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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The origin and evolution of viruses inferred from fold family structure

The canonical frameworks of viral evolution describe viruses as cellular predecessors, reduced forms of cells, or entities that escaped cellular control. The discovery of giant viruses has changed these standard paradigms. Their genetic, proteomic and structural complexities resemble those of cells, prompting a redefinition and reclassification of viruses. In a previous genome-wide analysis of the evolution of structural domains in proteomes, with domains defined at the fold superfamily level, we found the origins of viruses intertwined with those of ancient cells. In this review, we extend these data-driven analyses to the study of fold families confirming the co-evolution of viruses and ancient cells and the genetic ability of viruses to foster molecular innovation. The results support our suggestion that viruses arose by genomic reduction from ancient cells and validate a co-evolutionary ‘symbiogenic’ model of viral origins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Distinguishing Electron and Hole Dynamics in Functionalized CdSe/CdS Core/Shell Quantum Dots Using Complementary Ultrafast Spectroscopies and Kinetic Modeling

The evolution of excitation energy and photogenerated charges in semiconductor quantum dots (QDs) functionalized with molecular acceptors can be probed on ultrafast time scales using techniques such as transient absorption (TA) spectroscopy. However, historical interpretations that the 1S(e)-1S 3/2 (h) transition in Cd-chalcogenide QDs is fully attributable to electrons may be misleading, and multiexponential models used to fit TA kinetics do not correspond directly to specific photophysical processes. Here, we present visible-wavelength and mid-IR TA and time-resolved photoluminescence measurements to inform a comprehensive kinetic model of the photoexcited CdSe/CdS core/shell QDs functionalized with passivating oleic acid (OA), hole-accepting ferrocene, or electron-accepting naphthalene bisimide (NBI). We show that ~30% of the 1S signal and 72% of the IR signal can originate from holes in well-passivated core/shell QDs. We also demonstrate evidence of electron trapping in OA-capped core/shell QDs, with additional electron transfer and hole trapping in the QDs functionalized with NBI. Electron (hole) trapping and detrapping occur in 450 ± 100 ps (430 ± 70 ps) and 340 ± 100 ps (1.1 ± 0.4 ns) respectively, while the time constant for electron transfer to NBI is ~1.8 ns. The comprehensive picture of photophysical processes provided by the complementary ultrafast techniques and kinetic modeling can accelerate both the fundamental science and application development of nanostructured and molecular systems.

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

Target Affinity and Structural Analysis for a Selection of Norovirus Aptamers

Aptamers, single-stranded oligonucleotides that specifically bind a molecule with high affinity, are used as ligands in analytical and therapeutic applications. For the foodborne pathogen norovirus, multiple aptamers exist but have not been thoroughly characterized. Consequently, there is little research on aptamer-mediated assay development. This study characterized seven previously described norovirus aptamers for target affinity, structure, and potential use in extraction and detection assays. Norovirus-aptamer affinities were determined by filter retention assays using norovirus genotype (G) I.1, GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney virus-like particles. Of the seven aptamers characterized, equilibrium dissociation constants for GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney ranged from 71 ± 38 to 1777 ± 1021 nM. Four aptamers exhibited affinity to norovirus GII.4 strains; three aptamers additionally exhibited affinity toward GII.3 and GI.7. Aptamer affinity towards GI.1 was not observed. Aptamer structure analysis by circular dichroism (CD) spectroscopy showed that six aptamers exhibit B-DNA structure, and one aptamer displays parallel/antiparallel G-quadruplex hybrid structure. CD studies also showed that biotinylated aptamer structures were unchanged from non-biotinylated aptamers. Finally, norovirus aptamer assay feasibility was demonstrated in dot-blot and pull-down assays. This characterization of existing aptamers provides a knowledge base for future aptamer-based norovirus detection and extraction assay development and aptamer modification.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1985

The search for extraterrestrial life: Recent developments; Proceedings of the Symposium, Boston University, MA, June 18-21, 1984

The conference presents papers on the history of the search for extraterrestrial life, the scientific rationale and methods used in the search for other planetary systems, the detection of distant planets with the Space Telescope, planetary searches using optical astrometric interferometers, and infrared spectral identification of complex organic molecules in interstellar grains. Also considered are universal protein ancestors from hydrogen cyanide and water, astronomical sources of polarized light and their role in determining molecular chirality on earth, the universal diagrams and life in the universe, the precambrian evolution of terrestrial life and a thermodynamic approach to the occurrance and appearance of galactic life forms. Papers are also presented on the Ohio Seti program, lunar reflections of terrestrial radio leakage, the multichannel spectrum analyzer, software implementation of detection algorithms for the MCSA, the Serendip II design, galactic colonization and competition in a young galactic disk, implications of ancient and future migrations, extraterrestrial intelligence, the ineviability and the possible structures of supercivilizations, planetary, interplanetary and interstellar organic matter, and universal aspects of biological evolution.

Papagiannis, M. D.↗
NASA NTRS1989

Computer simulation of dust grain evolution

The latest results are reported from a Monte Carlo code that is being developed at NASA Ames. The goal of this program, is to derive from the observed and presumed properties of the interstellar medium (ISM) the following information: (1) the size spectrum of interstellar dust; (2) the chemical structure of interstellar dust; (3) interstellar abundances; and (4) the lifetime of a dust grain in the ISM. Presently this study is restricted to refractory interstellar material, i.e., the formation and destruction of ices are not included in the program. The program is embedded in an analytic solution for the bulk chemical evolution of a two-phase interstellar medium in which stars are born in molecular clouds, but new nucleosynthesis products and stellar return are entered into a complementary intercloud medium. The well-mixed matter of each interstellar phase is repeatedly cycled stochastically through the complementary phase and back. Refractory dust is created by thermal condensation as stellar matter flows away from sites of nucleosynthesis such as novae and supernovae and/or from the matter returned from evolved intermediate stars. The history of each particle is traced by standard Monte Carlo techniques as it is sputtered and fragmented by supernova shock waves in the intercloud medium. It also accretes an amorphous mantle of gaseous refractory atoms when its local medium joins with the molecular cloud medium. Finally it encounters the possibility of astration (destruction by star formation) within the molecular clouds.

Liffman, K.↗
NASA NTRS1992

The temporal evolution of the ionospheric signatures of subauroral ion drifts

The effects of an imposed westward plasma drift on O(+) and molecular ion behavior in the nightside ionosphere are investigated using a model of the ionosphere and plasmasphere. A closed subauroral tube of the plasma is considered, and the velocity input persists for 30 min. The rapid increase in the F-region ion temperature resulting from ion-neutral frictional heating causes an immediate surge in the O(+) field-aligned velocity, upwards in the topside ionosphere and downwards below the F2-peak, but after about 10 min into the event the surge in the topside disappears. After the event there is a return flow of O(+) from the plasmasphere. The relative abundance of O(+) decreases during the event due to the increased rate of conversion of O(+) into NO(+) and O2(+); the decrease is more marked for greater values of the imposed westward ion drift. The implications of these results for satellite observations of subauroral ion drifts events and on EISCAT incoherent scatter radar observations of ion heating events is discussed.

Moffett, R. J.↗
NASA NTRS2023

STXM-C-XANES, IR Microspectroscopy, and Raman Microspectroscopy Analysis of Organic Matter in the Chwichiya 002 C3.00-Ungrouped Chondrite

Chwichiya 002 is a C3.00-ungrouped carbonaceous chondrite discovered in Western Sahara in 2018. The presence of hydrated phases in Chwichiya 002 was not confirmed by XRD analysis, and only a faint water and Si-O band attributed to phyllosilicate were observed by infrared transmission spectroscopy, indicating a very low degree of aqueous alteration (Meteoritical Bulletin, 2020). The structural order of polycyclic aromatic hydrocarbons evaluated by Raman spectroscopy indicates that the effect of thermal metamorphism is less severe than in the Semarkona meteorite, an LL3.00 ordinary chondrite (Meteoritical Bulletin, 2020). Chiwichiya 002 is a very primitive carbonaceous chondrite and an important information source for the early stage of the evolution of organic matter in the solar system. In this study, we investigated the molecular structure and distribution of organic matter in Chiwichiya 002 by Carbon X-ray Absorption Near Edge Structure (C-XANES) analysis using a Scanning Transmission X-ray Microscope (STXM). The STXM-C-XANES analysis has a spatial resolution of 20~100 nm and can observe the spatial distribution of organic materials in microstructures. In addition, to investigate the degree of thermal metamorphism of the organic matter, micro-IR, and micro-Raman spectroscopic analyses were performed. In addition, the Murchison CM2 chondrite was also analyzed for comparison. To evaluate contamination during analytical procedures, antigorite, which was heated in air at 500°C for 5 hours to eliminate organic matter was also analyzed in the same manner. The samples were milled into 100 nm-thick, thin sections using a Focused Ion Beam (FIB), and C-XANES spectra were obtained using the STXM at the High Energy Accelerator Research Organization, Photon Factory (PF), BL-19B. The obtained C-XANES spectra were smoothed and then fitted with Gaussian functions using the method of Le Guillou et al. (2018). The C-XANES showed that the ratio of oxygenated functional group (ketone, phenolic) carbons in Chwichiya 002 was lower than in Murchison, whereas the ratio of aliphatic carbons was almost the same. This may reflect the low degree of aqueous alteration of Chwichiya 002. In addition, contamination peaks were detected at 287.3-287.7 eV and 288.3-288.7 eV in the C-XANES spectra of some of the antigorite samples. The source of these peaks is under investigation. Raman spectroscopic analysis showed that the intensity ratio of the D band to the G band of Chwichiya 002 was slightly higher than that of Murchison. IR absorption spectra showed aromatic absorption at 1630 cm -1 , but there was little absorption due to aliphatic C-H around 2900 cm -1 . These results suggest that the organic matter in Chwichiya 002 may be more heated than in Murchison.

Chwichiya 002↗
DOE OSTI2020

Optimal control of coupled quantum systems based on the first-order Magnus expansion: Application to multiple dipole-dipole-coupled molecular rotors

This paper presents a method for performing approximate optimal control simulations for quantum systems with multiple coupled degrees of freedom. In this work, the time evolution is simulated using the first-order Magnus expansion in the interaction picture, where the couplings between different degrees of freedom are treated as the perturbation. A numerical implementation procedure is presented that leverages upon pairwise couplings and the separability of the zeroth-order time evolution operator to achieve a reduced computational cost, which is analyzed with respect to the number of degrees of freedom. The formulation is compatible with gradient-free methods to optimize the control field, and a stochastic hill climbing algorithm is adopted for this purpose. As illustrations, optimal control simulations are performed for systems of two and three dipole-dipole-coupled molecular rotors under the influence of a control field. For the two-rotor system, the field is optimized to achieve either orientation or entanglement objectives. For the three-rotor system, the field is optimized either to orient all three rotors in the same direction or to orient one rotor in a particular direction while the other two rotors point in the opposite direction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Spatial influence of paramagnetic molecules on magnetic tunnel junction-based molecular spintronic devices (MTJMSD)

Magnetic Tunnel Junction-Based Molecular Spintronic Devices (MTJMSDs) are potential candidates for inventing highly correlated systems. Understanding MTJMSD's magnetic behavior is essential to designing and fabricating practical devices. This paper investigates the effect of two contributing factors on MTJMSD's magnetic properties via Monte Carlo Simulation. Here, we have systematically studied coupling strengths and nature between magnetic molecules and ferromagnetic electrodes at various temperatures. We have also investigated the effect of length and thickness increase on MTJMSD temporal and spatial evolution of magnetic moment, magnetic correlation, and magnetic susceptibility. Our results showed that thermal energy increase significantly affects molecular devices.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Effects of dimensionality on the electronic structure of Ruddlesden-Popper chromates Sr n+1 ⁢Cr n ⁢O 3⁢n+1

Transition-metal oxides host a wide variety of electronic phenomena that can be significantly influenced by the effective dimensionality of the system under consideration. These include charge, spin, and orbital orderings, as well as unconventional superconductivity. In this context, the Ruddlesden-Popper chromates Sr n+1 Cr n O 3n+1 emerge as a particularly intriguing series of materials. Formally, the chromium atom displays a rather special 4+ oxidation state throughout the entire series. However, the effective dimensionality changes from quasi-2D to 3D as n increases from 1 to ∞. As a result, the insulating antiferromagnetic behavior observed for n = 1, 2, 3 transforms into itinerant antiferromagnetism with reduced transition temperature for the n = ∞ end member of the series, i.e., the perovskite SrCrO 3 . Further, distinct orbital orderings with exotic singlet states have been predicted for these systems. However, the lack of single-crystal bulk or thin-film samples has made experimental progress difficult. Here we demonstrate the synthesis of thin films of the perovskite SrCrO 3 and the associated layered chromates via oxide molecular beam epitaxy for n = 1 to n = 5. Our electrical transport measurements reveal a gradual evolution from a strongly insulating state in Sr 2 CrO 4 to a metallic state in the end member SrCrO 3 . X-ray absorption spectroscopy measurements demonstrate a varying hybridization strength of the Cr 4+ valence electrons across the series, helping to explain the trend in conduction. Finally, density functional theory calculations further confirm the observed transport trend and identify additional distortions present in the system.

36 MATERIALS SCIENCE↗
NASA NTRS1994

Investigations of the dynamical evolution of protoplanetary nebulae

The spectral energy distributions (SED's) of all the known Class I (protostellar) sources in the Taurus molecular cloud were modelled. The Tereby, Shu, & Cassen (1984, TSC) density distribution for a rotating, infalling envelope was adopted. The radiative equilibrium temperature distribution from the spherical average of the TSC density distribution was calculated. The resulting spherically-symmetric temperature distribution then provides the source function to obtain the emergent spectrum at a given inclination angle i from the formal solution of the transfer equation, using the exact density (opacity) distribution. Results showed that the SED's of the protostar candidates in Taurus can be reproduced with TSC models having infall rates close to the values predicted by the theory of isothermal cloud collapse. Flat Spectrum T Tauri Stars were studied. The mid- to far-infrared fluxes of 'flat spectrum' T Tauri stars can be explained by radiative equilibrium emission from infalling dusty envelopes. This explanation indicated that models employing 'active' disks, in which the temperature distribution is a parameterized power law, should be invoked with caution. Infall also naturally explains the scattered light nebulae detected around many flat-spectrum sources. Results showed that the SED's of the protostar candidates in Taurus can be reproduced with TSC models having infall rates close to the values predicted by the theory of isothermal cloud collapse. Flattened infalling envelope models are also being studied.

Hartmann, Lee W.↗
DOE OSTI2023

Disentangling the evolution of electrons and holes in photoexcited ZnO nanoparticles

The evolution of charge carriers in photoexcited room temperature ZnO nanoparticles in solution is investigated using ultrafast ultraviolet photoluminescence spectroscopy, ultrafast Zn K-edge absorption spectroscopy, and ab initio molecular dynamics (MD) simulations. The photoluminescence is excited at 4.66 eV, well above the band edge, and shows that electron cooling in the conduction band and exciton formation occur in <500 fs, in excellent agreement with theoretical predictions. The x-ray absorption measurements, obtained upon excitation close to the band edge at 3.49 eV, are sensitive to the migration and trapping of holes. They reveal that the 2 ps transient largely reproduces the previously reported transient obtained at 100 ps time delay in synchrotron studies. In addition, the x-ray absorption signal is found to rise in ∼1.4 ps, which we attribute to the diffusion of holes through the lattice prior to their trapping at singly charged oxygen vacancies. Indeed, the MD simulations show that impulsive trapping of holes induces an ultrafast expansion of the cage of Zn atoms in <200 fs, followed by an oscillatory response at a frequency of ∼100 cm−1, which corresponds to a phonon mode of the system involving the Zn sub-lattice.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Fermentation Practices Select for Thermostable Endolysins in Phages

Endolysins are produced by (bacterio)phages and play a crucial role in degrading the bacterial cell wall and the subsequent release of new phage progeny. These lytic enzymes exhibit a remarkable diversity, often occurring in a multimodular form that combines different catalytic and cell wall-binding domains, even in phages infecting the same species. Yet, our current understanding lacks insight into how environmental factors and ecological niches may have influenced the evolution of these enzymes. In this study, we focused on phages infecting Streptococcus thermophilus, as this bacterial species has a well-defined and narrow ecological niche, namely, dairy fermentation. Among the endolysins found in phages targeting this species, we observed limited diversity, with a singular structural type dominating in most of identified S. thermophilus phages. Within this prevailing endolysin type, we discovered a novel and highly conserved calcium-binding motif. This motif proved to be crucial for the stability and activity of the enzyme at elevated temperatures. Ultimately, we demonstrated its positive selection within the host's environmental conditions, particularly under the temperature profiles encountered in the production of yogurt, mozzarella, and hard cheeses that rely on S. thermophilus.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2019

High-Resolution Mid-Infrared Molecular Line Survey of the Orion Hot Core

The basic building blocks of life are synthesized in space as part of the natural stellar evolutionary cycle, whereby elements ejected into the interstellar medium by dying stars are incorporated back into the dense clouds, which form the next generation of stars and planets. The formation of stars and planets are fundamental to the evolution of matter in the Universe as complex molecules are created and destroyed during this step. Understanding these processes will allow us to answer “What is the relation between the molecules we see in the ISM and the molecular inventory of Earth and the terrestrial planets in the Solar System?” Measuring and cataloging the inventory of organic molecules and understanding their evolution requires observations over a broad wavelength range (IR, MIR, FIR, (sub)mm, and radio) to cover all stages of this evolutionary cycle needed to link interstellar material to that delivered to planets. High-resolution molecular line surveys provide chemical inventories for star forming regions and are essential for studying their chemistry, kinematics and physical conditions. Previous high spectral resolution surveys have been limited to radio, sub-mm and FIR wavelengths; however, Mid-infrared observations are the only way to study symmetric molecules that have no dipole moment and thus cannot be detected in the (sub)mm line surveys from ALMA. Past midinfrared missions such as ISO and Spitzer had low to moderate resolving power that were only able to link broad features with particular molecular bands and could not resolve the individual rovibrational transitions. JWST will provide exceptional sensitivity in the MIR, but will also not have sufficient spectral resolution, which can lead to confusion in identifying the contribution from strong to moderate strength molecular species. We present new results from an on-going high resolution (R ~ 60,000) line survey of the Orion hot core between 12.5 - 28.3 μm and 7 - 8 μm, using the EXES instrument on the SOFIA airborne observatory. SOFIA's higher-resolution and smaller beam compared to ISO allows us to spatially and spectrally isolate the emission towards the hot core. This survey will provide the best infrared measurements (to date) of molecular column densities and physical conditions, providing strong constraints on the current chemical network models for star forming regions. This survey will greatly enhance the inventory of resolved line features in the MIR, making it an invaluable reference to be used by the JWST and ALMA scientific communities.

Rangwala, Naseem↗
NASA NTRS1994

The early evolution of life: solution to Darwin's dilemma

Recent studies of Precambrian fossils indicate that life on Earth originated earlier than assumed, microscopic life was prevalent in the Precambrian Eon, the tempo and mode of evolution during the Precambrian period were different from other periods, and that only the Precambrian fossil record can be used as evidence of early life. Implications for future research include directing the search for the origin of life away from the geological record, modification of hypotheses about molecular change, use of Precambrian microfossils in dating younger geological units, and progress in defining the nature of major events in early evolution.

Non-NASA Center↗
DOE OSTI2023

Unfaulting mechanisms of interstitial Frank loops in fluorite-structured ThO 2

Unfaulting of Frank loops in irradiated fluorite-structured oxides is of significance for understanding microstructural evolution. However, the mechanisms have not yet been directly observed. To this end, we utilize molecular dynamics to reveal the atomistic details related to the unfaulting process of interstitial Frank loops in ThO 2 , which involve a single pair or multiple pairs of co-propagating Shockley partials to annihilate the stacking faults. Here, we find that the unfaulting is achieved via a synchronous shear of the partial pairs to remove the extrinsic stacking fault in the cation sublattice and the intrinsic stacking fault in the anion sublattice. The high mobility of oxygen at the dislocation core may reduce the activation barriers of dislocation nucleation and migration. These findings provide a fundamental understanding of the transformation of faulted loops in irradiated ThO 2 , and could be transferable to other fluorite-structured oxides.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Time-Evolving Chirality Loss in Molecular Photodissociation Monitored by X-ray Circular Dichroism Spectroscopy

In this work, the ultrafast photoinduced chirality loss of 2-iodobutane is studied theoretically by time- and frequency-resolved X-ray circular dichroism (TRXCD) spectroscopy. Following an optical excitation, the iodine atom dissociates from the chiral center, which we capture by quantum non-adiabatic molecular dynamics simulations. At variable time delays after the pump, the resonant X-ray pulse selectively probes the iodine and carbon atom involved in the chiral dissociation through a selected core-to-valence transition. The TRXCD signal at the iodine L 1 edge accurately captures the timing of C–I photodissociation and thereby chirality loss, c.a 70 fs. The strong electric dipole–electric quadrupole (ED–EQ) response makes this signal particularly sensitive to vibronic coherence at the high X-ray regime. At the carbon K-edges, the signals monitor the molecular chirality of the 2-butyl radical photoproduct and the spin state of the iodine atom. The ED–EQ response is masked under the strong electric dipole-magnetic dipole response, making this signal intuitive for the electronic population. The evolution of the core electronic states and its chiral sensitivity is discussed. Overall, the element-specific TRXCD signal provides a detailed picture of molecular dynamics and offers a unique sensitive window into the time-dependent chirality of molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗