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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 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Global 1km Land Surface Parameters for Kilometer-Scale Earth System Modeling

Earth system models (ESMs) are progressively advancing towards the kilometer scale (k-scale). However, the surface parameters for Land Surface Models (LSMs) within ESMs running at the k-scale are typically derived from coarse resolution and outdated datasets. This study aims to develop a new set of global land surface parameters with a resolution of 1 km for multiple years from 2001 to 2020, utilizing the latest and most accurate available datasets. Specifically, the datasets consist of parameters related to land use and land cover, vegetation, soil, and topography. The new land surface parameters are tailored to meet the emerging needs of k-scale LSMs and ESMs modeling with significant implications for advancing our understanding of water, carbon, and energy cycles under global change. The data is published via PNNL DataHub.

Li, Lingcheng↗
DOE OSTI2020

Redox and Thiols in Archaea

Low molecular weight (LMW) thiols have many functions in bacteria and eukarya, ranging from redox homeostasis to acting as cofactors in numerous reactions, including detoxification of xenobiotic compounds. The LMW thiol, glutathione (GSH), is found in eukaryotes and many species of bacteria. Analogues of GSH include the structurally different LMW thiols: bacillithiol, mycothiol, ergothioneine, and coenzyme A. Many advances have been made in understanding the diverse and multiple functions of GSH and GSH analogues in bacteria but much less is known about distribution and functions of GSH and its analogues in archaea, which constitute the third domain of life, occupying many niches, including those in extreme environments. Archaea are able to use many energy sources and have many unique metabolic reactions and as a result are major contributors to geochemical cycles. As LMW thiols are major players in cells, this review explores the distribution of thiols and their biochemistry in archaea.

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

Spatial variation in soil microbial processes as a result of woody encroachment depends on shrub size in tallgrass prairie

Aims: As woody plants encroach into grassland ecosystems, we expect that altered plant-soil interactions will lead to changes in the microbial processes that affect carbon storage and nutrient cycling. Specifically, this research aimed to address how (1) soil chemistry, (2) microbial nutrient demand, and (3) the rate and source of potential soil C mineralization vary spatially under individual woody shrubs of varying size within a mesic grassland. Methods: Here, we collected soil samples from the center, the midpoint between the center and edge, the edge, and the shrub-grass ecotone of multiple Cornus drummondii shrubs across a shrub-size gradient in infrequently burned tallgrass prairie. Results: We found total soil carbon and total soil nitrogen increased with shrub size in every location but the edge. Microbial demand for nitrogen also increased as shrubs increased in size. Across all shrub sizes and sampling locations, potential soil carbon mineralization rates were higher when microbes broke down proportionally more shrub-derived (C 3 ) organic matter than grass-derived (C 4 ) organic matter. Conclusions: Our results suggest that the spatio-temporal context of woody encroachment is critical for understanding its impact on belowground microbial processes. In this ecosystem, a longer period of occupancy by woody plants increases potentially mineralizable carbon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Incorporating Full Elastodynamic Effects and Dipping Fault Geometries in Community Code Verification Exercises for Simulations of Earthquake Sequences and Aseismic Slip (SEAS)

ABSTRACT Numerical modeling of earthquake dynamics and derived insight for seismic hazard relies on credible, reproducible model results. The sequences of earthquakes and aseismic slip (SEAS) initiative has set out to facilitate community code comparisons, and verify and advance the next generation of physics-based earthquake models that reproduce all phases of the seismic cycle. With the goal of advancing SEAS models to robustly incorporate physical and geometrical complexities, here we present code comparison results from two new benchmark problems: BP1-FD considers full elastodynamic effects, and BP3-QD considers dipping fault geometries. Seven and eight modeling groups participated in BP1-FD and BP3-QD, respectively, allowing us to explore these physical ingredients across multiple codes and better understand associated numerical considerations. With new comparison metrics, we find that numerical resolution and computational domain size are critical parameters to obtain matching results. Codes for BP1-FD implement different criteria for switching between quasi-static and dynamic solvers, which require tuning to obtain matching results. In BP3-QD, proper remote boundary conditions consistent with specified rigid body translation are required to obtain matching surface displacements. With these numerical and mathematical issues resolved, we obtain excellent quantitative agreements among codes in earthquake interevent times, event moments, and coseismic slip, with reasonable agreements made in peak slip rates and rupture arrival time. We find that including full inertial effects generates events with larger slip rates and rupture speeds compared to the quasi-dynamic counterpart. For BP3-QD, both dip angle and sense of motion (thrust versus normal faulting) alter ground motion on the hanging and foot walls, and influence event patterns, with some sequences exhibiting similar-size characteristic earthquakes, and others exhibiting different-size events. These findings underscore the importance of considering full elastodynamics and nonvertical dip angles in SEAS models, as both influence short- and long-term earthquake behavior and are relevant to seismic hazard.

Geochemistry & Geophysics↗
DOE OSTI2024

Quantifying microbial roles in environmental iron oxidation via an integrated kinetics, `omics and metabolic modeling study (Final Report)

Iron oxyhydroxides are extremely reactive components of environmental systems, and therefore exert a strong influence on biogeochemical cycles. These oxyhydroxides strongly adsorb many biologically-relevant elements, including organic carbon and phosphate, as well as a wide range of metals including uranium and actinide species. Thus, the formation mechanism of iron oxyhydroxides are key to understanding both nutrient and contaminant cycling. Microorganisms can catalyze iron oxidation and promote the formation of Fe biominerals and thus are increasingly recognized as important players in biogeochemical cycling. However, it is completely unknown how much of environmental iron oxidation is biologically mediated versus abiotic, and various challenges in studying microbial iron oxidation have hindered accurate incorporation into hydrobiogeochemical models. The overarching goal of our work was to quantify and constrain microbial iron oxidation rates and use ‘omics to gain insight into the controls on this process, while developing tools to enable integration of biotic iron oxidation into hydrobiogeochemical models. Our work focused on the Savannah River Site (SRS) in South Carolina, where extensive microbial iron oxidation has been observed. At Tims Branch, part of the Argonne National Laboratory Wetland Hydrobiogeochemistry Science Focus Area (Argonne SFA), where groundwater discharges into a stream, iron-oxidizing microbial mats form and appear to be a major sink of uranium. In the wetlands that surround Tims Branch, there are wide swaths of iron microbial mats and flocs (mobilized mat). We measured biotic and abiotic iron oxidation rates using mats and water sampled from these sites and found that iron oxidation is primarily carried out by chemolithotrophic microorganisms. The resulting rate constants can be incorporated into models. These mats were characterized by metagenomics and metatranscriptomics, which showed that aerobic chemolithotrophs were the dominant iron-oxidizing bacteria (FeOB), and these included Gallionellaceae and Leptothrix, and possibly Rhodoferax, which is known as an Fe-reducer but may also oxidize Fe(II). This demonstrated that diverse FeOB can coexist and suggests that there are a range of niches and therefore drivers of chemolithotrophic iron oxidation. Analysis of reconstructed genomes strongly suggests that a major factor in diversity is carbon source, as genomes contained varied pathways for autotrophy and heterotrophy. We performed an in-depth analysis of Leptothrix ochracea genomes, since this sheath-former is one of the primary mat builders, yet its physiology remained unresolved. A combination of genomics, transcriptomics, and metabolic modeling suggest that L. ochracea grows mixotrophically using a combination of Fe(II) and organics for energy and both inorganic and organic carbon to create biomass. This contrasts with the largely autotrophic Gallionellaceae (Gallionella, Sideroxydans, and Ferriphaselus) also present in the mats and flocs. Remarkably, multiple FeOB, both Leptothrix and Gallionellaceae, showed activity in response to Fe(II) in live mat incubations. We tracked the gene expression of individual MAGs to Fe(II) and found that various autotrophic and heterotrophic FeOB responded to Fe(II), increasing expression of both carbon fixation and organic utilization genes. The results of the integrated field, kinetics, and omics studies give detailed insight into 1) the taxa that oxidize Fe, and 2) how they connect Fe, C, and N cycles. Towards the goal of connecting omics data to hydrobiogeochemical models, we worked with the KBase team to create a template metabolic model for chemolithotrophic iron oxidation. We initially modeled the well-characterized isolate Gallionellaceae Sideroxydans lithotrophicus, and also applied the model to the mixotroph L. ochracea. In all, we have characterized diverse FeOB in a representative wetland system and solved key problems that enable better incorporation of iron-oxidizing microbes into hydrobiogeochemical models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Leveraging Electrons for Electrochemical CO 2 Capture Using a Hemi‐Labile Iron Complex

Climate change, driven by anthropogenic carbon emissions, demands urgent action to prevent a 2050 tipping point. With CO 2 levels at 427 ppm (50% above pre-industrial levels), deploying energy-efficient carbon capture technologies is crucial. Electrochemical carbon capture processes that have been touted to have the potential to meet these needs rely on the applied cell voltage, and electron utilization (CO 2 molecules separated per electron), which has generally been asserted to have a theoretical limit of one. Here, we introduce an electron-leveraging strategy to enhance electron utilization beyond this limit to 1.43 by employing Fe-EDDHA, a redox-active coordination complex having a ligand with multiple hemi-labile coordination sites. The reversibility and robustness of the system were enabled by the efficient prevention of CO 2 reduction upon the introduction of nicotinamide as a guardian of the iron(2+) center. The proof-of-concept cyclic system exhibits a minimum operational energy of 22.6 kJ e mol −1 and an average of 63.7 kJ e mol −1 over 29 cycles, using a simulated flue gas (15% CO 2 ). Our electron-leveraging strategy holds promise for advancing energy-efficient electrochemical carbon capture technologies, and offers an alternative to prevalent redox potential shifting methods proposed to mitigate undesired electron transfer reactions in redox-active materials across diverse operational conditions.

carbon storage↗
DOE OSTI2024

Mechanical and electrical changes in electrochemically active polyimide binders for Li-ion batteries

Polyimide binders are often used in electrodes made with silicon for lithium-ion batteries for their mechanical strength and adhesion, which help mitigate mechanical issues associated with large volumetric expansion. These binders can be electrochemically active, but it is difficult to characterize what physical and chemical changes occur due to a composite electrode with multiple components and processes at play. Here, in this work, we study electrodes consisting only of polyimide binder and conductive carbon, using scanning probe-based techniques—contact resonance, force volume, and scanning spreading resistance microscopy—along with cryo-scanning transmission electron microscopy, electron energy loss spectroscopy, and energy dispersive X-ray spectroscopy. We show that lithium becomes trapped in the binder during cycling and results in large initial capacity losses, the formation of dendrite-like features, column-like domains of significantly increased mechanical modulus, and a slight increase in electronic resistivity.

25 ENERGY STORAGE↗
DOE OSTI2026

Characterization of UV optical components for photon detector calibration in liquid argon TPCs

Large liquid argon time projection chambers (LArTPCs)require stable and well-characterized delivery of ultraviolet (UV)light for in situ calibration of photosensors at cryogenictemperatures. This article reports bench-top and cryogenicmeasurements of the optical components used in a UV lightcalibration system, including multi-mode fused-silica fibers,SMA-to-SMA connectors, optical fiber feedthroughs, andlight-diffuser assemblies. Light loss in several fiber types and SMAconnectors was measured across wavelengths from275–970 mm. In addition,light-loss measurements of the tested fibers after severalliquid-nitrogen thermal cycles showed no statistically significantdegradation relative to baseline measurements, and high-rate pulsedexposure (30–90 million pulses from a275 nm LED) likewise showed nomeasurable aging in jacketed fibers. A compact, palm-sized,3D-printed PEEK diffuser housing with stacked UV-grade fused-silicadiffusers yields Lambertian emission and the most uniform angulardistribution. Optical components exhibiting improved UV transmissionwere deployed successfully in multiple DUNE small- and large-scaleprototypes, demonstrating reliable operation of UV light calibrationsystem. These findings inform component selection and calibrationprocedures for achieving reliable, uniform UV light delivery inlarge-scale cryogenic detectors such as DUNE.

Behera, B. [South Dakota Sch. Mines Tech.] (ORCID:↗
DOE OSTI2021

Lean-Stratified Combustion System with Miller Cycle for Downsized Boosted Application - Part I

Automotive manufacturers relentlessly explore engine technology combinations to achieve reduced fuel consumption under continued regulatory, societal and economic pressures. For example, technologies enabling advanced combustion modes, increased expansion to effective compression ratio, and reduced parasitics continue to be developed and integrated within conventional and hybrid propulsion strategies across the industry. A high-efficiency gasoline engine capable for use in conventional or hybrid electric vehicle platforms is highly desirable. This paper is the first to two papers describing the development of a combustion system combining lean-stratified combustion with Miller cycle for downsized boosted applications. The work was completed under a multi-year US DOE project. The goal was to define a light-duty engine package capable of achieving a 35% fuel economy improvement at US Tier 3 emission standards over a naturally aspirated stoichiometric baseline vehicle. A multi-mode combustion system was developed enabling highly efficient lean-stratified operation at light-load and stoichiometric Miller-cycle operation at mid- to highloads. Some of the unique challenges in synergistically combining the two concepts are highlighted in this paper. Here, a central direct-injection four-valve layout was designed with high-tumble ports and a bowl-in-piston capable of stable operation under highly dilute (lean plus EGR) mixtures when properly matched to fuel spray characteristics, a multiple-injection strategy, and a high-energy ignition system. Other challenges specific to meeting exhaust emissions requirements with a high-efficiency engine are also explored in this study. In this Part 1 of the paper, the single-cylinder combustion system design, analysis, and testing is described. Multicylinder engine system design, analysis and development is described in Part 2 of the paper.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2023

Characterization of Interconnects

Combined-accelerated stress testing (C-AST) simultaneously combines stress factors of the natural environment (including UV radiation, temperature, humidity, electrical current, and external mechanical force) into a single test that requires fewer modules, fewer chambers, and makes it possible to discover weaknesses in new designs that are not known a-priori. C-AST reduces risk, accelerates time to market, and improves bankability by reducing costly overdesign using test levels not exceeding those seen in the natural environment. This project seeks to evaluate strengths and weaknesses of modern cell interconnect designs with combined-accelerated stress testing (C-AST) to screen multiple climates along with finite element and failure analysis to determine the potential for a 50-year life. Supporting this, we seek to develop methods of characterization to assess the degradation of interconnects, enable predictive rate models with material forensics and FEA and show C-AST's ability to find interconnect failures and benchmark it relative to other accelerated stress test methods like temperature cycling and cyclic dynamic mechanical loading. Examples of modern interconnect designs covered are Canadian Solar Hetero Technology ribbon enabling closer cell interconnections, SmartWire (eg. Meyer-Berger technology), and shingled cells with new interconnect materials.

C-AST↗
DOE OSTI2021

Adaptation to the dietary sugar D-tagatose via genome instability in polyploid Candida albicans cells

The opportunistic fungal pathogen Candida albicans undergoes an unusual parasexual cycle wherein diploid cells mate to form tetraploid cells that can generate genetically diverse progeny via a nonmeiotic program of chromosome loss. The genetic diversity afforded by parasex impacts clinically relevant features including drug resistance and virulence, and yet the factors influencing genome instability in C. albicans are not well defined. To understand how environmental cues impact genome instability, we monitored ploidy change following tetraploid cell growth in a panel of different carbon sources. We found that growth in one carbon source, D-tagatose, led to high levels of genomic instability and chromosome loss in tetraploid cells. This sugar is a stereoisomer of L-sorbose which was previously shown to promote karyotypic changes in C. albicans. However, while expression of the SOU1 gene enabled utilization of L-sorbose, overexpression of this gene did not promote growth in D-tagatose, indicating differences in assimilation of the two sugars. In addition, genome sequencing of multiple progenies recovered from D-tagatose cultures revealed increased relative copy numbers of chromosome 4, suggestive of chromosome-level regulation of D-tagatose metabolism. Together, these studies identify a novel environmental cue that induces genome instability in C. albicans, and further implicate chromosomal changes in supporting metabolic adaptation in this species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An Intelligent Power Electronic System for Secondary Use Batteries

This paper presents a plug-and-play power electronic system for integration of multiple energy storage system technologies. The system uses a communication and control architecture with individual developed modules to support scaling to larger systems for the electric grid. An optimization framework is also presented to demonstrate the functionality of the system. This system is shown to work in hardware with a constructed testbed to demonstrate different use cases and systems. Results are presented for a full efficiency cycle test.

Starke, Michael↗
DOE OSTI2026

The 1990 San Francisco Bay Area Metropolitan Transportation Commission Household Survey

The San Francisco Bay Area's Metropolitan Transportation Commission (MTC) and the regional transportation planning agency for the nine-county Bay Area conducted the survey. The basic purpose for the survey was for the development of travel demand models to simulate the various components of travel behavior: auto ownership, trip frequency (trip generation), and the distribution of trips between origins and destinations by travel mode. Planners at MTC envisioned the 1990 survey as the first wave of a multi-wave household panel survey designed to capture both short- and long-term changes in regional travel behavior. The 1990 survey collected single-weekday travel data from nearly 9,900 Bay Area households and multiple-weekday travel data from nearly 1,500 households. The 1990 survey effort also included a separate sub-project, funded by the Bay Area Rapid Transit (BART) District, to collect multiple-weekday travel data from 1,000 BART-using households. The BART survey and the MTC multiple-weekday survey were completed in the spring of 1990; the MTC single-weekday survey was continued and completed during the autumn of 1990.

1Hz data↗
DOE OSTI2023

Characterization of Impure Plutonium Oxide Neutron Calibration Standards through Evaluation by Neutron Multiplicity Equations

Plutonium oxide calibration standards STD4C, STD6C and STD8C have been historically used, and are currently the only MT52 standards in use, for calibration and measurement control program of Passive/Active Neutron Coincidence Counter known as PAN1 at PF-4. In this paper, previously measured high-statistics data are used in conjunction with neutron multiplicity equations to determine multiplication M and α parameter of these standards as the explicit knowledge of these parameters may allow quantification of precision and bias of accountability measurements of different material types and matrices of items.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Studies on the Vitrification Potential of High Risk Spent Nuclear Fuels

This research explored vitrification of U-Zr nuclear fuel that exhibits an explosion hazard when processed by common nitric acid dissolution. Glass frits were chosen based on properties that had been previously measured as well as being demonstrated successfully in production at the Defense Waste Process Facility (DWPF). Zirconium and Aluminum metal powders were chosen to represent the spent fuels after literature demonstrated that the potential phase that causes the issue for explosive reaction in the effluent stream is tied to the Zirconium-III phase field. DSC measurements were carried out on various simulants and waste forms to better understand thermal behavior of these materials. Zirconium (Zr) was tested with both nitric acid and the new effluent flowsheet that is under development by the SRNL Chemical Process Control (CPC) group. The nitric acid test did show the expected exothermic behavior as well as how the behavior is affected by particle size of the powders used. In contrast, the effluent samples did not show an exothermic peak. However, the concentration of metal in the samples was orders of magnitude lower than in the nitric acid testing and further testing of the effect of concentration on the exothermicity that could be measured confirmed a dampened signal. Tests were run that included frit, both DWPF Frit 510 and Iron Phosphate frit, exhibiting complex curves that included multiple endothermic and exothermic peaks during heating and cooling. The final crucible samples appear similarly to the bulk glasses pointing to these peaks being a part of the dissolution of the simulant into the base glasses.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Validation of the Community Land Model Version 5 over the Contiguous United States (CONUS) using in-situ and remote sensing datasets

The Community Land Model (CLM) is an effective tool to simulate the biophysical and biogeochemical processes and their interactions with the atmosphere. Although CLM Version 5 (CLM5) constitutes various updates in these processes, its performance in simulating energy, water and carbon cycles over the Contiguous United States (CONUS) at scales which land surface changes and hydrometeorological and hydroclimatological applications are more locally relevant is yet to be assessed. In this study, we conducted three simulations at 0.125? during 1979-2018 over the CONUS using different configurations of CLM, namely CLM5-biogeochemistry (CLM5BGC), CLM4.5BGC, and CLM5-satellite phenology (CLM5SP). We validated and compared their simulations against multiple remote-sensed and in-situ datasets. Overall, the parametric and structural updates (e.g., carbon cost for nitrogen uptake, variable soil thickness, dry surface layer) in CLM5 improve its ability in capturing terrestrial biogeochemical dynamics. The low evapotranspiration in CLM5BGC is associated with biases in simulating vegetation phenological characteristics rather than soil water limitations. The mismatch between CLM5BGC-simulated peak leaf area index and reference data can be attributed to CLM5BGC's inability in simulating phenology of trees and grasses. The differences between CLM-simulated irrigation and reference estimates can be attributed to differences between processes represented in models and in reality, and uncertainties in input and validation datasets. Evaluation against observations at small catchments suggest that hydrologic parameters needed to be calibrated to improve simulations of runoff, especially subsurface runoff. Additional efforts are needed to incorporate spatially-distributed plant phenology and physiology parameters and regional-specific agricultural management practices (e.g., planting, harvest).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source

ABSTRACT Purple sulfur bacteria (PSB) are capable of anoxygenic photosynthesis via oxidizing reduced sulfur compounds and are considered key drivers of the sulfur cycle in a range of anoxic environments. In this study, we show that Allochromatium vinosum (a PSB species) is capable of autotrophic growth using pyrite as the electron and sulfur source. Comparative growth profile, substrate characterization, and transcriptomic sequencing data provided valuable insight into the molecular mechanisms underlying the bacterial utilization of pyrite and autotrophic growth. Specifically, the pyrite-supported cell cultures (“py”’) demonstrated robust but much slower growth rates and distinct patterns from their sodium sulfide-amended positive controls. Up to ~200-fold upregulation of genes encoding various c - and b -type cytochromes was observed in “py,” pointing to the high relevance of these molecules in scavenging and relaying electrons from pyrite to cytoplasmic metabolisms. Conversely, extensive downregulation of genes related to LH and RC complex components indicates that the electron source may have direct control over the bacterial cells’ photosynthetic activity. In terms of sulfur metabolism, genes encoding periplasmic or membrane-bound proteins (e.g., FccAB and SoxYZ) were largely upregulated, whereas those encoding cytoplasmic proteins (e.g., Dsr and Apr groups) are extensively suppressed. Other notable differentially expressed genes are related to flagella/fimbriae/pilin(+), metal efflux(+), ferrienterochelin(−), and [NiFe] hydrogenases(+). Characterization of the biologically reacted pyrite indicates the presence of polymeric sulfur. These results have, for the first time, put the interplay of PSB and transition metal sulfide chemistry under the spotlight, with the potential to advance multiple fields, including metal and sulfur biogeochemistry, bacterial extracellular electron transfer, and artificial photosynthesis. IMPORTANCE Microbial utilization of solid-phase substrates constitutes a critical area of focus in environmental microbiology, offering valuable insights into microbial metabolic processes and adaptability. Recent advancements in this field have profoundly deepened our knowledge of microbial physiology pertinent to these scenarios and spurred innovations in biosynthesis and energy production. Furthermore, research into interactions between microbes and solid-phase substrates has directly linked microbial activities to the surrounding mineralogical environments, thereby enhancing our understanding of the relevant biogeochemical cycles. Our study represents a significant step forward in this field by demonstrating, for the first time, the autotrophic growth of purple sulfur bacteria using insoluble pyrite (FeS2) as both the electron and sulfur source. The presented comparative growth profiles, substrate characterizations, and transcriptomic sequencing data shed light on the relationships between electron donor types, photosynthetic reaction center activities, and potential extracellular electron transfer in these organisms capable of anoxygenic photosynthesis. Furthermore, the findings of our study may provide new insights into early-Earth biogeochemical evolutions, offering valuable constraints for understanding the environmental conditions and microbial processes that shaped our planet’s history.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. In this study, we aim to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

60 APPLIED LIFE SCIENCES↗