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Results for “mechanistic modeling”

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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Heterogeneity in Permeability and Particulate Organic Carbon Content Controls the Redox Condition of Riverbed Sediments at Different Timescales

Abstract The hydrological and biogeochemical properties of the hyporheic zone in stream and riverine ecosystems have been extensively studied over the past two decades. Although it is widely acknowledged that sediment heterogeneity can influence biogeochemical reactions, little effort has been made to understand the role of heterogeneity on the spatiotemporal variability of riverbed redox conditions under changing flow dynamics at different timescales. Here we integrate a mechanistic model and field data to demonstrate that heterogeneity in permeability plays a vital role in modulating sediment redox conditions at both seasonal (annual) and event (daily‐to‐weekly) timescales, whereas heterogeneity in particulate organic carbon (POC) content only has a comparable influence on redox conditions at the seasonal timescale. These findings underscore the importance of accurately characterizing sediment heterogeneity, in terms of permeability and POC content, in quantifying biogeochemical dynamics in the riverbed and hyporheic zones of riverine ecosystems.

Geology↗
DOE OSTI2024

Integrated Effects of Site Hydrology and Vegetation on Exchange Fluxes and Nutrient Cycling at a Coastal Terrestrial‐Aquatic Interface

Abstract The complex interactions among soil, vegetation, and site hydrologic conditions driven by precipitation and tidal cycles control the biogeochemical transformations and bi‐directional exchange of carbon and nutrients across the terrestrial–aquatic interfaces (TAIs) in coastal regions. This study uses a highly mechanistic model, Advanced Terrestrial Simulator (ATS)‐PFLOTRAN, to explore how these interactions affect exchanges of materials and carbon and nitrogen cycling. We used a transect in the Chesapeake Bay region that spans zones of open water, coastal wetland, transition, and upland forest. We designed several simulation scenarios to parse the effects of the individual controlling factors and the sensitivity of carbon cycling to reaction rate parameters derived from laboratory experiments. Our simulations reveal an active zone for carbon cycling under the transition zones between the wetland and the upland. Evapotranspiration is found to enhance the exchange fluxes between the surface and subsurface domains, resulting in a higher dissolved oxygen concentration in the TAIs. The transport of organic carbon derived from plant leaves and roots provide an additional source of organic carbon needed for the aerobic respiration and denitrification processes in the TAIs. The variability in reaction rate parameters associated with microbial activities is also found to play a dominant role in controlling the heterogeneity and dynamics of the simulated redox conditions. This modeling‐focused exploratory study enabled us to better understand the complex interactions among soil, water and microbes that govern the hydro‐biogeochemical processes at the TAIs, which is an important step toward representing coastal ecosystems in larger‐scale Earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Potential impacts of mercury released from thawing permafrost

Abstract Mercury (Hg) is a naturally occurring element that bonds with organic matter and, when converted to methylmercury, is a potent neurotoxicant. Here we estimate potential future releases of Hg from thawing permafrost for low and high greenhouse gas emissions scenarios using a mechanistic model. By 2200, the high emissions scenario shows annual permafrost Hg emissions to the atmosphere comparable to current global anthropogenic emissions. By 2100, simulated Hg concentrations in the Yukon River increase by 14% for the low emissions scenario, but double for the high emissions scenario. Fish Hg concentrations do not exceed United States Environmental Protection Agency guidelines for the low emissions scenario by 2300, but for the high emissions scenario, fish in the Yukon River exceed EPA guidelines by 2050. Our results indicate minimal impacts to Hg concentrations in water and fish for the low emissions scenario and high impacts for the high emissions scenario.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Revealing the evolution of order in materials microstructures using multi-modal computer vision

The development of high-performance materials for microelectronics, energy storage, and extreme environments depends on our ability to describe and direct property-defining microstructural order. Our present understanding is typically derived from laborious manual analysis of imaging and spectroscopy data, which is difficult to scale, challenging to reproduce, and lacks the ability to reveal latent associations needed for mechanistic models. Here, we demonstrate a multi-modal machine learning (ML) approach to describe order from electron microscopy analysis of the complex oxide La 1−x Sr x FeO 3 . We construct a hybrid pipeline based on fully and semi-supervised classification, allowing us to evaluate both the characteristics of each data modality and the value each modality adds to the ensemble. We observe distinct differences in the performance of uni- and multi-modal models, from which we draw general lessons in describing crystal order using computer vision.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The role of ionic blockades in controlling the efficiency of energy recovery in forward bias bipolar membranes

Limited understanding exists about the operation of bipolar membranes (BPMs) in forward bias to convert protonic gradients into electrical work, despite their emerging role in many electrochemical devices. In these device contexts, the BPM is typically exposed to complex electrolyte mixtures, but their impact on polarization remains poorly understood. Here, for this work, we develop a mechanistic model explaining the forward bias polarization behaviour of BPMs in mixed electrolytes with different acidities/basicities. This model invokes that weak acids/bases accumulate in the BPM and impose an ionic blockade that inhibits the recombination of stronger acids/bases, resulting in a substantial neutralization overpotential. We demonstrate the utility of our model for fuel cells and redox flow batteries and introduce two materials design strategies for mitigating this inhibition. Lastly, we apply our findings to enhance the energy efficiency of carbonate management in CO 2 electrolysers. This work highlights how non-equilibrium local environments at membrane–membrane interfaces can define the efficiency of protonic-to-electrical energy conversion.

25 ENERGY STORAGE↗
DOE OSTI2026

Depth-resolved carbon dioxide and methane concentrations in 522 lakes, ponds, and reservoirs worldwide

Lakes, ponds, and reservoirs (hereafter: “lakes”) are important sources of the greenhouse gases carbon dioxide (CO 2 ) and methane (CH 4 ). Emissions of CO 2 and CH 4 from lakes are regulated in part by in-lake processes, including the production and storage of gases in the lower parts of the water column (bottom waters). However, while substantial efforts have been made to improve estimates of greenhouse gas emissions from lakes, limited data on gas concentrations along depth profiles have prevented the incorporation of bottom-water processes in global emission estimates. Here, we present GHG-depths: the largest existing dataset of depth-profile CO 2 and CH 4 measurements worldwide, including 522 lakes across 38 countries and all seven continents. These data include contributions from 45 research teams and 56 published studies, totaling 2558 discrete sampling events. As global change continues to alter biogeochemical cycling in lakes, these data can help improve mechanistic models to better predict greenhouse gas production and emission from lakes worldwide.

Rabaey, Joseph S. [University of Minnesota, Duluth↗
DOE OSTI2021

A correlation between grain boundary character and deformation twin nucleation mechanism in coarse-grained high-Mn austenitic steel

Abstract In polycrystalline materials, grain boundaries are known to be a critical microstructural component controlling material’s mechanical properties, and their characters such as misorientation and crystallographic boundary planes would also influence the dislocation dynamics. Nevertheless, many of generally used mechanistic models for deformation twin nucleation in fcc metal do not take considerable care of the role of grain boundary characters. Here, we experimentally reveal that deformation twin nucleation occurs at an annealing twin (Σ3{111}) boundary in a high-Mn austenitic steel when dislocation pile-up at Σ3{111} boundary produced a local stress exceeding the twining stress, while no obvious local stress concentration was required at relatively high-energy grain boundaries such as Σ21 or Σ31. A periodic contrast reversal associated with a sequential stacking faults emission from Σ3{111} boundary was observed by in-situ transmission electron microscopy (TEM) deformation experiments, proving the successive layer-by-layer stacking fault emission was the deformation twin nucleation mechanism, different from the previously reported observations in the high-Mn steels. Since this is also true for the observed high Σ-value boundaries in this study, our observation demonstrates the practical importance of taking grain boundary characters into account to understand the deformation twin nucleation mechanism besides well-known factors such as stacking fault energy and grain size.

36 MATERIALS SCIENCE↗
DOE OSTI2022

On the mechanism of marine fouling-prevention performance of oil-containing silicone elastomers

For many decades, silicone elastomers with oil incorporated have served as fouling-release coating for marine applications. In a comprehensive study involving a series of laboratory-based marine fouling assays and extensive global field studies of up to 2-year duration, we compare polydimethylsiloxane (PDMS) coatings of the same composition loaded with oil via two different methods. One method used a traditional, one-pot pre-cure oil addition approach (o-PDMS) and another method used a newer post-cure infusion approach (i-PDMS). The latter displays a substantial improvement in biofouling prevention performance that exceeds established commercial silicone-based fouling-release coating standards. We interpret the differences in performance between one-pot and infused PDMS by developing a mechanistic model based on the Flory–Rehner theory of swollen polymer networks. Using this model, we propose that the chemical potential of the incorporated oil is a key consideration for the design of future fouling-release coatings, as the improved performance is driven by the formation and stabilization of an anti-adhesion oil overlayer on the polymer surface.

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

Microbial contribution to post-fire tundra ecosystem recovery over the 21st century

Abstract Tundra ecosystems have experienced an increased frequency of fire, and this trend is predicted to continue throughout the 21 st Century. Post-fire recovery is underpinned by complex interactions between microbial functional groups that drive nutrient cycling. Here we use a mechanistic model to demonstrate an acceleration of the nitrogen cycle post-fire driven by changes in niche space and microbial competitive dynamics. We show that over the first 5-years post-fire, fast-growing bacterial heterotrophs colonize regions of the soil previously occupied by slower-growing saprotrophic fungi. The bacterial heterotrophs mineralize organic matter, releasing nutrients into the soil. This pathway outweighs new sources of nitrogen and facilitates the recovery of plant productivity. We broadly show here that while consideration of distinct microbial metabolisms related to carbon and nutrient cycling remains rare in terrestrial ecosystem models, they are important when considering the rate of ecosystem recovery post-disturbance and the feedback to soil nutrient cycles on centennial timescales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Binding of the substrate analog methanol in the oxygen-evolving complex of photosystem II in the D1-N87A genetic variant of cyanobacteria

The solar water-splitting protein complex, photosystem II (PSII), catalyzes one of the most energetically demanding reactions in nature by using light energy to drive a catalyst capable of oxidizing water. The water oxidation reaction is catalyzed at the Mn 4 Ca-oxo cluster in the oxygen-evolving complex (OEC), which cycles through five light-driven S-state intermediates (S 0 –S 4 ). A detailed mechanism of the reaction remains elusive as it requires knowledge of the delivery and binding of substrate water in the higher S-state intermediates. In this paper, we use two-dimensional (2D) hyperfine sublevel correlation spectroscopy, in conjunction with quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT), to probe the binding of the substrate analog, methanol, in the S 2 state of the D1-N87A variant of PSII from Synechocystis sp. PCC 6803. The results indicate that the size and specificity of the “narrow” channel is altered in D1-N87A PSII, allowing for the binding of deprotonated 13 C-labeled methanol at the Mn4(IV) ion of the catalytic cluster in the S 2 state. This has important implications on the mechanistic models for water oxidation in PSII.

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

Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations

The protein folding process often proceeds through partially folded transient states. Therefore, a structural understanding of these disordered states is crucial for developing mechanistic models of the folding process. Characterization of unfolded states remains challenging due to their disordered nature, and incorporating multiple methods is necessary. Combining the time-resolved x-ray solution scattering (TRXSS) signal with molecular dynamics (MD), we are able to characterize transient partially folded states of bovine α-lactalbumin, a model system widely used for investigation of molten globule states, during its unfolding triggered by a temperature jump. We track the unfolding process between 20 μs and 70 ms and demonstrate that it passes through three distinct kinetic states. The scattering signals associated with these transient species are then analyzed with TRXSS constrained MD simulations to produce protein structures that are compatible with the input signals. Without utilizing any experimentally extracted kinetic information, the constrained MD simulation successfully drove the protein to an intermediate molten globule state; signals for two later disordered states are refined to terminal unfolded states. From our examination of the structural characteristics of these disordered states, we discuss the implications disordered states have on the folding process, especially on the folding pathway. Finally, we discuss the potential applications and limitations of this method.

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

Photosynthetic reaction center variants made via genetic code expansion show Tyr at M210 tunes the initial electron transfer mechanism

Significance Reaction centers (RCs) are critical to photosynthetic energy conversion. RCs in all characterized photosynthetic organisms contain two symmetrically arranged branches of chromophores and enable light-induced electron transfer with high yield. We fine-tune the properties of a key bacterial RC symmetry-breaking tyrosine via its replacement with noncanonical tyrosine analogs and determine kinetic outcomes. Results are interpreted through energetic characterization made possible by resonance Stark spectroscopy. Analysis indicates this tyrosine modulates the mechanism of the initial light-induced electron transfer, affording an alternative functional pathway that maintains the RC’s robust electron transfer. Modern molecular biology, ultrafast spectroscopy, crystallography, and energetic characterization enable the mechanistic model we describe. Our results deepen understanding of RC function and may have implications for other photocatalysts and enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Leaky ribosomal scanning enables tunable translation of bicistronic ORFs in green algae

Advances in sequencing technology have unveiled examples of nucleus-encoded polycistrons, once considered rare. Exclusively polycistronic transcripts are prevalent in green algae, although the mechanism by which multiple polypeptides are translated from a single transcript is unknown. Here, we used bioinformatic and in vivo mutational analyses to evaluate competing mechanistic models for translation of bicistronic mRNAs in green algae. High-confidence manually curated datasets of bicistronic loci from two divergent green algae, Chlamydomonas reinhardtii and Auxenochlorella protothecoides, revealed a preference for weak Kozak-like sequences for ORF 1 and an underrepresentation of potential initiation codons before the ORF 2 start codon, which are suitable conditions for leaky ribosome scanning to allow ORF 2 translation. We used mutational analysis in A. protothecoides to test the mechanism. In vivo manipulation of the ORF 1 Kozak-like sequence and start codon altered reporter expression at ORF 2, with a weaker Kozak-like sequence enhancing expression and a stronger one diminishing it. A synthetic bicistronic dual reporter demonstrated inversely adjustable activity of green fluorescent protein expressed from ORF 1 and luciferase from ORF 2, depending on the strength of the ORF 1 Kozak-like sequence. Our findings demonstrate that translation of multiple ORFs in green algal bicistronic transcripts is consistent with episodic leaky scanning of ORF 1 to allow translation at ORF 2. This work has implications for the potential functionality of upstream open reading frames (uORFs) found across eukaryotic genomes and for transgene expression in synthetic biology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Growth instabilities shape morphology and genetic diversity of microbial colonies

Abstract Cellular populations assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of a population influences its ecology and evolution. Here, we investigate this relationship in the context of microbial colonies grown on hard agar plates. This a well-studied system that exhibits a transition from smooth circular disks to more irregular and rugged shapes as either the nutrient concentration or cellular motility is decreased. Starting from a mechanistic model of colony growth, we identify two dimensionless quantities that determine how morphology and genetic diversity of the population depend on the model parameters. Our simulations further reveal that population dynamics cannot be accurately described by the commonly-used surface growth models. Instead, one has to explicitly account for the emergent growth instabilities and demographic fluctuations. Overall, our work links together environmental conditions, colony morphology, and evolution. This link is essential for a rational design of concrete, biophysical perturbations to steer evolution in the desired direction.

Golden, Alexander↗
DOE OSTI2021

Correlation and co-localization of QTL for stomatal density, canopy temperature, and productivity with and without drought stress in Setaria

Abstract Mechanistic modeling indicates that stomatal conductance could be reduced to improve water use efficiency (WUE) in C4 crops. Genetic variation in stomatal density and canopy temperature was evaluated in the model C4 genus, Setaria. Recombinant inbred lines (RILs) derived from a Setaria italica×Setaria viridis cross were grown with ample or limiting water supply under field conditions in Illinois. An optical profilometer was used to rapidly assess stomatal patterning, and canopy temperature was measured using infrared imaging. Stomatal density and canopy temperature were positively correlated but both were negatively correlated with total above-ground biomass. These trait relationships suggest a likely interaction between stomatal density and the other drivers of water use such as stomatal size and aperture. Multiple quantitative trait loci (QTL) were identified for stomatal density and canopy temperature, including co-located QTL on chromosomes 5 and 9. The direction of the additive effect of these QTL on chromosome 5 and 9 was in accordance with the positive phenotypic relationship between these two traits. This, along with prior experiments, suggests a common genetic architecture between stomatal patterning and WUE in controlled environments with canopy transpiration and productivity in the field, while highlighting the potential of Setaria as a model to understand the physiology and genetics of WUE in C4 species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Impact of Blast Overpressure on the Pharmacokinetics of Various Antibiotics in Sprague Dawley Rats

ABSTRACT Introduction Combat injuries are complex and multimodal. Most injuries to the extremities occur because of explosive devices such as improvised explosive devices. Blast exposure dramatically increases the risk of infection in combat wounds, and there is limited available information on the best antibiotic treatments for these injuries. We previously demonstrated that mice exposed to blast displayed a delayed clearance of cefazolin from the plasma and liver; further semi-mechanistic modeling determined that cefazolin concentrations in the skin of these mice were reduced. Our objective was to investigate the effects of blast on the pharmacokinetics of antibiotics of different types used for the treatment of combat wounds in the rat model. Materials and Methods Male Sprague Dawley rats were exposed to blast overpressure followed by injection of a bolus of animal equivalent doses of an antibiotic (cefazolin, cefepime, ertapenem, or clindamycin) into the tail vein at 1-hour post-blast exposure. Blood was collected at predetermined time points via repeated sampling from the tail vein. Animals were also euthanized at predetermined time points, at which time liver, kidney, skin, and blood via cardiac puncture were collected. Antibiotic concentrations were determined by ultra-performance liquid chromatography–tandem mass spectrometry. Results Blast-exposed rats exhibited a similar rate of clearance compared to non-blasted rats in the blood, liver, kidney, and skin, which is inconsistent with the data regarding cefazolin in blast-exposed mice. Conclusions Our results in rats do not recapitulate our previous observation of delayed cefazolin clearance in mice following the blast overpressure exposure. Although using rats permitted us to collect multiple blood samples from the same animals, rats may not be a suitable model for measuring the pharmacokinetics of antibiotics following blast. The interpretation of the results may be challenging because of variation in data among rat subjects in the same sample groups.

General & Internal Medicine↗
DOE OSTI2026

Hypothesis on the dust-borne atmospheric transport of Coccidioides , causative fungal pathogen for coccidioidomycosis (Valley fever)

For many decades, the fungal pathogen (Coccidioides spp.) that causes coccidioidomycosis (Valley fever) has been associated with dust exposure. However, the mechanism of atmospheric transport of arthroconidia has yet to be defined. As such, it is unclear whether the association between dust exposure and Coccidioides is coincidental or not: do soil-disturbing events simultaneously cause both free-floating Coccidioides conidia and dust particles (i.e., particulate matter) to become entrained in the atmosphere, or is Coccidioides attached to dust particles and they are jointly suspended? In this short article, we propose the dust-borne atmospheric transport hypothesis: Coccidioides conidia are transported in the atmosphere attached to dust particles, which protect the fungi from harsh environmental conditions like desiccation and UV exposure, allowing them to travel far while remaining viable in comparison to free-floating aerial transport. If true, the dust-borne atmospheric transport hypothesis provides a means for mechanistically modeling the transport and exposure risk of Coccidioides via atmospheric dispersion modeling and suggests health implications from simultaneous exposure to dust and a fungal pathogen.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Structural basis for cloverleaf RNA-initiated viral genome replication

The genomes of positive-strand RNA viruses serve as a template for both protein translation and genome replication. In enteroviruses, a cloverleaf RNA structure at the 5' end of the genome functions as a switch to transition from viral translation to replication by interacting with host poly(C)-binding protein 2 (PCBP2) and the viral 3CD pro protein. We determined the structures of cloverleaf RNA from coxsackievirus and poliovirus. Cloverleaf RNA folds into an H-type four-way junction and is stabilized by a unique adenosine-cytidine-uridine (A•C-U) base triple involving the conserved pyrimidine mismatch region. The two PCBP2 binding sites are spatially proximal and are located on the opposite end from the 3CD pro binding site on cloverleaf. We determined that the A•C-U base triple restricts the flexibility of the cloverleaf stem–loops resulting in partial occlusion of the PCBP2 binding site, and elimination of the A•C-U base triple increases the binding affinity of PCBP2 to the cloverleaf RNA. Based on the cloverleaf structures and biophysical assays, we propose a new mechanistic model by which enteroviruses use the cloverleaf structure as a molecular switch to transition from viral protein translation to genome replication.

59 BASIC BIOLOGICAL SCIENCES↗