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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Bioinspired Supercharging of Photoredox Catalysis for Applications in Energy and Chemical Manufacturing

For more than a decade, photoredox catalysis has been demonstrating that when photoactive catalysts are irradiated with visible light, reactions occur under milder, cheaper, and environmentally friendlier conditions. Furthermore, this methodology allows for the activation of abundant chemicals into valuable products through novel mechanisms that are otherwise inaccessible. The photoredox approach, however, has been primarily used for pharmaceutical applications, where its implementation has been highly effective, but typically with a more rudimentary understanding of the mechanisms involved in these transformations. From a global perspective, the manufacture of everyday chemicals by the chemical industry as a whole currently accounts for 10% of total global energy consumption, and generates 7% of the world's greenhouse gases annually. In this context, the Bio-Inspired Light-Escalated Chemistry (BioLEC) Energy Frontier Research Center (EFRC) was founded to supercharge the photoredox approach for applications in chemical manufacturing aimed at reducing its energy consumption and emissions burden, by using bio-inspired schemes to harvest multiple electrons to drive endothermically uphill chemical reactions. The Center comprises a diverse group of researchers with expertise that includes synthetic chemistry, biophysics, physical chemistry, and engineering. Here the team works together to gain a deeper understanding of the mechanistic details of photoredox reactions while amplifying the applications of these light-driven methodologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1975

Chemical research projects office functions accomplishments programs

Basic and applied research in the fields of polymer chemistry, polymeric composites, chemical engineering, and biophysical chemistry is summarized. Emphasis is placed on fire safety and human survivability as they relate to commercial and military aircraft, high-rise buildings, mines and rapid transit transportation. Materials systems and other fire control systems developed for aerospace applications and applied to national domestic needs are described along with bench-scale and full-scale tests conducted to demonstrate the improvements in performance obtained through the utilization of these materials and fire control measures.

Heimbuch, A. H.↗
DOE OSTI2023

Single-cell multimodal imaging uncovers energy conversion pathways in biohybrids

Microbe–semiconductor biohybrids, which integrate microbial enzymatic synthesis with the light-harvesting capabilities of inorganic semiconductors, have emerged as promising solar-to-chemical conversion systems. Improving the electron transport at the nano–bio interface and inside cells is important for boosting conversion efficiencies, yet the underlying mechanism is challenging to study by bulk measurements owing to the heterogeneities of both constituents. Here we develop a generalizable, quantitative multimodal microscopy platform that combines multi-channel optical imaging and photocurrent mapping to probe such biohybrids down to single- to sub-cell/particle levels. We uncover and differentiate the critical roles of different hydrogenases in the lithoautotrophic bacterium Ralstonia eutropha for bioplastic formation, discover this bacterium’s surprisingly large nanoampere-level electron-uptake capability, and dissect the cross-membrane electron-transport pathways. Furthermore, this imaging platform, and the associated analytical framework, can uncover electron-transport mechanisms in various types of biohybrid, and potentially offers a means to use and engineer R. eutropha for efficient chemical production coupled with photocatalytic materials.

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

Ligand modulation of the conformational dynamics of the A 2A adenosine receptor revealed by single-molecule fluorescence

G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a complex conformational ensemble. The intra- and inter-state dynamics, however, is not well documented. Here, we used single-molecule fluorescence to measure ligand-modulated conformational dynamics of the adenosine A 2A receptor (A 2A R) on nanosecond to millisecond timescales. Experiments were performed on detergent-purified A 2R in either the ligand-free (apo) state, or when bound to an inverse, partial or full agonist ligand. Single-molecule Förster resonance energy transfer (smFRET) was performed on detergent-solubilized A 2A R to resolve active and inactive states via the separation between transmembrane (TM) helices 4 and 6. The ligand-dependent changes of the smFRET distributions are consistent with conformational selection and with inter-state exchange lifetimes ≥ 3 ms. Local conformational dynamics around residue 229 6.31 on TM6 was measured using fluorescence correlation spectroscopy (FCS), which captures dynamic quenching due to photoinduced electron transfer (PET) between a covalently-attached dye and proximal aromatic residues. Global analysis of PET-FCS data revealed fast (150–350 ns), intermediate (50–60 μs) and slow (200–300 μs) conformational dynamics in A 2A R, with lifetimes and amplitudes modulated by ligands and a G-protein mimetic (mini-G s ). Most notably, the agonist binding and the coupling to mini-G s accelerates and increases the relative contribution of the sub-microsecond phase. Molecular dynamics simulations identified three tyrosine residues (Y112, Y288 7.53 , and Y290 7.55 ) as being responsible for the dynamic quenching observed by PET-FCS and revealed associated helical motions around residue 229 6.31 on TM6. As a result, this study provides a quantitative description of conformational dynamics in A 2A R and supports the idea that ligands bias not only GPCR conformations but also the dynamics within and between distinct conformational states of the receptor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Extended experimental inferential structure determination method in determining the structural ensembles of disordered protein states

Proteins with intrinsic or unfolded state disorder comprise a new frontier in structural biology, requiring the characterization of diverse and dynamic structural ensembles. Here we introduce a comprehensive Bayesian framework, the Extended Experimental Inferential Structure Determination (X-EISD) method, which calculates the maximum log-likelihood of a disordered protein ensemble. X-EISD accounts for the uncertainties of a range of experimental data and back-calculation models from structures, including NMR chemical shifts, J-couplings, Nuclear Overhauser Effects (NOEs), paramagnetic relaxation enhancements (PREs), residual dipolar couplings (RDCs), hydrodynamic radii (R h ), single molecule fluorescence Förster resonance energy transfer (smFRET) and small angle X-ray scattering (SAXS). We apply X-EISD to the joint optimization against experimental data for the unfolded drkN SH3 domain and find that combining a local data type, such as chemical shifts or J-couplings, paired with long-ranged restraints such as NOEs, PREs or smFRET, yields structural ensembles in good agreement with all other data types if combined with representative IDP conformers.

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

Dehydration entropy drives liquid-liquid phase separation by molecular crowding

Complex coacervation driven liquid-liquid phase separation (LLPS) of biopolymers has been attracting attention as a novel phase in living cells. Studies of LLPS in this context are typically of proteins harboring chemical and structural complexity, leaving unclear which properties are fundamental to complex coacervation versus protein-specific. This study focuses on the role of polyethylene glycol (PEG)—a widely used molecular crowder—in LLPS. Significantly, entropy-driven LLPS is recapitulated with charged polymers lacking hydrophobicity and sequence complexity, and its propensity dramatically enhanced by PEG. Experimental and field-theoretic simulation results are consistent with PEG driving LLPS by dehydration of polymers, and show that PEG exerts its effect without partitioning into the dense coacervate phase. Furthermore, it is then up to biology to impose additional variations of functional significance to the LLPS of biological systems.

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

The structure of plastocyanin tunes the midpoint potential by restricting axial ligation of the reduced copper ion

Blue copper proteins are models for illustrating how proteins tune metal properties. Nevertheless, the mechanisms by which the protein controls the metal site remain to be fully elucidated. A hindrance is that the closed shell Cu(I) site is inaccessible to most spectroscopic analyses. Carbon deuterium (C-D) bonds used as vibrational probes afford nonperturbative, selective characterization of the key cysteine and methionine copper ligands in both redox states. The structural integrity of Nostoc plastocyanin was perturbed by disrupting potential hydrogen bonds between loops of the cupredoxin fold via mutagenesis (S9A, N33A, N34A), variably raising the midpoint potential. The C-D vibrations show little change to suggest substantial alteration to the Cu(II) coordination in the oxidized state or in the Cu(I) interaction with the cysteine ligand. They rather indicate, along with visible and NMR spectroscopy, that the methionine ligand distinctly interacts more strongly with the Cu(I) ion, in line with the increases in midpoint potential. Here we show that the protein structure determines the redox properties by restricting the interaction between the methionine ligand and Cu(I) in the reduced state.

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

Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors

The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds’ intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.

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

Employing artificial intelligence to steer exascale workflows with colmena

Computational workflows are a common class of application on supercomputers, yet the loosely coupled and heterogeneous nature of workflows often fails to take full advantage of their capabilities. We created Colmena to leverage the massive parallelism of a supercomputer by using Artificial Intelligence (AI) to learn from and adapt a workflow as it executes. Colmena allows scientists to define how their application should respond to events (e.g., task completion) as a series of cooperative agents. In this paper, we describe the design of Colmena, the challenges we overcame while deploying applications on exascale systems, and the science workflows we have enhanced through interweaving AI. The scaling challenges we discuss include developing steering strategies that maximize node utilization, introducing data fabrics that reduce communication overhead of data-intensive tasks, and implementing workflow tasks that cache costly operations between invocations. These innovations coupled with a variety of application patterns accessible through our agent-based steering model have enabled science advances in chemistry, biophysics, and materials science using different types of AI. In conclusion, our vision is that Colmena will spur creative solutions that harness AI across many domains of scientific computing.

Workflows↗
NASA NTRS1973

Investigation of the effect of stress on the chemistry, metabolism, and biophysics of collagen

The research is reported concerning the effect of stress on the chemistry in the connective tissue of the rat. It was found that within a day after administration of cortisol (stress harmone), a significant amount of the insoluble collagen disappeared from the skin. It is concluded that the abrupt catabolism of cutaneous collagen releases peptides. These peptides are rapidly degraded to free amino acids which are active in effecting liver glycogen synthesis, and provide a major energy source to assist the animal in the fight or flight reaction. It is proposed that cutaneous collagen represents a reserve energy pool, which can be mobilized via stress harmones.

Houck, J. C.↗
NASA NTRS2018

Advancing the Science of Both Coastal Ocean Biophysics and Atmospheric Pollution Chemistry: A Final Report to the Nasa Earth Science Division by the GEO-CAPE Team

The 2007 Decadal Survey (DS) included the recommendation for the Geostationary Coastal and Air Pollution Events (GEO-CAPE) mission to launch in 2013–2016 to advance the science of both coastal ocean biophysics and atmospheric-pollution chemistry. In 2009 the NASA Earth Science Division (ESD) initiated study activities for GEO-CAPE and 8 other near- to medium-term missions to help determine the readiness of these conceptual missions to begin the formulation phase. In FY15 the GEO-CAPE mission study team completed a white paper summarizing the results of the pre-formulation work accomplished to date: https://geo-cape.larc.nasa.gov/pdf/GEO-CAPE_2009-2015_SummativeWhitePaper.pdf The team was directed to complete a final report in FY18. This document, prepared as an addendum to the FY15 white paper, serves as the GEO-CAPE final report and focuses only on FY16-18 activities and on summarizing the final state.

Geostationary Coastal and Air Pollution Events↗
DOE OSTI2021

Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c

Abstract The dynamics of photodissociation and recombination in heme proteins represent an archetypical photochemical reaction widely used to understand the interplay between chemical dynamics and reaction environment. We report a study of the photodissociation mechanism for the Fe(II)-S bond between the heme iron and methionine sulfur of ferrous cytochrome c . This bond dissociation is an essential step in the conversion of cytochrome c from an electron transfer protein to a peroxidase enzyme. We use ultrafast X-ray solution scattering to follow the dynamics of Fe(II)-S bond dissociation and 1 s 3 p (Kβ) X-ray emission spectroscopy to follow the dynamics of the iron charge and spin multiplicity during bond dissociation. From these measurements, we conclude that the formation of a triplet metal-centered excited state with anti-bonding Fe(II)-S interactions triggers the bond dissociation and precedes the formation of the metastable Fe high-spin quintet state.

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

Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner

The reduction of dinitrogen to ammonia catalyzed by nitrogenase involves a complex series of events, including ATP hydrolysis, electron transfer, and activation of metal clusters for N 2 reduction. Early evidence shows that an essential part of the mechanism involves transducing information between the nitrogenase component proteins through conformational dynamics. Here, millisecond time-resolved hydrogen-deuterium exchange mass spectrometry was used to unravel peptide-level protein motion on the time scale of catalysis of Mo-dependent nitrogenase from Azotobacter vinelandii. Normal mode analysis calculations complemented this data, providing insights into the specific signal transduction pathways that relay information across protein interfaces at distances spanning 100 Å. Together, these results show that conformational changes induced by protein docking are rapidly transduced to the active site, suggesting a specific mechanism for activating the metal cofactor in the enzyme active site.

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

Differential sensitivity to oxygen among the bacteriochlorophylls g in the type-I reaction centers of Heliobacterium modesticaldum

The type-I, homodimeric photosynthetic reaction center (RC) of Heliobacteria (HbRC) is the only known RC in which bacteriochlorophyll g (BChl g) is found. It is also simpler than other RCs, having the smallest number of protein subunits and bound chromophores of any type-I RC. In the presence of oxygen, BChl g isomerizes to 8 1 -hydroxychlorophyll aF (Chl a F ). This naturally occurring process provides a way of altering the chlorophylls and studying the efect of these changes on energy and electron transfer. Transient absorbance diference spectroscopy reveals that triplet-state formation occurs in the antenna chlorophylls of HbRCs but does not provide site-specifc information. Herein, we report on an extended optically detected magnetic resonance (ODMR) study of the antenna triplet states in HbRCs with difering levels of conversion of BChl g to Chl a F . The data reveal pools of BChl g molecules with diferent triplet zero-feld splitting parameters and diferent susceptibilities to chemical oxidation. Finally, by relating the detailed spectroscopic characteristics derived from the ODMR data to the recently solved crystallographic structure, we have tentatively identifed BChl g molecules in which the probability of triplet formation is high and sites at which BChl g conversion is more likely, providing useful information about the fate of the excitation in the complex.

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

The development and applications of multidimensional biomolecular spectroscopy illustrated by photosynthetic light harvesting

The parallel and synergistic developments of atomic resolution structural information, new spectroscopic methods, their underpinning formalism, and the application of sophisticated theoretical methods have led to a step function change in our understanding of photosynthetic light harvesting, the process by which photosynthetic organisms collect solar energy and supply it to their reaction centers to initiate the chemistry of photosynthesis. The new spectroscopic methods, in particular multidimensional spectroscopies, have enabled a transition from recording rates of processes to focusing on mechanism. We discuss two ultrafast spectroscopies – two-dimensional electronic spectroscopy and two-dimensional electronic-vibrational spectroscopy – and illustrate their development through the lens of photosynthetic light harvesting. Both spectroscopies provide enhanced spectral resolution and, in different ways, reveal pathways of energy flow and coherent oscillations which relate to the quantum mechanical mixing of, for example, electronic excitations (excitons) and nuclear motions. The new types of information present in these spectra provoked the application of sophisticated quantum dynamical theories to describe the temporal evolution of the spectra and provide new questions for experimental investigation. While multidimensional spectroscopies have applications in many other areas of science, we feel that the investigation of photosynthetic light harvesting has had the largest influence on the development of spectroscopic and theoretical methods for the study of quantum dynamics in biology, hence the focus of this review. We conclude with key questions for the next decade of this review.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Three rate-determining protein roles in photosynthetic O 2 -evolution addressed by time-resolved experiments on genetically modified photosystems

Light-driven water splitting by plants, algae and cyanobacteria is pivotal for global bioenergetics and biomass formation. A manganese cluster bound to the photosystem II proteins catalyzes the complex reaction at high rate, but the rate-determining factors are insufficiently understood. Here we trace the oxygen-evolution transition by time-resolved polarography and infrared spectroscopy for cyanobacterial photosystems genetically modified at two strategic sites, complemented by computational chemistry. Our results highlight three rate-determining roles of the protein environment of the metal cluster: acceleration of proton-coupled electron transfer, acceleration of substrate-water insertion after O 2 -formation, and balancing of rate-determining enthalpic and entropic contributions. Whereas in general the substrate-water insertion step may be unresolvable in time-resolved experiments, here it likely becomes traceable because of deceleration by genetic modification. Our results may stimulate new time-resolved experiments on substrate-water insertion in photosynthesis, clarification of enthalpy-entropy compensation in enzyme catalysis, and knowledge-guided development of inorganic catalyst materials.

Bioenergetics↗
DOE OSTI2023

Ensuring thermodynamic consistency with invertible coarse-graining

Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insights by isolating the essential degrees of freedom that dictate the thermodynamic properties of a complex, condensed-phase system. The reduced complexity of the model typically leads to lower computational costs and more efficient sampling compared with atomistic models. Designing “good” coarse-grained models is an art. Generally, the mapping from fine-grained configurations to coarse-grained configurations itself is not optimized in any way; instead, the energy function associated with the mapped configurations is. In this work, we explore the consequences of optimizing the coarse-grained representation alongside its potential energy function. We use a graph machine learning framework to embed atomic configurations into a low-dimensional space to produce efficient representations of the original molecular system. Because the representation we obtain is no longer directly interpretable as a real-space representation of the atomic coordinates, we also introduce an inversion process and an associated thermodynamic consistency relation that allows us to rigorously sample fine-grained configurations conditioned on the coarse-grained sampling. We illustrate that this technique is robust, recovering the first two moments of the distribution of several observables in proteins such as chignolin and alanine dipeptide.

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

Quantitative Protein Corona Composition and Dynamics on Carbon Nanotubes in Biological Environments

When nanoparticles enter biological environments, proteins adsorb to form the "protein corona" which alters nanoparticle biodistribution and toxicity. Herein, we measure protein corona formation on DNA-functionalized single-walled carbon nanotubes (ssDNA-SWCNTs), a nanoparticle used widely for sensing and delivery, in blood plasma and cerebrospinal fluid. We characterize corona composition by mass spectrometry, revealing high-abundance corona proteins involved in lipid binding, complement activation, and coagulation. We investigate roles of electrostatic and entropic interactions driving selective corona formation. Lastly, we study real-time protein binding on ssDNA-SWCNTs, obtaining agreement between enriched proteins binding strongly and depleted proteins binding marginally, while highlighting cooperative adsorption mechanisms. Knowledge of protein corona composition, formation mechanisms, and dynamics informs nanoparticle translation from in vitro design to in vivo application.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗