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DOE OSTI2026

Predictive CRISPR-mediated gene downregulation for enhanced production of sustainable aviation fuel precursor in Pseudomonas putida

CRISPR interference (CRISPRi) has emerged as a valuable tool for redirecting metabolic flux to enhance bioproduction. However, its application is often constrained by two challenges: (i) rationally identifying effective gene targets for downregulation and (ii) efficiently constructing multiplexed CRISPRi systems. In this study, we address both challenges by integrating a computational prioritization tool with a versatile assembly method for building multiplexed CRISPRi systems. FluxRETAP (Flux-Reaction Target Prioritization) accurately identified gene targets whose knockdown led to substantial increase of isoprenol titers in Pseudomonas putida KT2440, outperforming a conventional non-computational, pathway-guided target selection. The highest isoprenol titer of nearly 1.5 g/L was achieved by knocking down PP_4118 (a gene encoding α-ketoglutarate dehydrogenase). The use of VAMMPIRE (Versatile Assembly Method for MultiPlexing CRISPRi-mediated downREgulation) enabled accurate assembly of CRISPRi constructs containing up to five sgRNA arrays, reducing context dependency and achieving uniform, position-independent gene downregulation. The integration of FluxRETAP and VAMMPIRE has the potential to advance metabolic engineering by rapidly identifying CRISPRi-mediated knockdowns and knockdown combinations that enhance bioproduction titers, with potential applicability to other microbial systems.

CRISPR interference↗

DOE OSTI2025

High Performance Solvent for NGCC Flue Gas CO 2 Capture (Final Technical Report)

Amine-based solvent absorption is the most mature and reliable technology for large scale CO 2 capture, dating back to the 1930s when monoethanolamine (MEA) was used to treat acid gases from oil refineries. However, while strategic advancements have optimized the CO2 capture process, the cost of capture remains high, where current estimates suggest that CO 2 capture costs are around $\$$72/tonne of CO 2 . To address this, solvent development and optimization have become a focus of current research. This project sought to develop a high-performance solvent to reduce the overall cost of CO 2 capture from NGCC flue gas. Here, solvent optimization focused on: (1) reducing the energy required for CO 2 desorption in a reboiler, (2) improving CO 2 absorption and desorption reaction kinetics, (3) improving solvent stability, and (4) reducing environmental impacts. Susteon has developed and evaluated a promoted solvent, Sustenol™, for NGCC flue gas CO 2 capture. The optimized Sustenol™ also shows a higher dynamic CO 2 absorption capacity of ~0.5 mol CO2 /mol amine compared to 0.25 mol CO2 /mol amine for 30 wt% MEA. Additionally, the solvent is oxidatively, thermally and hydrothermally stable, which leads to lower solvent loss and emissions. These advancements have resulted in a solvent regeneration energy of 2.16 GJ/tonne of CO 2 which is >30% lower than current state-of-the-art commercial and emerging solvents. Combined with empirical data from the bench and pilot scale testing, this preliminary TEA study indicated the cost of CO 2 capture by Sustenol™ for 97% CO 2 removal at $\$$54/tonne and for 90% removal at $\$$49/tonne, with a pathway to achieve $\$$45/tonne of CO 2 with continued process and solvent advancements. Susteon has developed a technology roadmap to reduce the cost of CO 2 capture to <$\$$45/tonne for NGCC flue gas. Susteon plans to derisk this technology for commercial deployment through comprehensive solvent degradation testing, long-term testing in a pilot plant at 5 tonne CO2 /day and demonstration scale testing at 100 tonne CO2 /day with NGCC flue gas and engineering design studies to qualify Sustenol™ as a drop-in replacement solvent.

03 NATURAL GAS↗

DOE OSTI2025

Gas-mediated defect engineering in earth-abundant Mn-rich layered oxides for non-aqueous sodium-based batteries

Gases are often by-products of battery materials during cell formation and degradation, affecting the cycle life and safety of rechargeable batteries. However, understanding gas-mediated (electro)-chemical reactions and nanoscale structural transformations during the synthesis of battery electrode materials remains challenging because of the lack of suitable characterization routes and the complexity of the interplay between thermodynamics and kinetics. Here, in this study, we use operando synchrotron X-ray diffraction, in situ transmission X-ray microscopy and multiscale modelling to elucidate the reaction pathways and microstructural defect development of earth-abundant Mn-rich layered oxides as positive electrode materials for sodium-based batteries. In particular, we demonstrate the dominant role of CO 2 over O 2 and H 2 O (g) in modulating the competition between entropy and enthalpy during solid-state synthesis. Using Ni 0.25 Mn 0.75 CO 3 as a model precursor, we reveal that CO 2 generation favours the formation of entropy-driven metastable intermediates, suppresses closed pore/nanovoids formation and decreases chemical heterogeneity and residual lattice strain of Mn-rich layered oxides during the synthesis. This result motivates a fast-sintering strategy to promote CO 2 release, which ultimately leads to improved chemo-mechanical and electrochemical stability of the Mn-rich positive electrodes when tested in non-aqueous Na metal coin cells.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Amino Acid Residues Controlling Domain Interaction and Interdomain Electron Transfer in Cellobiose Dehydrogenase

The function of cellobiose dehydrogenase (CDH) in biosensors, biofuel cells, and as a physiological redox partner of lytic polysaccharide monooxygenase (LPMO) is based on its role as an electron donor. Before donating electrons to LPMO or electrodes, an interdomain electron transfer from the catalytic FAD-containing dehydrogenase domain to the electron shuttling cytochrome domain of CDH is required. This study investigates the role of two crucial amino acids located at the dehydrogenase domain on domain interaction and interdomain electron transfer by structure-based engineering. The electron transfer kinetics of wild-type Myriococcum thermophilum CDH and its variants M309A, R698S, and M309A/R698S were analyzed by stopped-flow spectrophotometry and structural effects were studied by small-angle X-ray scattering. The data show that R698 is essential to pull the cytochrome domain close to the dehydrogenase domain and orient the heme propionate group towards the FAD, while M309 is an integral part of the electron transfer pathway – its mutation reducing the interdomain electron transfer 10-fold. Structural models and molecular dynamics simulations pinpoint the action of these two residues on the domain interaction and interdomain electron transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Colloidal AInSe 2 (A = K, Rb, Cs) Nanocrystals with Tunable Crystal and Band Structures

Wide band gap AInSe 2 (A = K, Rb, Cs) is an important interlayer material for improving the efficiency of Cu(In,Ga)(S,Se) 2 (CIGS) solar cells. Compared to high-vacuum deposition and solid-state synthesis, a less energyintensive method is of interest for its fabrication. Herein, we present the rapid, low-temperature colloidal synthesis of AInSe 2 nanocrystals that opens a pathway for convenient solution processing. The crystal structures and electronic band structures of the nanocrystals were studied, and their particle morphology was found to be dependent on the choice of alkali metal and selenium precursors. Homogeneous solid solution (K,Rb,Cs)InSe 2 nanocrystals were synthesized using a mixture of alkali metal precursors. Their compositions, lattice parameters, and band gaps were easily tuned based on the K:Rb:Cs precursor ratio, providing potential for interface engineering of CIGS nanocrystal-based solar cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Data for A Hybrid Biophysical-Machine Learning Framework for Diurnal Surface Energy Flux Estimation Using Proximal Sensing

Thermal infrared-based remote sensing of surface energy fluxes has traditionally relied on high spatial resolution satellite data with revisit frequencies on the order of weeks. In this study, we evaluate a biophysics-based analytical surface energy balance model for predicting latent energy (LE) and sensible heat (H) fluxes using proximal sensing observations. The Surface Temperature Initiated Closure (STIC1.2) model has been extensively validated across a wide range of spatial and temporal scales using various satellite-derived thermal infrared data sets. Here we extend this validation by applying STIC at sub-hourly temporal resolution over multiple growing seasons for four distinct agricultural systems. We further develop and evaluate novel STIC variants that incorporate machine learning (ML) techniques to eliminate the need for surface energy balance observations, specifically net radiation and soil heat flux, thereby enhancing model applicability in data-sparse settings. The integration of a ML component to estimate surface available energy is shown to have strong predictive performance for both LE (R2 = 0.81–0.94) and H (R2 = 0.46–0.72) across all agricultural systems examined here, demonstrating the potential of hybrid biophysical-machine learning approaches for surface energy balance modeling with minimal data requirements. This study concludes with a novel application of explainable machine learning (exML) to diagnose sources of model error. This exML framework attributes residual prediction errors to both model input variables and environmental drivers not explicitly included in the simulation experiments. This approach provides a new pathway for improving model design and integrating previously overlooked yet influential variables into future model iterations.

AI/ML↗

DOE OSTI2025

Development of emerging model microorganisms: Megasphaera elsdenii for biomass and organic acid upgrading to fuels and chemicals

The metabolic diversity of microorganisms in nature represents a largely untapped source of valuable compounds that are difficult or impossible to produce in the limited number of available model systems. Efforts to produce longer-chain alcohols, such as hexanol, in organisms like Escherichia coli have met with limited success; production of C6 and larger products remains low, highlighting the challenges of extending chain elongation pathways beyond a single cycle. Megasphaera elsdenii naturally condenses acetyl-CoA to efficiently generate C4–C8 organic acids, making it a promising candidate for producing fuels and chemicals from lactate and plant-derived carbohydrates. This high native flux through the chain elongation pathway offers the potential for higher yields and titers of medium-chain products, such as hexanol, compared to conventional hosts. Recent advances—most notably the development of a transformation method for M. elsdenii—have further opened the organism to detailed physiological studies and bioengineering. While full development of M. elsdenii as a hexanol-producing platform was not achieved, significant progress was made in understanding its metabolism and building foundational genetic tools for future engineering.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Developing novel electrodes with ultralow catalyst loading for high-efficiency hydrogen production in proton exchange membrane electrolyzer cells

Hydrogen plays more crucial roles for decarbonizing the planets and meeting the climate challenges because of its high energy density and zero-emission. It can be produced with proton exchange membrane electrolyzer cells (PEMECs) driven by sustainable and renewable energy resources. Although PEMECs have a number of advantages, including high purity production, quick response, and the ability to operate at high pressure facilitating the gas delivering, their performance and cost greatly hinder their commercial-scale applications. To achieve high-efficiency and cost-reduced hydrogen production in PEMECs, we proposed thin engineered liquid/gas diffusion layers (LGDLs) and associated electrodes, i.e., catalyst-coated LGDLs (CCLGDLs), over conventional porous transport layers (PTLs) and catalyst-coated membranes (CCMs). The research approaches in this project are based on material synthesis, in-situ and ex-situ characterizations, component design and treatment, numerical modeling, and cost analysis. The thin and tunable LGDLs (TT-LGDLs) and CCLGDLs were successfully developed with great performance improvement as demonstrated in lab-scale, bench-scale, and system-scale electrolyzer tests. The electrode thickness was reduced from 370 µm to less than 100 µm with simplified fabrication processes. With the catalytically enhanced Ir-based catalyst coating, the as-developed CCLGDLs with a catalyst loading of 0.34 mg Ir /cm 2 achieved a cell performance of 1.77 V at 2 A cm -2 , exhibiting the catalyst mass activity enhanced by >20 times with significant catalyst saving over conventional catalyst cell design. In-situ PEMEC characterizations, including the current distribution mapping and high-speed and multiscale visualizations, were conducted for a deeper understanding of mass transport and electrochemical reactions within an electrolyzer with LGDLs and CCLGDLs. A 2D cell model was developed and validated for the enhanced performance on TT-LGDL through reducing ohmic losses due to nonuniform hydration and water transport. Further, the cost analysis results have shown a path to move beyond equivalency and surpass costs associated with the project baseline. In this project, the design and fabrication of TT-LGDLs and CCLGDLs will contribute to the performance enhancement, manufacturing simplification, and cost reduction for PEMECs and other energy conversion devices, thus shortening their pathways towards commercialization. This project also provides a good foundation for furthering the in-situ reaction interface research.

08 HYDROGEN↗

DOE OSTI2026

Carbon source–driven metabolic and regulatory remodeling defines phenomic states in Lipomyces starkeyi

Lipomyces is a genus of oleaginous yeasts with potential for contributing to reliable biomanufacturing supply chains. However, progress in advanced strain designs and engineering efforts are still constrained by a lack of understanding of the underlying molecular drivers of Lipomyces phenotypes. To address this gap, we collected a suite of multi-omic data to dissect how carbon source availability reshapes the metabolic network, lipid allocation, and regulatory architecture of Lipomyces starkeyi. We observed that glucose promotes biosynthetic and proliferative processes supported by abundant energy and carbon intermediates, xylose enhances redox-balancing mechanisms centered on the pentose phosphate pathway, and glycerol activates respiratory metabolism, ß-oxidation, and the glyoxylate cycle. Lipid species distributions remained consistent in both nitrogen replete and depleted conditions across the carbon sources, indicating robust production mechanisms. Regulatory protein identification and network analysis revealed glycerol-driven respiratory growth favors regulatory programs integrating stress tolerance, redox balance, and lipid-associated metabolism, whereas xylose growth activates compensatory transcriptional responses aimed at maintaining mitochondrial function. Nitrogen limitation modulates the strength of these responses but does not fundamentally alter their direction, reinforcing carbon source as the dominant driver of regulatory architecture. Taken together, this data enhances the understanding of Lipomyces molecular rearrangements and provides a foundation for further development of predictive phenotypic tools in this genus.

Biotechnology↗

DOE OSTI2021

Unraveling the advances of trace doping engineering for potassium ion battery anodes via tomography

Doping have been considered as a prominent strategy to stabilize crystal structure of battery materials during the insertion and removal of alkali ions. The instructive knowledge and experience acquired from doping strategies predominate in cathode materials, but doping principle in anodes remains unclear. Here, we demonstrate that trace element doping enables stable conversion-reaction and ensures structural integrity for potassium ion battery (PIB) anodes. With a synergistic combination of X-ray tomography, structural probes, and charge reconfiguration, we encode the physical origins and structural evolution of electro-chemo-mechanical degradation in PIB anodes. By the multiple ion transport pathways created by the orderly hierarchical pores from “surface to bulk” and the homogeneous charge distribution governed in doped nanodomains, the anisotropic expansion can be significantly relieved with trace isoelectronic element doping into the host lattice, maintaining particle mechanical integrity. Our work presents a close relationship between doping chemistry and mechanical reliability, projecting a new pathway to reengineering electrode materials for next-generation energy storage.

25 ENERGY STORAGE↗

DOE OSTI2025

Theoretical study of CO2 capture mechanisms of SrO and Sr(OH)2.nH2O (n=0,1,8)

In this presentation, the adsorption reactions of CO2 on SrO surfaces and its hydrated counterparts are examined. The predicted energies of CO2 adsorption on follows the order of increasing H2O content. The carbonation on the monohydrate surface is barrierless, whereas the CO2 reaction on the Sr(OH)2 and the octahydrate surfaces follows pathways with finite activation barriers. The thermodynamics of bulk reaction is also addressed.

computational science and engineering↗

DOE OSTI2024

Cascade CO 2 Insertion in Carbanion Ionic Liquids Driven by Structure Rearrangement

The CO 2 chemisorption in state-of-the-art sorbents based on oxide/hydroxide/amine moieties is driven by strong chemical bonding formation in the carbonate/bicarbonate/carbamate products, which in turn leads to high energy input in sorbent regeneration. In addition, the CO 2 uptake capacity was limited by the active sites’ utilization efficiency, with each active site incorporating one CO 2 molecule or less. In this work, a new concept and generation of sorbent was developed to achieve cascade insertion of multiple CO 2 molecules by leveraging structure rearrangement as the driving force, leading to in situ generation of extra CO 2 -binding sites and significantly reduced energy input for CO 2 release. The designed ionic liquids (ILs) containing carbanions with conjugated and asymmetric structure, deprotonated (methylsulfonyl)acetonitrile ([MSA]) anion, allowed the cascade insertion of two CO 2 molecules via consecutive C–C and O–C bond formations. The proton transfer and structure rearrangement of the carboxylic acid intermediates played critical roles in stabilizing the first integrated CO 2 and generating extra electron-rich oxygen sites for the insertion of the second CO 2 . The structure variation and reaction pathway were confirmed by operando spectroscopy, magnetic resonance spectroscopy (NMR), mass spectroscopy, and computational chemistry. The energy input in sorbent regeneration could be further reduced by harnessing the phase-changing behavior of the carbanion salts in ether solutions upon reacting with CO 2 , avoiding the energy consumption in heating the solvent. In conclusion, the fundamental insights obtained herein provide a promising approach to greatly improve the CO 2 sorption performance via sophisticated molecular-scale structural engineering of the sorbents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Stabilization of three-dimensional charge order through interplanar orbital hybridization in Pr x Y 1–x Ba 2 Cu 3 O 6+δ

The shape of 3d-orbitals often governs the electronic and magnetic properties of correlated transition metal oxides. In the superconducting cuprates, the planar confinement of the d x 2 –y 2 orbital dictates the two-dimensional nature of the unconventional superconductivity and a competing charge order. Achieving orbital-specific control of the electronic structure to allow coupling pathways across adjacent planes would enable direct assessment of the role of dimensionality in the intertwined orders. Using Cu L 3 and Pr M 5 resonant x-ray scattering and first-principles calculations, we report a highly correlated three-dimensional charge order in Pr-substituted YBa 2 Cu 3 O 7 , where the Pr f-electrons create a direct orbital bridge between CuO 2 planes. With this we demonstrate that interplanar orbital engineering can be used to surgically control electronic phases in correlated oxides and other layered materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography

Pyridoxal 5’-phosphate (PLP)-dependent enzymes utilize a vitamin B 6 -derived cofactor to perform a myriad of chemical transformations on amino acids and other small molecules. Some PLP-dependent enzymes, such as serine hydroxymethyltransferase (SHMT), are promising drug targets for the design of small-molecule antimicrobials and anticancer therapeutics, while others have been used to synthesize pharmaceutical building blocks. Understanding PLP-dependent catalysis and the reaction specificity is crucial to advance structure-assisted drug design and enzyme engineering. Here we report the direct determination of the protonation states in the active site of Thermus thermophilus SHMT (TthSHMT) in the internal aldimine state using room-temperature joint X-ray/neutron crystallography. Conserved active site architecture of the model enzyme TthSHMT and of human mitochondrial SHMT (hSHMT2) were compared by obtaining a room-temperature X-ray structure of hSHMT2, suggesting identical protonation states in the human enzyme. The amino acid substrate serine pathway through the TthSHMT active site cavity was tracked, revealing the peripheral and cationic binding sites that correspond to the pre-Michaelis and pseudo-Michaelis complexes, respectively. At the peripheral binding site, the substrate is bound in the zwitterionic form. By analyzing the observed protonation states, Glu53, but not His residues, is proposed as the general base catalyst, orchestrating the retro-aldol transformation of L-serine into glycine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Structure of V-defects in long wavelength GaN-based light emitting diodes

The V-defect is a naturally occurring inverted hexagonal pyramid structure that has been studied in GaN and InGaN growth since the 1990s. Strategic use of V-defects in pre-quantum well superlattices or equivalent preparation layers has enabled record breaking efficiencies for green, yellow, and red InGaN light emitting diodes (LEDs) utilizing lateral injection of holes through the semi-polar sidewalls of the V-defects. In this article, we use advanced characterization techniques such as scattering contrast transmission electron microscopy, high angle annular dark field scanning transmission electron microscopy, x-ray fluorescence maps, and atom probe tomography to study the active region compositions, V-defect formation, and V-defect structure in green and red LEDs grown on (0001) patterned sapphire and (111) Si substrates. We identify two distinct types of V-defects. The “large” V-defects are those that form in the pre-well superlattice and promote hole injection, usually nucleating on mixed (Burgers vector b = ±a±c⁠) character threading dislocations. In addition, “small” V-defects often form in the multi-quantum well region and are believed to be deleterious to high-efficiency LEDs by providing non-radiative pathways. The small V-defects are often associated with basal plane stacking faults or stacking fault boxes. Furthermore, we show through scattering contrast transmission electron microscopy that during V-defect filling, the threading dislocation, which runs up the center of the V-defect, will “bend” onto one of the six {10$\overline{1}$1} semi-polar planes. In conclusion, this result is essential to understanding non-radiative recombination in V-defect engineered LEDs.

42 ENGINEERING↗

DOE OSTI2022

Real-time bioelectronic sensing of environmental contaminants

Real-time chemical sensing is crucial for applications in environmental and health monitoring. Biosensors can detect a variety of molecules through genetic circuits that use these chemicals to trigger the synthesis of a coloured protein, thereby producing an optical signal. However, the process of protein expression limits the speed of this sensing to approximately half an hour, and optical signals are often difficult to detect in situ. Here we combine synthetic biology and materials engineering to develop biosensors that produce electrical readouts and have detection times of minutes. Here we programmed Escherichia coli to produce an electrical current in response to specific chemicals using a modular, eight-component, synthetic electron transport chain. As designed, this strain produced current following exposure to thiosulfate, an anion that causes microbial blooms, within 2 min. This amperometric sensor was then modified to detect an endocrine disruptor. The incorporation of a protein switch into the synthetic pathway and encapsulation of the bacteria with conductive nanomaterials enabled the detection of the endocrine disruptor in urban waterway samples within 3 min. Our results provide design rules to sense various chemicals with mass-transport-limited detection times and a new platform for miniature, low-power bioelectronic sensors that safeguard ecological and human health.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Employing bacterial microcompartments to create privileged redox pools for biofuel production (Final report: Accomplishments)

Over the award period we made progress on all three objectives. We completed our goal of understanding the impact of cofactor recycling on pathway performance for a propanediol-related pathway (Objective 1) and coupled this data with kinetic metabolic models developed in Objective 3, resulting in several products (4 published research articles, 1 review and 3 other research manuscripts in preparation). We completed half of Objective 2 but found the pathway was incompatible with compartmentalization, which is an important but unexpected result. The details are relayed in the following sections, grouped by objective and task as applicable.

09 BIOMASS FUELS↗

DOE OSTI2025

An argument for using anaerobes as microbial cell factories to advance synthetic biology and biomanufacturing

Anaerobes thrive in the absence of oxygen and are an untapped reservoir of biotechnological potential. Therefore, bioprospecting efforts focused on anaerobic microbial diversity could rapidly uncover new enzymes, pathways, and chassis organisms to drive biotechnology innovation. Despite their potential utility, anaerobic fermenters are viewed as inefficient from a biochemical perspective because their metabolisms produce fewer ATP (~2) per molecule of glucose processed than heterotrophic respirers (~32–38 ATP). While aerobes excel at ATP generation, they are often less efficient than anaerobes at processes that compete with ATP generation for cellular resources. This perspective highlights how anaerobic adaptations are advantageous for synthetic biology and biomanufacturing applications through the engineering of microbial cell factories. We further highlight emerging applications of anaerobic bioprocessing, including the use of anaerobic metabolisms for lignocellulosic bioprocessing, human and environmental health, and value-added bioproduction.

59 BASIC BIOLOGICAL SCIENCES↗