or at the equator. Understanding this observed variability is critical to find the ultimate cause of the double ITCZ in climate models. Seasonal variation of ITCZ south of the eastern equatorial Pacific: By analyzing data from satellites, field measurements and atmospheric reanalysis, we have found that in the region where spurious ITCZ in models occurs, there is a “seasonal cloud transition” — from stratocumulus to shallow cumulus and eventually to deep convection —in the South Equatorial Pacific (SEP) from September to April that is similar to the spatial cloud transition from the California coast to the equator. This seasonal transition is associated with increasing sea surface temperature (SST), decreasing lower tropospheric stability and large-scale subsidence. This finding of seasonal cloud transition points to the same source of model errors in the ITCZ simulations as in simulation of stratocumulus-cumulus-deep convection transition. It provides a test for climate models to simulate the relationships between clouds and large-scale atmospheric fields in a region that features a spurious double Inter-tropical Convergence Zone (ITCZ) in most models. This work is recently published in Yu et al. (2016). Interannual variation of ITCZ south of the eastern equatorial Pacific: By analyzing data from satellites, field measurements and atmospheric reanalysis, we have characterized the interannual variation of boreal spring precipitation in the eastern tropical Pacific and found the cause of the observed interannual variability. We have shown that ITCZ in this region can occur as a single ITCZ along the Equator, single ITCZ north of the Equator, single ITCZ south of the Equator, and double ITCZ on both sides of the Equator. We have found that convective instability only plays a secondary role in the ITCZ interannual variability. Instead, the remote impact of the Pacific basin-wide SST on the horizontal gradient of surface pressure and wind convergence is the primary driver of this interannual variability. Results point to the need to include moisture convergence in convection schemes to improve the simulation of precipitation in the eastern tropical Pacific. This result has been recently submitted for publication (Yu and Zhang 2016). 2. Improvement of model parameterizations to reduce the double ITCZ bias We analyzed the current status of climate model performance in simulating precipitation in the equatorial Pacific. We have found that the double ITCZ bias has not been reduced in CMIP5 models relative to CMIP4 models. We have characterized the dynamic structure of the common bias by using precipitation, sea surface temperature, surface winds and sea-level. Results are published in Zhang et al. (2015): Since cumulus convection plays a significant role in the double ITCZ behavior in models, we have used measurements from ARM and other sources to carry out a systematic analysis of the roles of shallow and deep convection in the CAM. We found that in both CAM4 and CAM5, when the intensity of deep convection decreases as a result of parameterization change, the intensity of shallow convection increases, leading to very different changes in precipitation partitions but little change in the total precipitation. The different precipitation partition however can manifest themselves in other measures of model performances including temperature and humidity. This study points to the need to treat model physical parameterizations as integrated system rather than individual components. Results from this study are published in Wang and Zhang (2013). Since shallow convection interacts with the deep convection scheme and surface turbulence to trigger the double ITCZ, we studied methods to improve the shallow convection scheme in climate models. We investigated the bulk budgets of the vertical velocity and its parameterization in convective cores, convective updrafts, and clouds by using large-eddy simulation (LES) of four shallow convection cases including one from ARM. We proposed optimal forms of the Simpson and Wiggert equation to calculate the vertical velocity in bulk mass flux convection schemes for convective cores, convective updrafts, and convective clouds as parameterization schemes. The new scheme is published in Wang and Zhang (2014). By using long-term radar-based ground measurements from ARM, we derived a scale-aware inhomogeneity parameterization of cloud liquid water in climate models. We found a relationship between the inhomogeneity parameter and the model grid size as well as atmospheric stability. This relationship is implemented in the CESM to describe the subgrid-scale cloud inhomogeneity. Relative to the default CESM with the finite-volume dynamic core at 2-degree resolution, the new parameterization leads to smaller cloud inhomogeneity and larger cloud liquid-water path in high latitudes, and the opposite effect in low latitudes, with the regional impact on shortwave cloud radiation effect of up to 10 W/m 2 . This is due to both the smaller (larger) grid size in high (low) latitudes in the longitude-latitude grid setting of CESM and the more stable (unstable) atmosphere. This parameterization is expected lead to more realistic simulation of tropical precipitation in high-resolution models. Results from this study are reported in Xie and Zhang (2015).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Mixed Integer Nonlinear Programming Approaches to Enhance Resiliency and Response Strategies in Critical Infrastructure

Motivation. Critical infrastructures are large, complex engineered systems that must be operated robustly under abnormal conditions resulting from natural hazards or intentional acts. For example, electric power systems must be robust to line faults, water utilities must rapidly mitigate contamination incidents, and computing networks must adapt to adversarial intrusions to protect critical information. Problem. It is difficult for decision-makers within resiliency analysis in critical infrastructure to optimize designs and develop effective response strategies that can account for uncertainties. Facing incomplete information and the sheer scope that a natural hazard or attack vector may incorporate, response can be ineffective without reliable, scalable decision support tools. These problems are intrinsically nonlinear and involve discrete decisions, and unfortunately, existing off-the-shelf mathematical programming methods cannot support optimization-based decision-making of these nonlinear at scale. Method/Approach and Results. This project emphasized development of fundamental optimization strategies that supported real- time mitigation and response for critical infrastructures. In particular, the project developed multi- tree approaches based on piecewise outer-approximations for solution of mixed-integer nonlinear programming (MINLP) problems. These techniques alternate between an MILP or MISOCP relaxation to obtain a lower bound and candidate discrete solutions and an NLP subproblem to obtain upper bounds. Using tailored relaxations based on problem structure, these methods were used to solve several key applications in resilience and response of critical infrastructure. This work resulted in two open-source, copyrighted software packages: CORAMIN (https://github.com/Coramin/Coramin) -- an object-oriented mathematical programming framework that supports tailored multi-tree algorithms for solution of large- scale mixed-integer nonlinear programming; and EGRET (Electrical Grid Research and Engineering Toolkit) (https://github.com/grid- parity-exchange/Egret) -- a declarative mathematical programming framework built upon CORAMIN and Pyomo for formulation and solution of resilience and operations problems in power grid systems. Furthermore, these tools resulted in several important published results, including the following: The first known global optimization approach that could solve the unit-commitment problem with nonlinear power flow constraints on medium-sized test problems; Improved parallel optimization-based bounds tightening and strengthening of relaxations of AC power flow constraints; and, Optimization-based approaches for improved grid resilience and use of demand response to improve grid resilience with reduction in capital requirements. Result Implications. This project developed first-of-a-kind algorithms for decision-making in critical infrastructure resilience operations and planning, as well as a next-generation toolkit for MINLP researchers. These approaches leveraged high-performance computing architectures to solve some of the largest, most challenging nonlinear discrete optimization problems to global optimality, and these successes were captured in open-source software to enable optimization-based decision-making, and efficient solution of MINLP formulations for electric power transmission grids.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Comparison of genotyping assays for detection of targeted CRISPR/Cas mutagenesis in highly polyploid sugarcane

Sugarcane (Saccharum spp.) is an important biofuel feedstock and a leading source of global table sugar. Saccharum hybrid cultivars are highly polyploid (2n = 100–130), containing large numbers of functionally redundant hom(e)ologs in their genomes. Genome editing with sequence-specific nucleases holds tremendous promise for sugarcane breeding. However, identification of plants with the desired level of co-editing within a pool of primary transformants can be difficult. While DNA sequencing provides direct evidence of targeted mutagenesis, it is cost-prohibitive as a primary screening method in sugarcane and most other methods of identifying mutant lines have not been optimized for use in highly polyploid species. In this study, non-sequencing methods of mutant screening, including capillary electrophoresis (CE), Cas9 RNP assay, and high-resolution melt analysis (HRMA), were compared to assess their potential for CRISPR/Cas9-mediated mutant screening in sugarcane. These assays were used to analyze sugarcane lines containing mutations at one or more of six sgRNA target sites. All three methods distinguished edited lines from wild type, with co-mutation frequencies ranging from 2% to 100%. Cas9 RNP assays were able to identify mutant sugarcane lines with as low as 3.2% co-mutation frequency, and samples could be scored based on undigested band intensity. CE was highlighted as the most comprehensive assay, delivering precise information on both mutagenesis frequency and indel size to a 1 bp resolution across all six targets. This represents an economical and comprehensive alternative to sequencing-based genotyping methods which could be applied in other polyploid species.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

WE-G-204-06: Grid-Line Artifact Minimization for High Resolution Detectors Using Iterative Residual Scatter Correction

Purpose: Anti-scatter grid-line artifacts are more prominent for high-resolution x-ray detectors since the fraction of a pixel blocked by the grid septa is large. Direct logarithmic subtraction of the artifact pattern is limited by residual scattered radiation and we investigate an iterative method for scatter correction. Methods: A stationary Smit-Rοntgen anti-scatter grid was used with a high resolution Dexela 1207 CMOS X-ray detector (75 µm pixel size) to image an artery block (Nuclear Associates, Model 76-705) placed within a uniform head equivalent phantom as the scattering source. The image of the phantom was divided by a flat-field image obtained without scatter but with the grid to eliminate grid-line artifacts. Constant scatter values were subtracted from the phantom image before dividing by the averaged flat-field-with-grid image. The standard deviation of pixel values for a fixed region of the resultant images with different subtracted scatter values provided a measure of the remaining grid-line artifacts. Results: A plot of the standard deviation of image pixel values versus the subtracted scatter value shows that the image structure noise reaches a minimum before going up again as the scatter value is increased. This minimum corresponds to a minimization of the grid-line artifacts as demonstrated in line profile plots obtained through each of the images perpendicular to the grid lines. Artifact-free images of the artery block were obtained with the optimal scatter value obtained by this iterative approach. Conclusion: Residual scatter subtraction can provide improved grid-line artifact elimination when using the flat-field with grid “subtraction” technique. The standard deviation of image pixel values can be used to determine the optimal scatter value to subtract to obtain a minimization of grid line artifacts with high resolution x-ray imaging detectors. This study was supported by NIH Grant R01EB002873 and an equipment grant from Toshiba Medical Systems Corp.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Minimum Cost Multi-way Data Association for Optimizing Multitarget Tracking of Interacting Objects

This paper presents a general formulation for a minimum cost data association problem which associates data features via one-to-one, m-to-one and one-to-n links with minimum total cost of the links. A motivating example is a problem of tracking multiple interacting nanoparticles imaged on video frames, where particles can aggregate into one particle or a particle can be split into multiple particles. Many existing multitarget tracking methods are capable of tracking non-interacting targets or tracking interacting targets of restricted degrees of interactions. The proposed formulation solves a multitarget tracking problem for general degrees of inter-object interactions. The formulation is in the form of a binary integer programming problem. We propose a polynomial time solution approach that can obtain a good relaxation solution of the binary integer programming, so the approach can be applied for multitarget tracking problems of a moderate size (for hundreds of targets over tens of time frames). The resulting solution is always integral and obtains a better duality gap than the simple linear relaxation solution of the corresponding problem. The proposed method was validated through applications to simulated multitarget tracking problems and a real multitarget tracking problem.

Binary Integer Programming↗