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DOE OSTI2024

Optimized CRISPR Interference System for Investigating Pseudomonas alloputida Genes Involved in Rhizosphere Microbiome Assembly

Pseudomonas alloputida KT2440 (formerly P. putida) has become both a well-known chassis organism for synthetic biology and a model organism for rhizosphere colonization. Here, we describe a CRISPR interference (CRISPRi) system in KT2440 for exploring microbe–microbe interactions in the rhizosphere and for use in industrial systems. Our CRISPRi system features three different promoter systems (XylS/P m , LacI/P lac , and AraC/P BAD ) and a dCas9 codon-optimized for Pseudomonads, all located on a mini-Tn7-based transposon that inserts into a neutral site in the genome. It also includes a suite of pSEVA-derived sgRNA expression vectors, where the expression is driven by synthetic promoters varying in strength. We compare the three promoter systems in terms of how well they can precisely modulate gene expression, and we discuss the impact of environmental factors, such as media choice, on the success of CRISPRi. We demonstrate that CRISPRi is functional in bacteria colonizing the rhizosphere, with repression of essential genes leading to a 10–100-fold reduction in P. alloputida cells per root. Finally, we show that CRISPRi can be used to modulate microbe–microbe interactions. When the gene pvdH is repressed and P. alloputida is unable to produce pyoverdine, it loses its ability to inhibit other microbes in vitro. Furthermore, our design is amendable for future CRISPRi-seq studies and in multispecies microbial communities, with the different promoter systems providing a means to control the level of gene expression in many different environments.

Bacteria↗

DOE OSTI2024

Shape Matters: Understanding the Effect of Electrode Geometry on Cell Resistance and Chemo-Mechanical Stress

Rechargeable batteries that incorporate shaped three-dimensional electrodes have been shown to have increased power and energy densities when compared to a conventional geometry, i.e. a planar cathode and anode that sandwich an electrolyte. Electrodes can be shaped to enable a higher active material loading, while keeping ion transport distances small. However, the relationship between electrical and mechanical performance of shaped electrodes remains poorly understood. Many electrode designs have been explored, where the electrodes are individually shaped or intertwined, and advances in manufacturing and shape/topology optimization have made such designs a reality. Here, we explore sinusoidal half cells and interdigitated full cells. First, we use a simple electrostatics model to understand the cell resistance as a function of shape. Here we focus on low-temperature conditions, where the electrolyte conductivity decreases relative to that of the electrode; here, LiPF 6 EC:DMC electrolyte and MnO 2 electrode are considered. Next, we use a chemo-mechanics model to examine the stress that arises due to intercalation-driven volume expansion. We show that shaped electrodes provide a significant reduction in resistance in low-temperature conditions, however, they exhibit unfavorable stress concentrations. Overall, we find that the fully interdigitated electrodes may provide the best balance with respect to this resistance-stress trade-off.

25 ENERGY STORAGE↗

DOE OSTI2025

Supporting Information for manuscript: “A latitudinal gradient in S/G lignin monomer ratio driven by laccase in natural poplar variants”

Lignin composition plays a crucial role in plant structural integrity and environmental adaptation. However, the genetic and molecular mechanisms underlying natural variation in lignin composition remain poorly understood. This study investigates the syringyl-to-guaiacyl (S/G) lignin monomer ratio across a natural population of Populus trichocarpa spanning a latitudinal gradient along the Northwest coast of North America. By integrating biochemical, genomic, and geographic analysis, we identify key gene variants associated with S/G ratio differences. These datasets provide valuable insights into the evolutionary and functional genomics of lignin composition and serve as a resource for developing poplar variants optimized for forestry and bioenergy applications.

Poplar, lignin composition, laccases, latitude, ad↗

DOE OSTI2022

Neural Network-Based Electric Vehicle Range Prediction for Smart Charging Optimization

Range prediction is a standard feature in most modern road vehicles, allowing drivers to make informed decisions about when to refuel. Most vehicles make range predictions through data- or model-driven means, monitoring the average fuel consumption rate or using a tuned vehicle model to predict fuel consumption. The uncertainty of future driving conditions makes the range prediction problem challenging, particularly for less pervasive battery electric vehicles (BEV). Most contemporary machine learning-based methods attempt to forecast the battery SOC discharge profile to predict vehicle range. In this work, we propose a novel approach using two recurrent neural networks (RNNs) to predict the remaining range of BEVs and the minimum charge required to safely complete a trip. Each RNN has two outputs that can be used for statistical analysis to account for uncertainties; the first loss function leads to mean and variance estimation (MVE), while the second results in bounded interval estimation (BIE). These outputs of the proposed RNNs are then used to predict the probability of a vehicle completing a given trip without charging, or if charging is needed, the remaining range and minimum charging required to finish the trip with high probability. Training data was generated using a low-order physics model to estimate vehicle energy consumption from historical drive cycle data collected from medium-duty last-mile delivery vehicles. Here, the proposed method demonstrated high accuracy in the presence of day-to-day route variability, with the root-mean-square error (RMSE) below 6% for both RNN models.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

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

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

Altarjami, Ibrahim↗

DOE OSTI2023

Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome

Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa. Metaproteomics often generates less data than other omics techniques, but analytical workflows can be improved to increase usable data in metaproteomic outputs. Identification of peptides in the metaproteomic analysis is performed by comparing mass spectra of sample peptides to a reference database of protein sequences. Although these protein databases are an integral part of the metaproteomic analysis, few studies have explored how database composition impacts peptide identification. Here, we used cervicovaginal lavage (CVL) samples from a study of bacterial vaginosis (BV) to compare the performance of databases built using six different strategies. We evaluated broad versus sample-matched databases, as well as databases populated with proteins translated from metagenomic sequencing of the same samples versus sequences from public repositories. Smaller sample-matched databases performed significantly better, driven by the statistical constraints on large databases. Additionally, large databases attributed up to 34% of significant bacterial hits to taxa absent from the sample, as determined orthogonally by 16S rRNA gene sequencing. We also tested a set of hybrid databases which included bacterial proteins from NCBI RefSeq and translated bacterial genes from the samples. These hybrid databases had the best overall performance, identifying 1,068 unique human and 1,418 unique bacterial proteins, ~30% more than a database populated with proteins from typical vaginal bacteria and fungi. Our findings can help guide the optimal identification of proteins while maintaining statistical power for reaching biological conclusions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Development of an interatomic potential for the W–Ta system

A physics-inspired, data-driven interatomic potential framework for multi-element system is presented. This potential is based on the generalization of the embedded atom method potential and systematically incorporates two-, three- and many-body effects. Different atomic environments are described by atom-centered Gaussian basis sets which provides sufficient flexibility to capture diverse atomic environments and allows for easy optimization of the free parameters. An interatomic potential model for the tungsten–tantalum (W–Ta) system is developed using this framework by training on data from ab initio density functional theory (DFT) calculations. The potential is thoroughly tested at various compositions by comparing bulk and defect properties from experimental and DFT data. It is shown that the potential predicts the elastic constants, defect properties, such as vacancy and interstitial formation energies, core structures of dislocations, and melting points for both pure and tantalum and tungsten with an accuracy comparable to other single element machine learning based potentials. In conclusion, the potential model is used to investigate the formation energies of ordered alloys and vacancy formation energies for chemically random W–Ta alloys.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Thermodynamic assessment of nonstoichiometric oxides for solar thermochemical fuel production

Two-step solar thermochemical cycling (STC) based on nonstoichiometric oxides is an ideal means of solar fuel (e.g., H 2 , CO) production. Screening of nonstoichiometric oxides with excellent thermodynamic performance is key to achieving high solar-to-fuel efficiency. However, application-driven materials assessment intended for reactor-level solar fuel production performance requires mimicking realistic operating conditions of on-sun tests in a laboratory setting, which makes oxides assessment and screening an onerous task to accomplish experimentally. In this work, a rapid assessment and screening model of nonstoichiometric oxides for two-step solar thermochemical cycling assuming fixed-bed flow pattern and quasi-equilibration of the solid with the flowing gas phase is developed, with solar-to-fuel efficiency being the target function of optimization. The model accounts for the thermodynamic parameters of oxide materials and typical operating conditions of experimental thermochemical cycling. This study employed the model to explore and compare two groups of typical nonstoichiometric oxides (CeO 2 - and (LaSr)MnO 3 -based) for their maximum efficiency under their uniquely optimized cycling conditions. The results show that CeO 2 can reach a maximum efficiency of 12.9% at reduction temperature of 1500 °C, which is superior to other candidate materials, including 20 mol% Zr-doped CeO 2 (10.1%), La 0.6 Sr 0.4 MnO 3 (2.5%) and La 0.8 Sr 0.2 MnO 3 (3.3%). Even when the reduction temperature is lowered to 1350 °C, ceria yields the highest efficiency amongst the candidate STC materials considered. The optimal cycling strategy depends on the inherent thermodynamic properties of the oxides. This approach serves as a framework for assessing the maximum efficiency and optimal conditions of candidate thermochemical materials within a range of constraints rather than comparing materials under arbitrary cycling conditions, which may inherently favor one material over another. For oxidation temperatures below 800–1000 °C, the model could be further improved by considering reaction kinetics.

14 SOLAR ENERGY↗

DOE OSTI2026

Local Structural Coherence and Interfacial Charge Transfer in Cu 2 ⁢S/Mo⁢S 2 Heterostructure

Precise control over electronic coupling at nanoscale interfaces is critical for designing materials with tunable charge-transfer behavior and catalytic function. Heterostructures with locally coherent interfaces provide a platform for interrogating interfacial charge redistribution in coupled material systems. Here, we report Cu 2 ⁢S/Mo⁢S 2 heterostructures exhibiting nanoscale crystallographic alignment, which are synthesized through a rapid thermal transformation pathway. We employed electrochemical reduction reactions to probe interfacial charge transfer, revealing shifts in product distribution attributable to modified interfacial energetics, even in the absence of optimized catalytic performance. The observed formate Faradaic efficiency suggests that interfacial electronic modulation in the heterostructure shifts product selectivity towards formate, highlighting how interface-driven electronic modulation can direct reaction pathways and influence product selectivity. Optimizing catalyst loading, architecture, and reactor configuration will be critical for future improvement. Structural and compositional integrity were confirmed through powder x-ray diffraction, x-ray photoelectron spectroscopy, and high-resolution transmission electron microscopy. Electron transfer between Cu 2 ⁢S and Mo⁢S 2 domains was further evaluated by electrochemical impedance spectroscopy, while selected-area electron diffraction revealed local crystallographic alignment consistent with a local epitaxial relationship at the Cu 2 S/Mo⁢S 2 heterointerface. To illustrate the broader applicability of this approach, a Zn⁢S/Mo⁢S 2 heterostructure was also synthesized using the same microwave strategy, confirming the generalizability of interfacial engineering principles across metal sulfide-Mo⁢S 2 systems. Collectively, these findings demonstrate that controlled local epitaxial alignment serves as an effective design principle for tuning interfacial energetics and catalytic reactivity in complex heterostructure materials.

carbon capture & utilization↗

DOE OSTI2025

Electrically Conductive Amine Functionalized Reduced Graphite Oxide Foam for CO 2 Removal from the Air

Rapid regeneration of CO 2 adsorbents is critical to improving the productivity of direct air capture (DAC) systems. In this study, we codesigned a material to have appropriate electrical conductivity and CO 2 adsorption properties to enable efficient CO 2 capture from air. Specifically, we present a poly(ethylenimine) (PEI)-impregnated thermally annealed graphite oxide (TAGO900) foam adsorbent tailored for vacuum-assisted electrically driven thermal swing adsorption (V-ETSA). This structured adsorbent leverages the high electrical conductivity of the reduced graphite oxide framework to enable fast and direct heating of the adsorbent material by electrical resistance heating (Joule heating). An optimal sample, 40 wt % PEI (molecular weight 25k) impregnated TAGO900, shows the best balance between adsorption capacity (1.54 mmol g –1 ) and adsorption rates (0.016 mmol g –1 min –1 ) using fixed bed breakthrough experiments at 25 °C and 70% RH using 50 sccm 400 ppm of CO 2 /N 2 flow. Compared to conventional temperature vacuum swing adsorption (TVSA), the V-ETSA approach achieves substantially faster CO 2 desorption, achieving average desorption rates (including cooling time) of 0.09 mmol g –1 min –1 ─approximately 2.5 times faster than TVSA under similar operating conditions. The maximum desorption rate reaches 0.23 mmol/g/min during the desorption stage. These results underscore the importance of the direct heating strategy, such as Joule heating, for fast and highly productive vacuum swing adsorption in DAC systems.

amines↗

DOE OSTI2020

Mapped Moments to a Cartesian Grid (MMCG) Value-Added Product Report

Objective analysis (OA) is a method of mapping unstructured data to a structured grid. In the context of scanning radar data, OA is used to interpolate data in antenna coordinates (range, azimuth, and elevation) onto a regularly spaced Cartesian grid (Trapp and Doswell 2000). The U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility’s Mapped Moments to a Cartesian Grid (MMCG) Value-Added Product (VAP) uses the Python ARM Radar Toolkit (Py-ART), a data model-driven interactive architecture for working with weather radar data, to map the data to a Cartesian grid (Helmus and Collis 2016). MMCG, with Py-ART built in, has the ability to take radar data in antenna coordinates and map the gates to a Cartesian grid using inverse distance weight functions such as Cressman (square) and Barnes (exponential), but also can filter the data during the interpolation. MMCG also allows arbitrary formulations for the radius of influence, which are matched to particular radar scanning strategies. This creates a complex parameter space for optimizing the retention of storm structure detail while minimizing artifacts. MMCG takes data processed with ARM’s Corrected Precipitation Radar Moments in Antenna Coordinates (CMAC) VAP and maps it to a Cartesian grid as the output product. A variety of fields that have been mapped to the Cartesian grid are then saved to plots to complement each grid file.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

A Nonlocal Feature-Driven Exemplar-Based Approach for Image Inpainting

Here, we present a nonlocal variational image completion technique which admits simultaneous inpainting of multiple structures and textures in a unified framework. The recovery of geometric structures is achieved by using general convolution operators as a measure of behavior within an image. These are combined with a nonlocal exemplar-based approach to exploit the self-similarity of an image in the selected feature domains and to ensure the inpainting of textures. We also introduce an anisotropic patch distance metric to allow for better control of the feature selection within an image and present a nonlocal energy functional based on this metric. Finally, we derive an optimization algorithm for the proposed variational model and examine its validity experimentally with various test images.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Multigene engineering in plants: Technologies, applications, and future prospects

The emerging bioeconomy presents a promising solution to both economic and environmental challenges. Within the bioeconomy, plants serve as a renewable, sustainable, and cost-effective source of foods, fuels, chemicals, and materials. However, traditional breeding and single-gene engineering approaches fall short in addressing complex traits (e.g., drought tolerance, disease resistance, yield, nutrient use efficiency) which are controlled by multiple genes. The complexity of plant biology often necessitates the use of multigene engineering (MGE), which involves simultaneous ectopic expression, up/down-regulation, or editing of multiple genes, to enhance plant traits relevant to the bioeconomy. These genes may be associated with distinct traits or function as components of specific metabolic and regulatory pathways. This review summarizes current technologies for MGE within the synthetic biology-driven Design-Build-Test-Learn (DBTL) framework, detailing its four key stages: Design – gene construct development; Build – DNA assembly and plant transformation; Test – the molecular, biochemical, and physiological characterization of engineered plants; and Learn – computational modeling to refine, multiplex and iterate the process. Despite good progress in the applications of MGE in biofortification, metabolic engineering, and stress resilience, challenges remain in construct stability, coordinated gene expression, and regulatory predictability. We identified optimization paths and future directions to accelerate MGE deployment in sustainable agriculture, with possible societal benefits including reduced production costs, increased yield, and improved food and nutritional security.

AI-aided plant engineering↗

DOE OSTI2021

Human-automated vehicle interactions

This dissertation is proposed to answer the question: how can the interactions between human and automated vehicles be used to improve the overall performance of automated driving technology? Multiple different modules in automated vehicles such as the perception, motion plan and motion control modules can potentially be benefitted from human-automated vehicle interactions. For perception module, the self-correction of faulty sensors can be achieved using human demonstration data. For motion plan and motion control modules, the performance of the low-level motion controller can be improved with the help of human demonstration, and the behavior of the motion planner can be improved using human intervention data during automated driving. Moreover, a better model for a human driver could improve the overall efficiency and comfort of vehicles in connected mixed traffic. In this dissertation, the technical research toward these goals has been completed and has resulted in several peer-reviewed publications. Optimization methods and model predictive control are used extensively to improve energy efficiency while maintaining safe and comfort driving. An inverse model predictive control (IMPC) method has been developed and it has been proven to be effective in modeling the motion of human driven vehicles. The proposed method has demonstrated its benefits in both connected automated highway driving and the bilateral adaptation of human driver and automated driving controller in human-in-the loop simulations. The proposed future research seeks to broaden the application of IMPC by considering a more comprehensive cost function design and applying it to more complex driving situations.

Guo, Longxiang↗

DOE OSTI2021

HUMAN-AUTOMATED VEHICLE INTERACTIONS

Guo, Longxiang↗

DOE OSTI2022

Learning Local Volt/VAR Controllers Toward Efficient Network Operation with Stability Guarantees: Preprint

This paper considers the problem of voltage regulation in distribution network. The primary motivation is to keep voltages within pre-assigned operating limits by commanding the reactive power output of distributed energy resources (DERs) deployed in the grid. We develop a framework for developing local Volt/Var control that comprises of two main steps. In the first, exploiting historical data and for each DER, we learn a function representing desirable equilibrium points for the power network. These points approximate solutions of an Optimal Power Flow problem. In the second, we propose a control scheme for steering the network towards these favorable configurations. Theoretical conditions are derived to formally guarantee the stability of the developed control scheme and numerical simulations illustrate the effectiveness of the proposed approach.

data-driven control↗

DOE OSTI2025

Network Slicing for Federated Learning in Operational Technology Environment

Industrial Control Systems (ICS) and Supervisory Control and Data Acquisition (SCADA) environments are essential to modern infrastructure, facing challenges in ensuring low-latency, high-throughput communication while mitigating cyber threats. This paper presents a framework integrating Federated Learning (FL) and network slicing with Quality of Service (QoS) to enable real-time monitoring without disrupting OT operations. Leveraging digital twin technology and Network Function Virtualization (NFV), the architecture supports predictive analytics and Industry 4.0 requirements. FL facilitates decentralized model training, preserving data privacy and scalability, though it introduces potential throughput constraints. Network slicing addresses this by creating dedicated virtualized segments optimized for performance and security. Advanced fault tolerance at the container and instance levels enhances system reliability. The proposed architecture ensures high throughput, low latency, and secure orchestration for real-time anomaly detection in OT networks. Performance evaluations validate its efficiency in throughput, deployment, and learning accuracy, providing a robust foundation for future ICS automation and data-driven decision-making.

Delgado, Brian G. Rodiles [University of Texas at ↗

DOE OSTI2025

Operational resilience of additively manufactured parts to stealthy cyberphysical attacks using geometric and process digital twins

Cyberphysical attacks on the digital backbone of Additive Manufacturing (AM) can compromise the printed part’s functionality. They can alter features in the digital geometry to introduce geometric defects (e.g., missing fillets) or alter process parameters to create local defects (e.g., voids). Addressing the downtime, waste, and quality deterioration associated with existing solutions requires operational resilience, i.e., rapid elimination or disruption of defect formation (to retain part function) without production stoppage or part disposal (to retain yield). This need is unmet due to the inherently unpredictable nature of attack-induced alterations, lack of access to the original geometric model for identification of altered geometric features, and in-process imposition of unknown process dynamics via attack-driven alteration of real-time-uncontrolled (or exogenous) parameters. This work establishes the above-mentioned operational resilience for the first time by creating two Digital Twins (DT). The Geometric DT (Geo-DT) is based on a unique physical-field-driven soft sensor and topology optimization method. The Process Digital Twin (Pro-DT) combines local defect quantification with a novel Reinforcement Learning formulation and training method. The importance of these methodological advances and the scalability of our approach are examined on a real AM testbed. It is shown that Geo-DT can correct geometric defects without access to the original digital geometry or explicit knowledge of attack-altered geometric features. Further, Pro-DT can accelerate real-time disruption of local defects despite attack-driven imposition of unknown process dynamics. We discuss how our framework goes beyond the contemporary focus on pre-attack security and in-attack detection towards resilience for AM and beyond.

Additive Manufacturing↗