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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Engineering a Non‐Natural Photoenzyme for Improved Photon Efficiency**

Abstract Photoenzymes are biological catalysts that use light to convert starting materials into products. These catalysts require photon absorption for each turnover, making quantum efficiency an important optimization parameter. Flavin‐dependent “ene”‐reductases (EREDs) display latent photoenzymatic activity for synthetically valuable hydroalkylations; however, protein engineering has not been used to optimize this non‐natural function. We describe a protein engineering platform for the high throughput optimization of photoenzymes. A single round of engineering results in improved catalytic function toward the synthesis of γ, δ, ϵ‐lactams, and acyclic amides. Mechanistic studies show that key mutations can alter the enzyme's excited state dynamics, enhance its photon efficiency, and ultimately increase catalyst performance. Transient absorption spectroscopy reveals that engineered variants display dramatically decreased radical lifetimes, indicating an evolution toward a concerted mechanism.

Nicholls, Bryce T.↗
DOE OSTI2021

Cylindrical Confinement of Nanocolloidal Cholesteric Liquid Crystal

The organization of nanocolloidal liquid crystals in constrained geometries has fundamental and practical importance, since under confinement, liquid crystals contain stable topological defects that can serve as templates for nanoparticle organization. Three-dimensional confinement of cholesteric (Ch) liquid crystals formed by cellulose nanocrystals (CNCs) have been extensively studied; however, their two-dimensional confinement remains underinvestigated. In this work, we report the results of systematic experimental studies of two-dimensional confinement of Ch–CNC liquid crystal in cylindrical capillaries with varying inner diameters. Confinement resulted in phase separation of the Ch–CNC liquid crystal into a Ch shell formed by concentric CNC pseudolayers with the helicoidal axis perpendicular to the inner surface of the capillary walls, and a micrometer-diameter isotropic core thread running parallel to the long axis of the capillary. The morphology of the confined Ch–CNC liquid crystal varied when progressively increasing the degree confinement. Finally, we show that phase separation of the Ch–CNC liquid crystal into a Ch shell and an isotropic core is preserved in flexible capillary tubing, suggesting the applicability of this system for the fabrication of flexible optical waveguides.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms

Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. Here we find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

MixPI: Mixed-time slicing path integral software for quantized molecular dynamics simulations

We introduce the MixPI software to implement path integral molecular dynamics (PIMD) simulations for the study of condensed phase systems where nuclear quantum effects (NQEs) are important. In contrast to existing PIMD simulation software, MixPI enables the implementation of mixed quantum–classical path integral simulations where only a subset of system degrees of freedom (dofs) are treated quantum mechanically in an extended phase space while the remaining dofs are described classically. We expect this software to be particularly useful for simulations of electron and proton transfer in condensed phase systems, as well as for the study of biological and material systems where only a handful of dofs contribute significantly to the observed NQEs. We demonstrate the use of MixPI in two different systems. The first is a simple water model where we implement a set of mixed quantum–classical simulations to compute average energy and radial distribution functions. We use these simulations to benchmark the effectiveness of MixPI and to demonstrate how it enables systematic investigation into the origin of observed NQEs. We then compute radial distribution functions for a system where MixPI is essential: a solvated metal (M 2+ ) cation described using an explicit quantized electron localized on an M 3+ ion in water.

chemical physics↗
DOE OSTI2020

Direct evidence for low-energy electron emission following O LVV Auger transitions at oxide surfaces

Abstract Oxygen, the third most abundant element in the universe, plays a key role in the chemistry of condensed matter and biological systems. Here, we report evidence for a hitherto unexplored Auger transition in oxides, where a valence band electron fills a vacancy in the 2s state of oxygen, transferring sufficient energy to allow electron emission. We used a beam of positrons with kinetic energies of $$\sim 1$$ ∼ 1 eV to create O 2s holes via matter-antimatter annihilation. This made possible the elimination of the large secondary electron background that has precluded definitive measurements of the low-energy electrons emitted through this process. Our experiments indicate that low-energy electron emission following the Auger decay of O 2s holes from adsorbed oxygen and oxide surfaces are very efficient. Specifically, our results indicate that the low energy electron emission following the Auger decay of O 2s hole is nearly as efficient as electron emission following the relaxation of O 1s holes in $$\hbox {TiO}_2$$ TiO 2 . This has important implications for the understanding of Auger-stimulated ion desorption, Coulombic decay, photodynamic cancer therapies, and may yield important insights into the radiation-induced reactive sites for corrosion and catalysis.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Can improved canopy light transmission ameliorate loss of photosynthetic efficiency in the shade? An investigation of natural variation in Sorghum bicolor

Abstract Previous studies have found that maximum quantum yield of CO2 assimilation (Φ CO2,max,app) declines in lower canopies of maize and miscanthus, a maladaptive response to self-shading. These observations were limited to single genotypes, leaving it unclear whether the maladaptive shade response is a general property of this C4 grass tribe, the Andropogoneae. We explored the generality of this maladaptation by testing the hypothesis that erect leaf forms (erectophiles), which allow more light into the lower canopy, suffer less of a decline in photosynthetic efficiency than drooping leaf (planophile) forms. On average, Φ CO2,max,app declined 27% in lower canopy leaves across 35 accessions, but the decline was over twice as great in planophiles than in erectophiles. The loss of photosynthetic efficiency involved a decoupling between electron transport and assimilation. This was not associated with increased bundle sheath leakage, based on 13C measurements. In both planophiles and erectophiles, shaded leaves had greater leaf absorptivity and lower activities of key C4 enzymes than sun leaves. The erectophile form is considered more productive because it allows a more effective distribution of light through the canopy to support photosynthesis. We show that in sorghum, it provides a second benefit, maintenance of higher Φ CO2,max,app to support efficient use of that light resource.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

QuDPy: A Python-based tool for computing ultrafast non-linear optical responses

Nonlinear Optical Spectroscopy is a well-developed field with theoretical and experimental advances that have benefited multiple disciplines, including chemistry, biology, and physics. However, for the accurate interpretation of the corresponding multi-dimensional spectra, there is a need for precise quantum dynamical simulations based on model Hamiltonians. In this article, we present the initial release of our code, QuDPy (Quantum Dynamics in Python), which provides a robust numerical platform for performing quantum dynamics simulations based on model systems, including open quantum systems. Furthermore, a distinguishing feature of our approach is the ability to specify various high-order optical response pathways in the form of double-sided Feynman diagrams through a straightforward input syntax. This syntax outlines the time-ordering of ket-sided or bra-sided optical interactions acting on the time-evolving density matrix of the system. We utilize the quantum dynamics capabilities of QuTip to simulate the spectral response of complex systems, allowing us to compute virtually any $n$-th order optical response of the model system. To illustrate the utility of our approach, we provide a series of example calculations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Extremely Bright, Near-IR Emitting Spontaneously Blinking Fluorophores Enable Ratiometric Multicolor Nanoscopy in Live Cells

New bright, photostable, emission-orthogonal fluorophores that blink without toxic additives are needed to enable multicolor, live-cell, single-molecule localization microscopy (SMLM). Here we report the design, synthesis, and biological evaluation of Yale676sb, a photostable, near-IR-emitting fluorophore that achieves these goals in the context of an exceptional quantum yield (0.59). When used alongside HMSiR, Yale676sb enables simultaneous, live-cell, two-color SMLM of two intracellular organelles (ER + mitochondria) with only a single laser and no chemical additives.

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

Fluorescent, phosphorescent, magnetic resonance contrast and radioactive tracer labelling of extracellular vesicles

This review focusses on the significance of fluorescent, phosphorescent labelling and tracking of extracellular vesicles (EVs) for unravelling their biology, pathophysiology, and potential diagnostic and therapeutic uses. Various labeling strategies, such as lipid membrane, surface protein, luminal, nucleic acid, radionuclide, quantum dot labels, and metal complex-based stains, are evaluated for visualizing and characterizing EVs. Direct labelling with fluorescent lipophilic dyes is simple but generally lacks specificity, while surface protein labelling offers selectivity but may affect EV-cell interactions. Luminal and nucleic acid labelling strategies have their own advantages and challenges. Here, each labelling approach has strengths and weaknesses, which require a suitable probe and technique based on research goals, but new tetranuclear polypyridylruthenium(II) complexes as phosphorescent probes have strong phosphorescence, selective staining, and stability. Future research should prioritize the design of novel fluorescent probes and labelling platforms that can significantly enhance the efficiency, accuracy, and specificity of EV labeling, while preserving their composition and functionality. It is crucial to reduce false positive signals and explore the potential of multimodal imaging techniques to gain comprehensive insights into EVs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2002

Research in Computational Astrobiology

We present results from several projects in the new field of computational astrobiology, which is devoted to advancing our understanding of the origin, evolution and distribution of life in the Universe using theoretical and computational tools. We have developed a procedure for calculating long-range effects in molecular dynamics using a plane wave expansion of the electrostatic potential. This method is expected to be highly efficient for simulating biological systems on massively parallel supercomputers. We have perform genomics analysis on a family of actin binding proteins. We have performed quantum mechanical calculations on carbon nanotubes and nucleic acids, which simulations will allow us to investigate possible sources of organic material on the early earth. Finally, we have developed a model of protobiological chemistry using neural networks.

Chaban, Galina↗
DOE OSTI2026

Final Technical Report for U.S.-Japan Hadronic Physics Exchange Program for Studies of Hadron Structure and QCD

Nuclear physics explores the fundamental properties of matter -- how protons and neutrons emerge as quantum systems of elementary particles, how they form the atomic nuclei, and how they give rise to the wide variety of phenomena and applications at biological, technical, and astronomical scales. It is a global scientific effort centered around large-scale experimental user facilities (particle accelerators and detectors), advanced theoretical methods and concepts, and computational techniques and resources. Exchange of knowledge and ideas, scientific collaboration, and workforce development on a global scale are essential for the future of the field. The nuclear physics program envisaged in the 2023 DOE/NSF NSAC Long-Range Plan and pursued at the U.S. National Labs has strong synergies with programs at other facilities worldwide and will realize significant benefits from international collaboration. Nuclear physics is also recognized for promoting international cooperation in the broadest sense through joint construction and operation of experimental equipment, personal contacts between scientists, and education and training. The U.S.-Japan Hadronic Physics Exchange Program (USJPHE) supported collaborative scientific research in hadronic physics and quantum chromodynamics. USJHPE focused on subject areas related to the programs at current and future experimental facilities in the U.S.\ and Japan and supported both experimental and theoretical studies. USJHPE particularly aimed to realize synergies between the hadronic physics programs at Jefferson Lab 12 GeV and J-PARC resulting from the complementarity of electromagnetic and hadronic probes in the multi-GeV energy range. Subject areas of common interest included the quark-gluon structure of hadrons and nuclei, meson and baryon spectroscopy, strangeness and hypernuclear physics, and other related topics. USJHPE also supported research in hadronic physics and nuclear-physics-enabled tests of fundamental symmetries related to the programs at Brookhaven National Lab, Fermilab, KEK, Spring-8, and university-based facilities in the U.S. and Japan. USJHPE especially promoted collaboration between the U.S. and Japanese nuclear physics communities in developing the physics program and instrumentation for the future Electron-Ion Collider. USJHPE was intended to provide travel grants to U.S.-based scientists (primary institutional affiliation with a U.S.\ university, national laboratory, or other research center) to visit Japanese institutions and conduct collaborative research there. The program supported senior researchers, postdoctoral fellows, and students. Continuing the setup of the preceding grant period, J-PARC served as the Japanese “hub” for U.S. physicists for short- and long-term visits, and JLab served as the corresponding U.S. “hub”. The program was officially managed through the U. of Connecticut in Storrs, CT. Support for Japanese physicists visiting the U.S. was provided through funds from Japanese funding agencies. The USJHPE program promoted the scientific exchange and the collaborative spirit in hadronic physics between the two countries.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Photophysics of nanographenes: from polycyclic aromatic hydrocarbons to graphene nanoribbons

Graphene quantum dots (GQDs) and nanoribbons (GNRs) are classes of nanographene molecules that exhibit highly tunable photophysical properties. There have been great strides in recent years to advance our understanding of nanographene photophysics and develop their use in light-harvesting systems, such as artificial photosynthesis. Here, we review the latest studies of GQDs and GNRs which have shed new light onto their photophysical underpinnings through computational and advanced spectroscopic techniques. We discuss how the size, symmetry, and shape of nanographenes influence their molecular orbital structures and, consequentially, their spectroscopic signatures. The scope of this review is to comprehensively lay out the general photophysics of nanographenes starting with benzene and building up to larger polycyclic aromatic hydrocarbons, GQDs, and GNRs. We also explore a collection of publications from recent years that build upon the current understanding of nanographene photophysics and their potential application in light-driven processes from display, lasing, and sensing technology to photocatalytic water splitting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Substitution of distal and active site residues reduces product inhibition of E1 from Acidothermus Cellulolyticus

Abstract Cellulases are largely afflicted by inhibition from their reaction products, especially at high-substrate loading, which represents a major challenge for biomass processing. This challenge was overcome for endoglucanase 1 (E1) from Acidothermus cellulolyticus by identifying a large conformational change involving distal residues upon binding cellobiose. Having introduced alanine substitutions at each of these residues, we identified several mutations that reduced cellobiose inhibition of E1, including W212A, W213A, Q247A, W249A and F250A. One of the mutations (W212A) resulted in a 47-fold decrease in binding affinity of cellobiose as well as a 5-fold increase in the kcat. The mutation further increased E1 activity on Avicel and dilute-acid treated corn stover and enhanced its productivity at high-substrate loadings. These findings were corroborated by funnel metadynamics, which showed that the W212A substitution led to reduced affinity for cellobiose in the +1 and +2 binding sites due to rearrangement of key cellobiose-binding residues.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1986

Increased Spectral Response for Charge-Coupled Devices

Significant improvement in charge-coupled-device (CCD) spectral sensitivity is demonstrated over remarkable range. Improvement in quantum efficiency, in conjunction with CCD low-read-noise floor (less than 4e) opens up new scientific opportunities in fields of biology, nuclear science, laboratory plasma diagnositcs, and host of other physical and astronomical applications in the UV, X-UV, and X-ray regimes.

Janesick, J. R.↗
DOE OSTI2024

Structure of a biohybrid photosystem I-platinum nanoparticle solar fuel catalyst

Biohybrid solar fuel catalysts leverage natural light-driven enzymes to produce valuable fuel products. One useful biological platform for such a system is photosystem I, a pigment-protein complex that captures sunlight and converts it into chemical energy with near unity quantum efficiency, which generates low potential reducing equivalents for metabolism. Realizing and understanding the molecular basis for an approach that utilizes those electrons and stores solar energy as a fuel is therefore appealing. Here, we report the 2.27-Å global resolution cryo-EM structure of a photosystem I complex with bound platinum nanoparticles that catalyzes light-driven H 2 production. The platinum nanoparticle binding sites and possible stabilizing interactions are described. Overall, the investigation reveals a direct structural look at a photon-to-fuels photosynthetic biohybrid system.

59 BASIC BIOLOGICAL SCIENCES↗