SEARCH · Engineering Papers

Results for “sequence alignment”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

205 records · Page 12

All sources NASA NTRS DOE OSTI

DOE OSTI2023

Improved Biofuel Production through Discovery and Engineering of Terpene Metabolism in Switchgrass

Project Objectives - Of the myriad specialized metabolites that plants deploy to adapt to environmental challenges, terpenes form the largest group. In many major crops, unique terpene blends serve as key stress defenses that directly impact plant fitness and yield. In addition, terpenes, such as bisabolene and pinene, are used for producing renewable biofuels. Essential to advancing a broader use of terpenes for biofuel feedstock engineering is a system-wide knowledge of the diverse biosynthetic machinery and defensive potential of often species-specific terpene blends. The proposed project would merge genome-wide enzyme discovery with comparative –omics, protein structural and plant microbiome studies to define the biosynthesis and stress-defensive functions of the switchgrass (Panicum virgatum) terpene network. These insights would be combined with developing and applying non-transgenic genome editing tools to design plants with desirable terpene blends for higher productivity and biofuel production on marginal lands. As a dedicated lignocellulosic feedstock for U.S. biofuel production with high net energy yield, stress tolerance, and available genome resources, switchgrass is well-suited for devising new avenues for biofuel production. Project Description – The diversity of plant terpene defenses is governed by species-specific families of terpene synthase (TPS) and cytochrome P450 monooxygenase (P450) enzymes. Mining of the switchgrass genome (genotype Alamo) identified ~100 TPS and P450 candidate genes, and combinatorial biochemical analysis of synthesized TPSs and P450s revealed more than a dozen enzymes with common and novel activities. In addition, several identified terpene metabolites and the corresponding transcripts were up-regulated in response to abiotic stressors. These findings demonstrate a unique switchgrass terpene network with probable importance to abiotic stress tolerance, thus providing a large chemical portfolio for optimizing crop resistance, yield, and biofuel composition. Leveraging these preliminary data, we propose to generate a genome-wide map of the switchgrass terpene metabolic network through multi-gene co-expression analyses that allow the efficient cross-validation of TPS and P450 functions. Key enzymes would further be applied to structure-function studies via X-ray protein crystallography, homology modeling and site-directed mutagenesis to gain mechanistic insight into the catalytic specificity of switchgrass terpene metabolism and provide gene and amino acid targets for genome editing. In tandem with terpene pathway discovery, system-wide metabolomics, transcriptomics and proteomics studies in switchgrass accessions of contrasting drought tolerance would define the role of switchgrass terpene metabolism in conferring abiotic stress resilience. Metabolic changes would be assessed in a combined approach of targeted (terpenes) and untargeted metabolite profiling using a high-resolution LC-MS/MS approach, differential gene expression analyses through multiplexed Illumina RNA sequencing, and quantitative analysis of high-priority pathway enzymes using multiple reaction monitoring (MRM). Drawing on these insights, knock-down/out mutants of stress-associated pathway nodes would be generated by optimizing transient virus-induced gene silencing (VIGS) and CRISPR/Cas9 systems under control of the Tobacco Rattle Virus (TRV). The resulting mutant lines would then be analyzed for stress susceptibility and the impact on the root microbiome to define gene functions in planta. Knowledge of terpene pathways, enzyme mechanisms and bioactivities would be applied to enhance switchgrass stress resilience and to tailor-make terpene blends for biofuel production. Here, TRV-enabled CRISPR/Cas9 genome editing, including allele-specific knock-out of redundant genes, engineering of enzyme specificity via structure-guided point mutations, and overexpression of terpene genes relevant to stress-protection or biofuel production, would be used to increase metabolic flux toward desired pathways. Broader Impacts - Integrating the system-wide discovery, mechanistic analysis and non-transgenic genome engineering of the switchgrass terpene network aligns the required steps to unlock the chemical potential of this important metabolite class to generate crops that are more resistant to stress and provide advanced biofuel production in light of rising climate pressures as foreseeable challenges for bioenergy crop cultivation. The proposed project would further offer interdisciplinary student training through active involvement in the project and integration of research concepts and outcomes into newly-developed graduate and undergraduate courses on Plant Biotechnology.

09 BIOMASS FUELS↗

DOE OSTI2021

A Deeper Look at DES Dwarf Galaxy Candidates: Grus i and Indus ii

We present deep g- and r-band Magellan/Megacam photometry of two dwarf galaxy candidates discovered in the Dark Energy Survey (DES), Grus i and Indus ii (DES J2038–4609). For the case of Grus i, we resolved the main sequence turn-off (MSTO) and ~2 mags below it. The MSTO can be seen at g 0 ~24 with a photometric uncertainty of 0.03 mag. We show Grus i to be consistent with an old, metal-poor (~13.3 Gyr, [Fe/H] ~ -1.9) dwarf galaxy. We derive updated distance and structural parameters for Grus i using this deep, uniform, wide-field data set. We find an azimuthally-averaged halflight radius more than two times larger (~151 +21 -31 pc; ~$4\buildrel{\,\prime}\over{.} {16}_{-0.74}^{+0.54}$) and an absolute V-band magnitude ~-4.1 that is ~1 magnitude brighter than previous studies. We obtain updated distance, ellipticity, and centroid parameters that are in agreement with other studies within uncertainties. Although our photometry of Indus ii is ~2–3 magnitudes deeper than the DES Y1 public release, we find no coherent stellar population at its reported location. The original detection was located in an incomplete region of sky in the DES Y2Q1 data set and was flagged due to potential blue horizontal branch member stars. The best-fit isochrone parameters are physically inconsistent with both dwarf galaxies and globular clusters. We conclude that Indus ii is likely a false positive, flagged due to a chance alignment of stars along the line of sight.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Depth-dependent links between microbial taxa and nitrous oxide emissions in a long-term cotton cropping system employing soil health practices

Long-term management practices can shape soil microbial communities in ways that influence nitrogen (N) dynamics and nitrous oxide (N 2 O) emissions. We leverage a 41-year continuous cotton cropping experiment with contrasting tillage, cover cropping, and N fertilization regimes to investigate how these long-term strategies influence soil microbial communities and their associations with N 2 O fluxes during the cotton growing season. Using 16S rRNA gene metabarcoding, we assessed microbial composition in surface and subsurface soils and evaluated its relationship with temporal N 2 O emissions. Among the management practices, N fertilization – a known driver of N 2 O emissions – had the strongest effect on microbial community composition and was linked to a greater number of taxa correlated to N 2 O emissions, particularly in surface soils. Soil pH emerged as a key variable influencing microbial structure across depth and was negatively associated with both N 2 O emissions and microbial composition in the surface layers of fertilized soils. In total, 57 archaeal/bacterial taxa were correlated with N 2 O fluxes, but only seven were shared across depths, suggesting distinct microbial contributors in surface and subsurface soils. Several of these taxa have been previously reported to be associated with N and C cycling processes such as nitrate respiration or carbon turnover, indicating functional context to their correlation with N 2 O fluxes. Temporal shifts in the abundance of key taxa aligned with seasonal peaks in N 2 O emissions, notably in early and late August, and were most pronounced under conventional tillage, hairy vetch cover cropping, and N fertilization. While 16S-based associations cannot confirm functional gene presence or activity, these findings demonstrate that long-term fertilization and associated soil acidification are dominant drivers of microbial shifts linked to N 2 O emissions and highlight the importance of accounting for depth-specific and seasonal microbial dynamics when evaluating management impacts on greenhouse gas emissions.

16S rRNA gene sequencing↗

DOE OSTI2026

Supervisory Control and Data Acquisition for Electrochemical Separation Experimentation

The Python-based program is a laboratory automation tool designed to control and monitor electrochemical systems. The tool was developed for capacitive deionization (CDI) experiments, but it can be used for any system that requires controlled voltage or current segments and multi-parameter monitoring. The program integrates hardware components to run user-defined experimental parameters, providing operational control of a programmable power supply, peristaltic pump, and data acquisition devices. Currently, the program is structured with a workflow that includes an initialization (or pre-run) phase, a main loop, and a post-experiment stabilization (or post-run) phase. The initialization phase prepares and stabilizes the cell, ensuring that the electrodes and solution reach a baseline state before the experiment begins. The main loop consists of multiple voltage segments that repeat, controlling the experiment while recording key parameters such as time, voltage, current, pH, and conductivity. Finally, the post-experiment stabilization phase allows the system to stabilize after the experiment, returning the cell and solution to equilibrium conditions before ending the sequence. The program is designed with four variations, each tailored to different experimental needs. All variations include both the initialization and post-experiment stabilization stages, which run for a set amount of time, voltage, current, and flow rate before and after the main experiment block. The main loop runs for a set number of cycles, as defined by the user input, and each cycle is composed of 2 or 4 segments. The 4 program variations are described as follows: Program 1: The main program includes 2 segments. Each segment is defined to have a set duration, flow rate, voltage, and current. This program measures conductivity, flow rate, voltage, and current. Program 2: The main program expands Program 1 to include 4 segments. Each segment has a specified duration, flow rate, voltage, and current. Like Program 1, it measures conductivity, flow rate, voltage, and current. Program 3: The main program consists of 2 segments, each defined by time, flow rate, voltage, and current. In addition to conductivity, flow rate, voltage, and current, Program 3 collects pH and temperature data through a 4-channel data acquisition device. Program 4: This program independently controls two channels of a multi-channel power supply simultaneously. While conductivity can only be measured for one cell at a time, the dual-channel control makes it possible to operate two cells simultaneously under different voltage/current conditions. The main program includes 2 segments.For each program, all measurements are automatically logged and integrated into a single Excel output file. Data are displayed in numerical format and plotted, both in real time, to track system performance. A key feature of the program is its ability to synchronize all outputs so that every measurement shares a single timestamp, ensuring accurate alignment of voltage, current, pH, conductivity, and pH data.By combining hardware control, real-time monitoring, and unified data collection, this program significantly reduces manual workload and minimizes errors, making it a reliable platform for researchers, engineers, and laboratory technicians conducting CDI experiments, among other electrochemical tests.

Valentino, Lauren [Argonne National Laboratory (AN↗

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 OSTI2023

The Zintl Concept Applied to Intergrowth Structures: Electron‐Hole Matching, Stacking Preferences, and Chemical Pressures in Pd 5 InAs

Abstract Enumerating the potential stacking sequences of layers is a fundamental way to account for the structure diversity of solid state compounds. In many cases, these stacking variations represent polymorphs with only small energetic differences. Here, we examine a compound for which the preferred stacking pattern instead reveals key aspects about its chemical bonding: Pd 5 InAs. Its structure is based on the intergrowth of slabs of the AuCu 3 and PtHg 2 (or alternatively, fluorite) structure types. Two basic stacking arrangements are available to this compound, represented by the Pd 5 TlAs and HoCoGa 5 structure types. DFT total energy calculations reveal that the former outcompetes the latter by a staggering 0.65 eV/formula unit. Through a combination of DFT‐reversed approximation Molecular Orbital (DFT‐raMO) and DFT‐Chemical Pressure (DFT‐CP) analysis we trace this preference to two factors. First, with DFT‐raMO analysis, we derive a Zintl‐like bonding scheme of Pd 5 InAs. This scheme, along with the inspection of selected crystal orbitals, is then connected to preferred stacking through the coordination environments of the Pd atoms at the interface between the Pd−In and Pd−As layers. In the hypothetical HoCoGa 5 ‐type and observed Pd 5 InAs‐type structures, different Pd coordination environments arise at the interfaces. The hypothetical structure features square planar PdIn 2 As 2 units, in each of which the same 4d‐orbital serves in the Pd sublattice's role as both Lewis acid (for interactions with the As) and Lewis base (for interactions with the In). In the observed structure, tetrahedral PdIn 2 As 2 units occur instead, so that these contradictory roles are distributed to separate 4d‐orbitals, leading to more effective bonding. DFT‐CP analysis illustrates that this driving force for the Pd 5 TlAs‐type arrangement is supplemented by a favorable alignment of the packing tensions in the parent structures. Altogether, the resulting picture demonstrates how the reaction of simple intermetallic structures to form intergrowths can be guided by recognizable chemical interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Integrated Mid-Continent Stacked Carbon Storage Hub Project Phase II (Final Summary Report)

The Phase II Integrated Midcontinent Stacked Carbon Storage Hub (IMSCS-HUB) is part of the Carbon Storage Assurance Facility Enterprise (CarbonSAFE) established by the United States Department of Energy (DOE) National Energy Technology Laboratory (NETL). CarbonSAFE is phased to support the development of commercial-scale (50 million metric tonnes [Mt] over a 30-year period) carbon capture, utilization, and storage (CCUS) in the United States. The IMSCS-HUB study area comprises carbon dioxide (CO 2 ) sources in Iowa, Kansas, and Nebraska (the source corridor), and CO 2 sinks in Kansas and Nebraska (the storage corridor), representing the first large-scale project for the Midcontinent region. The stacked storage corridor is characterized by alternating sequences of deep saline formations, oil-bearing reservoirs, shale, and evaporite units that are conducive to vertically stacked CO 2 injection for geologic storage and enhanced oil recovery (EOR). Three sites within the IMSCS-HUB stacked storage corridor were evaluated in Phase II for commercial CCUS feasibility: one in southwest-central Nebraska, Sleepy Hollow Field (SHF), a second in southwestern Nebraska near Madrid (Madrid), and a third in southwestern Kansas, the Patterson Site (composed of the Patterson, Heinitz, Hartland, and Oslo fields). In Phase II, the team assessed the feasibility of storage complexes at the potential storage sites in Nebraska and Kansas to support a commercial-scale storage hub that integrates proven CO 2 capture technology and transport from nearby ethanol sources. Building on lessons learned from the DOE-NETL Regional Carbon Sequestration Partnerships (RCSPs), the Project Team has identified a clear strategy to meet DOE’s 2025 objective of commercial carbon capture and storage (CCS) implementation by developing a CO 2 market and infrastructure that relies on multiple ethanol-based CO 2 sources in the short term and the incorporation of multiple coal-fired power plant CO 2 sources when commercial capture is economically viable. The team also leveraged the updated 45Q tax credit to develop capture and transport infrastructure. Commercial-scale CCUS is feasible at two candidate storage sites studied, the Madrid, Nebraska Site and the Patterson Site in Kearny County, Kansas. The Sleepy Hollow Field in Nebraska was found to be an attractive candidate for stacked storage with CO 2 -EOR (Battelle 2020e). Outreach efforts facilitated engagement from industry, government, and research sectors (Battelle and GPI, 2020) and an outreach plan for future phases of the project was developed to address issues that are of concern in the IMSCS-HUB project area (Battelle, 2020f). All components of a CCUS project were determined to be feasible in the IMSCS-HUB region and Risk Mitigation Plan was developed and includes strategies to mitigate risks associated with each project component (Battelle, 2020j). A roadmap was developed to obtain the required UIC permits for an integrated CCUS project (Battelle, 2020k). The regional storage resource characterization demonstrated significant opportunity for commercial-scale projects in the IMSCS-HUB storage corridor with 577.4 Mt of stacked CO 2 storage capacity and the potential to produce 181.9 MMbbls of oil via EOR across 17 individual storage areas (Battelle and ARI, 2020). The pipeline assessment study found viable pipeline routes that connected 45Q-eligible ethanol plants, coal fired power plants, and other sources in the IMSCS-HUB corridor. The comprehensive results of subsurface characterization, modeling efforts, outreach assessment, and regulatory analysis from were integrated to develop a Detailed Commercial Development Plan for the IMSCS-HUB (Battelle, 2020n). Commercialization efforts will involve obtaining Class VI UIC permits, establishing and finalizing the pipeline route, and evaluating capture projects at participating CO 2 sources. Phases I and II of the IMSCS-HUB CarbonSAFE provide a strong foundation for safely, efficiently, and cost-effectively characterizing and permitting commercial-scale project sites in the region. The plan for implementation of commercial-scale CCUS projects in the IMSCS-HUB is aligned with the objectives of CarbonSAFE Phase III: Site Characterization and CO 2 Capture Assessment.

20 FOSSIL-FUELED POWER PLANTS↗