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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Distinct roles of land cover in regulating spatial variabilities of temperature responses to radiative effects of aerosols and clouds

Surface temperature responses to radiative perturbations due to aerosols and clouds are complicated by the land surface properties. To disentangle these complexities, this study, from a terrestrial surface energy budget perspective, isolates the underlying biophysical processes from the instantaneous radiative effects of aerosols and clouds on surface temperature using the National Center for Atmospheric Research Community Earth System Model version 1.2.1. It is found that in comparison with the global heterogeneous distributions of instantaneous radiative perturbations at the surface induced by aerosols and clouds, the spatial variations of the corresponding surface temperature responses to aerosol direct radiative effects (DRE) during the daytime and cloud radiative effects (CRE) during the nighttime are amplified. It is because of the consistent global distribution of the local surface climate sensitivity (a function of land cover properties such as surface roughness and Bowen ratio) with those of daytime DRE and nighttime CRE. By applying identical anthropogenic aerosol and precursor emissions over eight major past, present and projected future anthropogenic aerosol emitting regions (i.e. Brazil, China, East Africa, India, Indonesia, South Africa, United States and Western Europe), surface temperature responses to aerosol radiative cooling in the daytime and cloud radiative warming in the nighttime over these regions positively regulated by local surface climate sensitivities are prominent.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410–DNA interaction using small angle X-ray scattering

ZNF410 is a highly-conserved transcription factor, remarkable in that it recognizes a 15-base pair DNA element but has just a single responsive target gene in mammalian erythroid cells. ZNF410 includes a tandem array of five zinc-fingers (ZFs), surrounded by uncharacterized N- and C-terminal regions. Unexpectedly, full-length ZNF410 has reduced DNA binding affinity, compared to that of the isolated DNA binding ZF array, both in vitro and in cells. AlphaFold predicts a partially-folded N-terminal subdomain that includes a 30-residue long helix, preceded by a hairpin loop rich in acidic (aspartate/glutamate) and serine/threonine residues. This hairpin loop is predicted by AlphaFold to lie against the DNA binding interface of the ZF array. In solution, ZNF410 is a monomer and binds to DNA with 1:1 stoichiometry. Surprisingly, the single best-fit model for the experimental small angle X-ray scattering profile, in the absence of DNA, is the original AlphaFold model with the N-terminal long-helix and the hairpin loop occupying the ZF DNA binding surface. For DNA binding, the hairpin loop presumably must be displaced. After combining biophysical, biochemical, bioinformatic and artificial intelligence-based AlphaFold analyses, we suggest that the hairpin loop mimics the structure and electrostatics of DNA, and provides an additional mechanism, supplementary to sequence specificity, of regulating ZNF410 DNA binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cell-free Scaled Production and Adjuvant Addition to a Recombinant Major Outer Membrane Protein from Chlamydia muridarum for Vaccine Development

Subunit vaccines offer advantages over more traditional inactivated or attenuated whole-cell-derived vaccines in safety, stability, and standard manufacturing. To achieve an effective protein-based subunit vaccine, the protein antigen often needs to adopt a native-like conformation. This is particularly important for pathogensurface antigens that are membrane-bound proteins. Cell-free methods have been successfully used to produce correctly folded functional membrane protein through the co-translation of nanolipoprotein particles (NLPs), commonly known as nanodiscs. This strategy can be used to produce subunit vaccines consisting of membrane proteins in a lipid-bound environment. However, cell-free protein production is often limited to small scale (<1 mL). The amount of protein produced in small-scale production runs is usually sufficient for biochemical and biophysical studies. However, the cell-free process needs to be scaled up, optimized, and carefully tested to obtain enough protein for vaccine studies in animal models. Other processes involved in vaccine production, such as purification, adjuvant addition, and lyophilization, need to be optimized in parallel. This paper reports the development of a scaled-up protocol to express, purify, and formulate a membrane-bound protein subunit vaccine

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Accurate determination of solvation free energies of neutral organic compounds from first principles

The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Nanoscopic lipid domains determined by microscopy and neutron scattering

Biological membranes are highly complex supramolecular assemblies, which play central roles in biology. However, their complexity makes them challenging to study their nanoscale structures. To overcome this challenge, model membranes assembled using reduced sets of membrane-associated biomolecules have been found to be both excellent and tractable proxies for biological membranes. Due to their relative simplicity, they have been studied using a range of biophysical characterization techniques. Here, in this review article, we will briefly detail the use of fluorescence and electron microscopies, and X-ray and neutron scattering techniques used over the past few decades to study the nanostructure of biological membranes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Quantitative X-ray tomographic analysis reveals calcium precipitation in cataractogenesis

Cataracts, named for pathological light scattering in the lens, are known to be associated with increased large protein aggregates, disrupted protein phase separation, and/or osmotic imbalances in lens cells. We have applied synchrotron phase contrast X-ray micro-computed tomography to directly examine an age-related nuclear cataract model in Cx46 knockout (Cx46KO) mice. High-resolution 3D X-ray tomographic images reveal amorphous spots and strip-like dense matter precipitates in lens cores of all examined Cx46KO mice at different ages. The precipitates are predominantly accumulated in the anterior suture regions of lens cores, and they become longer and dense as mice age. Alizarin red staining data confirms the presence of calcium precipitates in lens cores of all Cx46KO mice. This study indicates that the spatial and temporal calcium precipitation is an age-related event associated with age-related nuclear cataract formation in Cx46KO mice, and further suggests that the loss of Cx46 promotes calcium precipitates in the lens core, which is a new mechanism that likely contributes to the pathological light scattering in this age-related cataract model.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering

Abstract Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.6 Å. The collapse is monophasic and is complete in <600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, showing that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Large global variations in the carbon dioxide removal potential of seaweed farming due to biophysical constraints

Abstract Estimates suggest that over 4 gigatons per year of carbon dioxide (Gt-CO 2 year −1 ) be removed from the atmosphere by 2050 to meet international climate goals. One strategy for carbon dioxide removal is seaweed farming; however its global potential remains highly uncertain. Here, we apply a dynamic seaweed growth model that includes growth-limiting mechanisms, such as nitrate supply, to estimate the global potential yield of four types of seaweed. We estimate that harvesting 1 Gt year −1 of seaweed carbon would require farming over 1 million km 2 of the most productive exclusive economic zones, located in the equatorial Pacific; the cultivation area would need to be tripled to attain an additional 1 Gt year −1 of harvested carbon, indicating dramatic reductions in carbon harvest efficiency beyond the most productive waters. Improving the accuracy of annual harvest yield estimates requires better understanding of biophysical constraints such as seaweed loss rates (e.g., infestation, disease, grazing, wave erosion).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Empirical Dynamic Modeling Reveals Complexity of Methane Fluxes in a Temperate Salt Marsh

Abstract Methane dynamics within salt marshes are complex because vegetation types, temperature, oscillating water levels, and changes in salinity and redox conditions influence CH 4 production, consumption, oxidation, and emissions. These non‐linear and complex interactions among variables affect the traditionally expected functional relationships and present challenges for interpreting and developing process‐based models. We employed empirical dynamic modeling (EDM) and convergent cross mapping (CCM) as a novel approach for characterizing seasonal/multiday and diurnal CH 4 dynamics by inferring causal variables, lags, and interconnections among multiple biophysical variables within a temperate salt marsh using 5 years of eddy covariance data. EDM/CCM is a nonparametric approach capable of quantifying the coupling between variables while determining time scales where variable interactions are the most relevant. We found that gross primary productivity, tidal creek dissolved oxygen, and temperature were important for seasonal/multiday dynamics (rho = 0.73–0.80), while water level was most important for diurnal dynamics during both the growing and dormancy phenoperiods (rho = 0.72 and 0.56, respectively). Lags for the top‐ranked variables (i.e., gross primary productivity, dissolved oxygen, temperature, water level) occurred between 1 and 5 weeks at the seasonal scale and 1–24 hr at the diurnal scale. The EDM had high prediction capabilities for intra‐/inter‐seasonal patterns and annual CH 4 sums but had limitations in representing large, infrequent fluxes. Results highlight the importance of non‐linearity, drivers, lag times, and interconnections among multiple biophysical variables that regulate CH 4 fluxes in tidal wetlands. This research introduces a novel approach to examining CH 4 fluxes, which will aid in evaluating current paradigms in wetlands and other ecosystems.

Environmental Sciences & Ecology↗
DOE OSTI2021

Leaf 13 C data constrain the uncertainty of the carbon dynamics of temperate forest ecosystems

Stable carbon isotope discrimination occurred in plant biophysical and biogeochemical processes can help understand plant physiology and soil biogeochemistry with respect to carbon cycling. Here, we incorporated the photosynthetic carbon isotope discrimination into a process-based land surface model (iTEM) to test if stable carbon isotope composition (δ 13 C) can impose additional constraint on model parameters. Sequential data assimilation was implemented at six eddy covariance flux tower sites using carbon flux observations including gross primary productivity (GPP) and net ecosystem exchange (NEE) with and without considering foliar δ 13 C (δ 13 C f ) measurement constraints, respectively. Our model-data fusion showed that δ 13 C f can provide useful constraint on photosynthetic (V cmax25 , the maximum rate of carboxylation at 25°C) and stomatal (g1, the slope of stomatal function) parameters as well as the posterior carbon fluxes. When including δ 13 C f measurement, g1 spatially varies among the six sites and is significantly correlated with annual precipitation. We incorporated the statistical relationship between g1 and annual precipitation into iTEM, which is then used to quantify the regional carbon dynamic in temperate forest ecosystems of the Northern Hemisphere. Compared with the simulation only conditioned on carbon flux observations, regional carbon flux estimations performed slightly better against the FLUXCOM products and the uncertainties of modeled carbon fluxes were reduced by 27%. Our study demonstrated that δ 13 C f data constrains carbon flux uncertainties across space.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase

Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid–base catalysis upon loop closure. These enzymes also have a conserved phosphate-binding loop that is typically highly rigid and forms a well-defined anion-binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have often evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTP’s high sequence similarity to its natural counterparts, it presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active-site cysteine, mechanistic promiscuity, and, most notably, hyperthermostability, with a denaturation temperature likely >130 °C (>8 °C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical, and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme and showcases the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions.

archaea↗
DOE OSTI2022

cabbi-bio/BECT-ABM

The emergence of the cellulosic bioeconomy requires not only adequate technological, economic, and policy advances, but also effective communication and coordination among the multiple stakeholders in the bioeconomy community. Aiming to facilitate stakeholder communication and collaboration for cellulosic bioeconomy growth, an agent-based model is developed as a community communication tool in this study. The tool simulates the behaviors and interactions of key stakeholders, as well as the responses and interactions between the stakeholders and biophysical, socioeconomic, and environmental conditions. The agent behavior rules are developed and validated based on behavior and economic theories and information attained from a stakeholder focus group study and a land use survey.

Yang, Pan↗
DOE OSTI2022

De novo designed protein inhibitors of amyloid aggregation and seeding

Neurodegenerative diseases are characterized by the pathologic accumulation of aggregated proteins. Known as amyloid, these fibrillar aggregates include proteins such as tau and amyloid-β (Aβ) in Alzheimer’s disease (AD) and alpha-synuclein (αSyn) in Parkinson’s disease (PD). The development and spread of amyloid fibrils within the brain correlates with disease onset and progression, and inhibiting amyloid formation is a possible route toward therapeutic development. Recent advances have enabled the determination of amyloid fibril structures to atomic-level resolution, improving the possibility of structure-based inhibitor design. In this work, we use these amyloid structures to design inhibitors that bind to the ends of fibrils, “capping” them so as to prevent further growth. Using de novo protein design, we develop a library of miniprotein inhibitors of 35 to 48 residues that target the amyloid structures of tau, Aβ, and αSyn. Biophysical characterization of top in silico designed inhibitors shows they form stable folds, have no sequence similarity to naturally occurring proteins, and specifically prevent the aggregation of their targeted amyloid-prone proteins in vitro. The inhibitors also prevent the seeded aggregation and toxicity of fibrils in cells. In vivo evaluation reveals their ability to reduce aggregation and rescue motor deficits in Caenorhabditis elegans models of PD and AD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cell-Free Screening, Production and Animal Testing of a STI-Related Chlamydial Major Outer Membrane Protein Supported in Nanolipoproteins

Background: Vaccine development against Chlamydia, a prevalent sexually transmied infection (STI), is imperative due to its global public health impact. However, significant challenges arise in the production of effective subunit vaccines based on recombinant protein antigens, particularly with membrane proteins like the Major Outer Membrane Protein (MOMP). Methods: Cellfree protein synthesis (CFPS) technology is an aractive approach to address these challenges as a method of high-throughput membrane protein and protein complex production coupled with nanolipoprotein particles (NLPs). NLPs provide a supporting scaffold while allowing easy adjuvant addition during formulation. Over the last decade, we have been working toward the production and characterization of MOMP-NLP complexes for vaccine testing. Results: The work presented here highlights the expression and biophysical analyses, including transmission electron microscopy (TEM) and dynamic light scaering (DLS), which confirm the formation and functionality of MOMP-NLP complexes for use in animal studies. Moreover, immunization studies in preclinical models compare the past and present protective efficacy of MOMP-NLP formulations, particularly when co-adjuvanted with CpG and FSL1. Conclusion: Ex vivo assessments further highlight the immunomodulatory effects of MOMP-NLP vaccinations, emphasizing their potential to elicitrobust immune responses. However, further research is warranted to optimize vaccine formulations further, validate efficacy against Chlamydia trachomatis, and beer understand the underlying mechanisms of immune response.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Data-driven prediction of α IIb β 3 integrin activation paths using manifold learning and deep generative modeling

The integrin heterodimer is a transmembrane protein critical for driving cellular process and is a therapeutic target in the treatment of multiple diseases linked to its malfunction. Activation of integrin involves conformational transitions between bent and extended states. Some of the conformations that are intermediate between bent and extended states of the heterodimer have been experimentally characterized, but the full activation pathways remain unresolved both experimentally due to their transient nature and computationally due to the challenges in simulating rare barrier crossing events in these large molecular systems. An understanding of the activation pathways can provide new fundamental understanding of the biophysical processes associated with the dynamic interconversions between bent and extended states and unveil new putative therapeutic targets. In this work, we apply nonlinear manifold learning to coarse-grained molecular dynamics simulations of bent, extended, and two intermediate states of αI I b β3 integrin to learn a low-dimensional embedding of the configurational phase space. We then train deep generative models to learn an inverse mapping between the low-dimensional embedding and high-dimensional molecular space and use these models to interpolate the molecular configurations constituting the activation pathways between the experimentally characterized states. Furthermore, this work furnishes plausible predictions of integrin activation pathways and reports a generic and transferable multi-scale technique to predict transition pathways for biomolecular systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Insights Into the Aerodynamic Versus Radiometric Surface Temperature Debate in Thermal-Based Evaporation Modeling

Global evaporation monitoring from Earth observation thermal infrared satellite missions is historically challenged due to the unavailability of any direct measurements of aerodynamic temperature. State-of-the-art one-source evaporation models use remotely sensed radiometric surface temperature as a substitute for the aerodynamic temperature and apply empirical corrections to accommodate for their inequality. This introduces substantial uncertainty in operational drought mapping over complex landscapes. By employing a non-parametric model, we show that evaporation can be directly retrieved from thermal satellite data without the need of any empirical correction. Independent evaluation of evaporation in a broad spectrum of biome and aridity yielded statistically significant results when compared with eddy covariance observations. While our simplified model provides a new perspective to advance spatio-temporal evaporation mapping from any thermal remote sensing mission, the direct retrieval of aerodynamic temperature also generates the highly required insight on the critical role of biophysical interactions in global evaporation research.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Future increase in compound soil drought-heat extremes exacerbated by vegetation greening

Compound soil drought and heat extremes are expected to occur more frequently with global warming, causing wide-ranging socio-ecological repercussions. Vegetation modulates air temperature and soil moisture through biophysical processes, thereby influencing the occurrence of such extremes. Global vegetation cover is broadly expected to increase under climate change, but it remains unclear whether vegetation greening will alleviate or aggravate future increases in compound soil drought-heat events. Here, using a suite of state-of-the-art model simulations, we show that the projected vegetation greening will increase the frequency of global compound soil drought-heat events, equivalent to 12-21% of the total increment at the end of 21st century. This increase is predominantly driven by reduced albedo and enhanced transpiration associated with increased leaf area. Although greening-induced transpiration enhancement has counteracting cooling and drying effects, the excessive water loss in the early growing season can lead to later soil moisture deficits, amplifying compound soil drought-heat extremes during the subsequent warm season. These changes are most pronounced in northern high latitudes and are dominated by the warming effect of CO 2 . Our study highlights the necessity of integrating vegetation biophysical effects into mitigation and adaptation strategies for addressing compound climate risks.

54 ENVIRONMENTAL SCIENCES↗