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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Systems Analysis and Engineering of Biofuel Production in Chromochloris zofingiensis , an Emerging Model Green Alga

As a core component of a sustainable bioeconomy, microalgae have the potential to become a major source of biofuels and bioproducts. These photosynthetic microbes utilize solar energy, grow quickly, consume CO 2 , and can be cultivated on non-arable land. However, there are presently considerable practical limitations in the photosynthetic production of biofuels from microalgae, resulting in low productivity and high costs. Algae are a strikingly diverse group and understudied algae can reveal new opportunities for biofuels. Integrative systems biology and engineering of emerging model systems are needed to expand the possibilities of microbial production of biofuels and bioproducts. Our long-term goal is to design and engineer high-level production of biofuel precursors in microalgae.

09 BIOMASS FUELS↗
DOE OSTI2025

Data for Discovery, Characterization, and Application of Chromosomal Integration Sites for Stable Heterologous Gene Expression in Rhodotorula toruloides

Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides . We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. We validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides . These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides .

Conversion↗
DOE OSTI2025

Advances and Challenges in Low‐Temperature Upcycling of Waste Polyolefins via Tandem Catalysis

Abstract Polyolefin waste is the largest polymer waste stream that could potentially serve as an advantageous hydrocarbon feedstock. Upcycling polyolefins poses significant challenges due to their inherent kinetic and thermodynamic stability. Traditional methods, such as thermal and catalytic cracking, are straightforward but require temperatures exceeding 400 °C for complete conversion because of thermodynamic constraints. We summarize and critically compare recent advances in upgrading spent polyolefins and model reactants via kinetic (and thermodynamic) coupling of the endothermic C─C bond cleavage of polyolefins with exothermic reactions including hydrogenation, hydrogenolysis, metathesis, cyclization, oxidation, and alkylation. These approaches enable complete conversion to desired products at low temperatures (<300 °C). The goal is to identify challenges and possible pathways for catalytic conversions that minimize energy and carbon footprints.

Zhang, Wei [State Key Laboratory of Petroleum Mole↗
DOE OSTI2025

Advances and Challenges in Low‐Temperature Upcycling of Waste Polyolefins via Tandem Catalysis

Abstract Polyolefin waste is the largest polymer waste stream that could potentially serve as an advantageous hydrocarbon feedstock. Upcycling polyolefins poses significant challenges due to their inherent kinetic and thermodynamic stability. Traditional methods, such as thermal and catalytic cracking, are straightforward but require temperatures exceeding 400 °C for complete conversion because of thermodynamic constraints. We summarize and critically compare recent advances in upgrading spent polyolefins and model reactants via kinetic (and thermodynamic) coupling of the endothermic C─C bond cleavage of polyolefins with exothermic reactions including hydrogenation, hydrogenolysis, metathesis, cyclization, oxidation, and alkylation. These approaches enable complete conversion to desired products at low temperatures (<300 °C). The goal is to identify challenges and possible pathways for catalytic conversions that minimize energy and carbon footprints.

C-C cleavage↗
DOE OSTI2023

Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii

Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, the engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs respond across sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome of Azotobacter vinelandii engineered with a phylogenetically inferred ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to the introduced nitrogenase sequence-level perturbations. Rather the sustained physiological compatibility with the ancestral nitrogenase variant is accompanied by reduced expression of genes that support trace metal and electron resource allocation to nitrogenase. Our results spotlight gene expression changes in cellular processes adjacent to nitrogen fixation as productive engineering considerations to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Development, optimization, and application of an episomal plasmid system for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre- loxP -mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

CRISPR-Cas9↗
DOE OSTI2023

A structural model of the long-term degradation of the concrete biological shield

The concrete biological shield (CBS) of light water reactors is exposed to high neutron radiation dose in the long term, which may lead to the degradation of the concrete’s mechanical properties. Given the important shielding role of the CBS, it is necessary to investigate the irradiation effects at the structural scale and provide estimates of the damage extent from the wall’s inner surface to study potential license renewals. For this purpose, we developed a mechanical model accounting for radiation-induced expansion, creep, and damage in concrete using the Grizzly finite element code, informed by ex-core neutron flux calculations using the VERA tool. The model was applied to a 3D CBS structure represented by the CBS wall, a steel liner, reinforcement bars, and a concrete base mat and evaluated damage at 40, 60, and 80 years of operation. The VERA model predicted a maximum fluence of approximately 2 x 10 19 ncm -2 at 80 years of operation. The results showed that damage is highest at the inner surface of the CBS wall and gradually decreases with depth. It extends beyond the rebar after 60 years and reaches a depth of approximately 12 cm at 80 years.

42 ENGINEERING↗
DOE OSTI2026

Beyond sequence similarity: toward function-based screening of nucleic acid synthesis

Synthetic nucleic acids are a key input to modern biotechnology, yet they represent dual-use materials that require robust screening to mitigate biosecurity risks. The prevailing screening paradigm, which identifies sequences of concern (SoCs) through sequence similarity to controlled pathogens and toxins, may not fully capture risks posed by AI tools that can decouple biomolecular function from reliance on known sequences. Rapidly advancing biodesign capabilities enable the generation of genes and proteins that might evade sequence-based detection. We highlight the critical need for function-based screening approaches that can detect sequences capable of hazardous biological functions, regardless of similarity to known SoCs. We examine the feasibility of function-based screening with an initial focus on proteins, arguing that, while protein sequence space is vast, biologically functional proteins are significantly constrained by biophysical and biochemical requirements that can be learned and modeled. We propose a concrete implementation framework organized along a continuum of complexity, starting with toxins as the most tractable targets before expanding to more complex pathogenic functions. We then discuss open challenges and describe a research and development strategy to address them.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Water, Solute, and Ion Transport in De Novo-Designed Membrane Protein Channels

Biological organisms engineer peptide sequences to fold into membrane pore proteins capable of performing a wide variety of transport functions. Synthetic de novo-designed membrane pores can mimic this approach to achieve a potentially even larger set of functions. Here, in this work, we explore water, solute, and ion transport in three de novo designed β-barrel membrane channels in the 5–10 Å pore size range. We show that these proteins form passive membrane pores with high water transport efficiencies and size rejection characteristics consistent with the pore size encoded in the protein structure. Ion conductance and ion selectivity measurements also show trends consistent with the pore size, with the two larger pores showing weak cation selectivity. MD simulations of water and ion transport and solute size exclusion are consistent with the experimental trends and provide further insights into structure–function correlations in these membrane pores.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Atomically Dispersed Ni‐N‐C Catalysts for Electrochemical CO 2 Reduction

Abstract The atomic dispersion of nickel in Ni‐N‐C catalysts is key for the selective generation of carbon monoxide through the electrochemical carbon dioxide reduction reaction (CO 2 RR). Herein, the study reports a highly selective, atomically dispersed Ni 1.0% ‐N‐C catalyst with reduced Ni loading compared to previous reports. Extensive materials characterization fails to detect Ni crystalline phases, reveals the highest concentration of atomically dispersed Ni metal, and confirms the presence of the proposed Ni‐N x active site at this reduced loading. The catalyst shows excellent activity and selectivity toward CO generation, with a faradaic efficiency for CO generation (FE CO ) of 97% and partial current density for CO (j co ) of ‐9.0 mA cm −2 at ‐0.9 V in an electrochemical H‐type cell. CO 2 RR activity and selectivity are also studied by rotating disk electrode (RDE) measurements where transport limitations can be suppressed. It is expected that the utility of these Ni‐N‐C catalysts will lie with tandem CO 2 RR reaction schemes to multi‐carbon (C 2+ ) products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Generative design of de novo proteins based on secondary-structure constraints using an attention-based diffusion model

We report two generative deep-learning models that predict amino acid sequences and 3D protein structures on the basis of secondary-structure design objectives via either the overall content or the per-residue structure. Both models are robust regarding imperfect inputs and offer de novo design capacity because they can discover new protein sequences not yet discovered from natural mechanisms or systems. The residue-level secondary-structure design model generally yields higher accuracy and more diverse sequences. These findings suggest unexplored opportunities for protein designs and functional outcomes within the vast amino acid sequences beyond known proteins. Our models, based on an attention-based diffusion model and trained on a dataset extracted from experimentally known 3D protein structures, offer numerous downstream applications in the conditional generative design of various biological or engineering systems. Future work could include additional conditioning and an exploration of other functional properties of the generated proteins for various properties beyond structural objectives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Influence of functional groups on low-temperature combustion chemistry of biofuels

Ongoing progress in synthetic biology, metabolic engineering, and catalysis continues to produce a diverse array of advanced biofuels with complex molecular structure and functional groups. In order to integrate biofuels into existing combustion systems, and to optimize the design of next-generation combustion systems, understanding connections between molecular structure and ignition at low-temperature conditions (< 1000 K) remains a priority that is addressed in part using chemical kinetics modeling. The development of predictive models relies on detailed information, derived from experimental and theoretical studies, on molecular structure and chemical reactivity, both of which influence the balance of chain reactions that occur during combustion – propagation, termination, and branching. In broad context, three main categories of reactions affect ignition behavior: (i) initiation reactions that generate a distribution of organic radicals, ; (ii) competing unimolecular decomposition of and bimolecular reaction of with O2; (iii) decomposition mechanisms of peroxy radical adducts (RO), including isomerization via RO ⇌ OOH. Furthermore, all three categories are influenced by functional groups in different ways, which causes a shift in the balance of chain reactions that unfold over complex temperature- and pressure-dependent mechanisms.

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

Thermodynamic and Kinetic Transitions of Liquids in Nanoconfinement

Core principles of chemistry are ubiquitously invoked to shed light on the nature of molecular level interactions in nanoconfined fluids, which play a pivotal role in a wide range of processes in geochemistry, biology, and engineering. A detailed understanding of the physicochemical processes involved in the flow, structural transitions, and freezing or melting behavior of fluids confined within nanometer-sized pores of solid materials is thus of enormous importance for both basic research and technological applications. This Account provides a perspective on new insights into the thermodynamic and kinetic transitions of nanoconfined fluids in their stable and metastable forms. After briefly introducing the unique properties of mesoporous silicas from the SBA, MCM, and FDU families that serve as the confinement matrices, combining highly ordered single and bimodal mesopore architectures with tunable pore sizes in the ~2-15 nm range and narrow size distributions, recent studies on melting/freezing behavior of water confined in these host matrices are reviewed. While differential scanning calorimetry (DSC) reveals a linear relationship between melting point depression and pore size (independent of the pore shape), as predicted by the Gibbs-Thomson relation, variable temperature 2 H wide-line nuclear magnetic resonance (NMR) spectroscopy studies confirm the core-shell model of water and give evidence for a layer-by-layer freezing mechanism, which gives rise to an apparent fragile-to-strong transition in the solidification dynamics. In contrast to the freezing/melting behavior of water, the effect of nanoconfinement on the glass transition of supercooled liquids is nonuniversal and the glass transition temperature T g can either increase or decrease with the dimensionality and extent of confinement. This nonuniversal behavior is exemplified by the two glass-forming molecular liquids, glycerol and ortho-terphenyl (OTP). While glycerol shows an increase in T g and a pronounced slowdown of the rotational dynamics of the constituent molecules due to a change in the molecular packing between the bulk and the confined liquid, OTP displays a linear and confining-media-dependent depression of T g with increased confinement that is strongly influenced by the pore-liquid interface characteristics. This Account concludes with a focus on recent experimental evidence of extreme spatial and dynamical heterogeneity in both freezing and glass transition processes. This discovery was enabled by the unique mesoporous structures of SBA-16 and FDU-5, possessing bimodal architectures with two interconnected pore types of different size and shape (spherical and cylindrical). For the very first time, two melting points for water and two glass transitions for supercooled OTP, corresponding to a specific pore type, were observed. Collectively, these observations strongly suggest a close mechanistic connection between the local fluctuations in the structure and dynamics of nanoconfined liquids. Finally, while the findings reviewed in this Account provide new insights into thermodynamic and kinetic transitions of fluids, there remain many unanswered questions regarding the effects of nanoconfinement on the fundamental properties of fluids, which offer exciting future opportunities in chemical research.

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

Membrane Bioreactor Pretreatment of High-Salinity O&G Produced Water

Produced water (PW) from oil and gas production contains variable constituents that are difficult to remove with conventional treatment processes. The focus of this study was to explore the long-term performance of a membrane bioreactor (MBR) for the removal of organic constituents from PW and how performance and microbial community composition are affected by progressively increasing salinity and introduction of PW from different shale basins around the United States. Dissolved organic carbon removal from the PW remained consistent throughout the study, averaging 86% from the Denver-Julesburg basin PW and 66% removal from the Permian basin PW. Surfactant removal was less consistent, showing 87% removal of poly(ethylene glycols) (PEGs) at a total dissolved solid (TDS) concentration of 40 g/L but only 58% removal at a TDS concentration of 100 g/L. Diversity in the microbial community decreased during reactor establishment but increased at TDS concentrations above 80 g/L. Finally, the results of this study suggest that MBRs can be effective PW pretreatment processes even at high salinities.

42 ENGINEERING↗
DOE OSTI2024

Aerosol jet printing of surface acoustic wave microfluidic devices

Abstract The addition of surface acoustic wave (SAW) technologies to microfluidics has greatly advanced lab-on-a-chip applications due to their unique and powerful attributes, including high-precision manipulation, versatility, integrability, biocompatibility, contactless nature, and rapid actuation. However, the development of SAW microfluidic devices is limited by complex and time-consuming micro/nanofabrication techniques and access to cleanroom facilities for multistep photolithography and vacuum-based processing. To simplify the fabrication of SAW microfluidic devices with customizable dimensions and functions, we utilized the additive manufacturing technique of aerosol jet printing. We successfully fabricated customized SAW microfluidic devices of varying materials, including silver nanowires, graphene, and poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS). To characterize and compare the acoustic actuation performance of these aerosol jet printed SAW microfluidic devices with their cleanroom-fabricated counterparts, the wave displacements and resonant frequencies of the different fabricated devices were directly measured through scanning laser Doppler vibrometry. Finally, to exhibit the capability of the aerosol jet printed devices for lab-on-a-chip applications, we successfully conducted acoustic streaming and particle concentration experiments. Overall, we demonstrated a novel solution-based, direct-write, single-step, cleanroom-free additive manufacturing technique to rapidly develop SAW microfluidic devices that shows viability for applications in the fields of biology, chemistry, engineering, and medicine.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Engineering regulatory networks for complex phenotypes in E. coli

Regulatory networks describe the hierarchical relationship between transcription factors, associated proteins, and their target genes. Regulatory networks respond to environmental and genetic perturbations by reprogramming cellular metabolism. Here we design, construct, and map a comprehensive regulatory network library containing 110,120 specific mutations in 82 regulators expected to perturb metabolism. We screen the library for different targeted phenotypes, and identify mutants that confer strong resistance to various inhibitors, and/or enhanced production of target compounds. These improvements are identified in a single round of selection, showing that the regulatory network library is universally applicable and is convenient and effective for engineering targeted phenotypes. The facile construction and mapping of the regulatory network library provides a path for developing a more detailed understanding of global regulation in E. coli , with potential for adaptation and use in less-understood organisms, expanding toolkits for future strain engineering, synthetic biology, and broader efforts.

59 BASIC BIOLOGICAL SCIENCES↗