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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Table-Top High Photon Energy Sources for Chemical Dynamics Investigations

Time-resolved spectroscopies using high-energy photons in the vacuum ultraviolet (VUV) to the X-ray region of the electromagnetic spectrum, have proven to be powerful probes of chemical dynamics. These high-energy photons can access valence and core orbitals of molecules and materials, providing key information on molecular and electronic structure and their time evolution. This report details the development of table-top sources of extreme ultraviolet (XUV) and VUV pulses at Sandia National Laboratories for use in studies of gas phase chemical dynamics. Femtosecond duration XUV pulses are produced using laser-driven high harmonic generation and their detected range span ~40-140 eV photon energies. These pulses are used in conjunction with ultraviolet pulses in a pump-probe scheme to study excited state dynamics of gas phase molecules. VUV pulses at 7.75 eV are generated using a four-wave-mixing scheme driven by 800 nm and 266 nm pulses in an argon-filled hollow-core fiber.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1967

Chemical evolution

Chemical evolution and geologic history of earth, and molecular structures of organic compounds

Calvin, M.↗
NASA NTRS1999

Archaea: From Genomics to Physiology and the Origin of Life

This document represents a report on a meeting about Archaea. The meeting had an unusually diversified mix of topics all related to Archaea highlighting their differences and similarities with other kingdoms of life. Thus, a large number of scientists from others areas of biology participated in this conference. One-third of the speakers (11 of 33) represented laboratories whose main interests have not been archaea and who have not previously participated in similar symposia or workshops. Thus, this symposium provided a unique opportunity for archaeal researchers to interact in a wider forum. Because of the broad range of topics covered, the conference also introduced many of the participants to new areas of archaeal research. The discussions of genomics, molecular mechanisms of transcription, metabolic pathways and evolution were at a very high level. Talks and posters provided detailed discussions of the state of the current knowledge in RNA processing, transcriptional initiation, chromatin structure, aminoacyl-tRNA synthetases, autotrophic CO2 fixation, Upid biosynthesis and a wide range of other topics. In addition to providing overviews, major areas of scientific argument were clearly delineated, particularly in the discussions of genomics and evolution. Some of the questions raised included: how representative are individual gene trees of organismal evolution, how prevalent is horizontal evolution, how reliable are functional assignments in genomics? On these topics, the different points of view were well represented. The future of any field depends on the enthusiasm and intellectual engagement of young scientists working in the area. Therefore, the participation of 29 graduate and postdoctoral students (out of about 135 participants) was a highlight of the meeting. This was the consequence of funding contributions by NSF and NASA.

Vothknecht, Ute C.↗
NASA NTRS2003

Membrane-Based Functions in the Origin of Cellular Life

How simple membrane peptides performed such essential proto-cellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we investigate how these peptides insert into membranes, self-assemble into higher-order structures and acquire functions. We have studied the insertion of an a-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)S into a model membrane. The transmembrane state is metastable, and approximately 15 kcal/mol is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)S and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self- assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to reengineering the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.

Wilson, Michael A.↗
NASA NTRS2003

Membrane peptides and their role in protobiological evolution

How simple membrane peptides performed such essential protocellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we explain how these peptides fold at water-membrane interfaces, insert into membranes, self-assemble into higher-order structures and acquire functions. We have investigated the interfacial behavior and folding of several peptides built of leucine and glutamine residues and have demonstrated that many of them tend to adopt ordered structures. Further, we have studied the insertion of an alpha-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)3 into a model membrane. The transmembrane state is metastable, and approximately 15 kcal mol(-1) is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)3 and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self-assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to re-engineer the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.

Models, Chemical↗
DOE OSTI2023

WISDOM project – XVIII. Molecular gas distributions and kinematics of three megamaser galaxies

ABSTRACT The co-evolution of galaxies and supermassive black holes (SMBHs) underpins our understanding of galaxy evolution, but different methods to measure SMBH masses have only infrequently been cross-checked. We attempt to identify targets to cross-check two of the most accurate methods, megamaser, and cold molecular gas dynamics. Three promising galaxies are selected from all those with existing megamaser SMBH mass measurements. We present Atacama Large Millimeter/sub-millimeter Array (ALMA) 12CO (2–1) and 230-GHz continuum observations with angular resolutions of ≈0${_{.}^{\prime\prime}}$5. Every galaxy has an extended rotating molecular gas disc and 230-GHz continuum source(s), but all also have irregularities and/or non-axisymmetric features: NGC 1194 is highly inclined and has disturbed and lopsided central 12CO (2–1) emission; NGC 3393 has a nuclear disc with fairly regular but patchy 12CO (2–1) emission with little gas near the kinematic major axis, faint emission in the very centre, and two brighter structures reminiscent of a nuclear ring and/or spiral; NGC 5765B has a strong bar and very bright 12CO (2–1) emission concentrated along two bisymmetric offset dust lanes and two bisymmetric nuclear spiral arms. 12CO (2–1) and 12CO (3–2) observations with the James Clerk Maxwell Telescope are compared with the ALMA observations. Because of the disturbed gas kinematics and the impractically long integration times required for higher angular resolution observations, none of the three galaxies is suitable for a future SMBH mass measurement. None the less, increasing the number of molecular gas observations of megamaser galaxies is valuable, and the ubiquitous disturbances suggest a link between large-scale gas properties and the existence of megamasers.

Liang, Fu-Heng (ORCID:0000000324961247)↗
DOE OSTI2025

Convergent evolution of NFP -facilitated root nodule symbiosis

The origin and phylogenetic distribution of symbiotic associations between nodulating angiosperms and nitrogen-fixing bacteria have long intrigued biologists. Recent comparative evolutionary analyses have yielded alternative hypotheses: a multistep pathway of independent gains and losses of root nodule symbiosis vs. a single gain followed by numerous losses. A detailed reconstruction of the history of genes involved in signaling between nitrogen-fixing bacteria and potential hosts, particularly lipo-chitooligosaccharide (LCO) signaling, is needed to distinguish between these hypotheses. LCO recognition by plants involves the Nod Factor Perception ( NFP ) gene family; in the legume model Medicago truncatula (Fabales), MtNFP is essential for establishing rhizobial symbiosis. Here, we document convergent evolution of NFP , indicating multiple origins of LCO-driven symbiosis. In contrast to previous models that explain the recruitment of NFP via a single duplication in the ancestor of the nitrogen-fixing clade, our phylogenomic and synteny results suggest this duplication does not span the entire clade. Tandem duplication in a common ancestor of Cucurbitales and Rosales resulted in the NFP1 and NFP2 groups. In contrast, the phylogenetically closest paralog of MtNFP is MtLYR1 , located on a different chromosome within a large syntenic block. All available data indicate that a large-scale duplication resulted in MtNFP and MtLYR1 , likely corresponding to a whole-genome duplication in an ancestor of subfamily Papilionoideae of Fabaceae. We show that MtNFP and the NFP2 -like group are not orthologous, indicating multiple independent gains of NFP -based LCO signaling. This molecular convergence provides a possible mechanism for multiple gains of root nodule symbiosis across the nitrogen-fixing clade.

LCO signaling↗
DOE OSTI2023

An idealized model for collapse of a molecular core within a filament

Here, we present an analytic treatment of the self-similar collapse of a uniform density ellipsoid to linear order in the deviations from sphericity. First we obtain a self-consistent closed-form solution for the evolution of an isolated ellipsoid and then impose the effects of an external forcing. This model describes the evolution under gravity of a pre-stellar core of molecular gas embedded in a much larger and lower-density filament. We compare with numerical solutions for the collapse without the limitation of small deviations. These show how the external perturbing force producing the initial deviation from sphericity is eventually surpassed by the anisotropic forces generated by the collapsing ellipsoid itself. This model should be useful in interpreting the way in which environment shapes the evolution of pre-stellar cores.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2005

From Astrochemistry to Astrobiology

Tremendous strides have been made in our understanding of interstellar material over the past twenty five years thanks to significant developments in observational astronomy and laboratory astrophysics. Twenty years ago the composition of interstellar dust was largely guessed at, the concept of ices in dense molecular clouds ignored, and the notion of large, abundant, gas phase, carbon-rich molecules widespread throughout the interstellar medium (ISM) considered impossible. Today the composition of interstellar dust is reasonably well understood. In molecular clouds, the birthplace of stars and planets, these cold dust particles are coated with mixed molecular ices whose composition is very well constrained. Lastly, the signature of carbon-rich polycyclic aromatic hydrocarbons (PAHs), shockingly large molecules by early interstellar chemistry standards, is widespread throughout the Universe. The first part of this talk will describe how infrared spectroscopic studies of interstellar space, combined with laboratory simulations of interstellar ice chemistry, have revealed the widespread presence of interstellar PAHs and the composition of interstellar ices, the building blocks of comets. The remainder of the presentation will focus on the photochemical evolution of these materials and astrobiology. Within a molecular cloud, and especially the presolar nebula, materials frozen into the ices are photoprocessed by ultraviolet light and produce more complex molecules. As these materials are the building blocks of comets and related to carbonaceous micrometeorites, they are likely to have been important sources of complex materials delivered to the early Earth and their composition may be related to the origin of life.

Allamandola, L. J.↗
DOE OSTI2023

A High-Speed Rotational Diamond Anvil Cell for In Situ Analysis of Hierarchical Microstructural Evolution of Metallic Alloys during Extreme Shear Deformation

High speed shear deformation is ubiquitous in engineering applications, ranging from material processing methods such as friction stir processing/extrusion and in tribological contacts. However, analyzing the microstructural evolution of materials while they are undergoing high speed shear deformation have been a long-standing challenge. This led to predominant reliance on ex situ microscopy before and after shear deformation. But ex situ microscopy lacks the ability to analyze dynamic and transient hierarchical microstructural evolution mechanisms that could occur during shear deformation of materials. Therefore, to better understand the dynamic mechanisms of mass and energy transfer in materials under shear deformation, we developed a first of its kind high-speed rotational diamond anvil cell (HS-RDAC) for synchrotron-based in situ high-energy x-ray diffraction (XRD). We studied the time resolved lattice strain evolution, XRD peak broadening and changes in spatial variation of shear deformation induced alloying in pure metal and metal alloy sheets and powder mixture using the HS-RDAC. These in situ results were combined with detailed ex situ microstructural characterization before and after the shear deformation using transmission electron microscopy and atom probe tomography, which revealed the different stages of evolution of a shear deformation induced hierarchical nanostructure. Multiscale computational simulations including computational fluid dynamics, crystal plasticity, molecular dynamic simulation and density functional theory uncovered the mechanisms behind morphological changes, evolution of defect structures and changes in driving force for shear deformation induced intermixing. In conclusion, this in situ HS-RDAC capability, in combination with ex situ microstructural characterization and computational simulations, can provide new insights into the hierarchical microstructural evolution pathway during shear deformation.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Microstructural and phase changes in alpha uranium investigated via in-situ studies and molecular dynamics

A deeper knowledge of thermally induced microstructural and phase evolution in nuclear metallic fuel can be obtained using novel in-situ microscopic analyses. Such studies can provide information on the dynamics of phase transitions which is not possible with conventional postmortem characterization (post-irradiation examination). In this work, the behavior of alpha uranium (α-U) was investigated via in-situ heating tests in a transmission electron microscope. Here, the main objective is to understand the microstructural and phase changes, such as defect annihilation and ß phase formation and retention, observed in reactor in-pile transient studies at the Transient Reactor Test facility. Indeed, defect migration and rearrangement were observed within the α phase starting at 673 K; α→ß phase transition was observed between 773 K and 1,073 K during the heating ramp (which is in the temperature window reported for α→ß transition temperatures). Recrystallization and formation of nano grains was observed at high temperatures (over 1,073 K). Such recrystallization was possibly related to the formation of the γ phase. Finally, it was indeed observed that the ß phase (but not γ phase) was retained at room temperature upon rapid cooling. Molecular dynamics studies support these experimental results and shows that the γ phase of pure uranium cannot be retained at room temperature if not stabilized with the addition of an alloying element.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
NASA NTRS1991

The nature, origin and evolution of embedded star clusters

The recent development of imaging infrared array cameras has enabled the first systematic studies of embedded protoclusters in the galaxy. Initial investigations suggest that rich embedded clusters are quite numerous and that a significant fraction of all stars formed in the galaxy may begin their lives in such stellar systems. These clusters contain extremely young stellar objects and are important laboratories for star formation research. However, observational and theoretical considerations suggest that most embedded clusters do not survive emergence from molecular clouds as bound clusters. Understanding the origin, nature, and evolution of embedded clusters requires understanding the intimate physical relation between embedded clusters and the dense molecular cloud cores from which they form.

Lada, Charles J.↗
NASA NTRSDate not supplied

Low-Temperature Production of Cosmic Grains Analogs From Gas-Phase Molecular Precursors with the NASA Ames' COSmIC Facility

Complex carbon molecules and ions are ubiquitous in space and form the building blocks of carbonaceous cosmic dust grains, ultimately contributing to the formation of planets. Here, we report the first experimental investigations of the low temperature chemical pathways leading to the production of cosmic grain analogs from gas phase molecular precursors in order to better understand the evolution of cosmic carbon. The experiments were performed using the COsmic SImulation Chamber (COSmIC) to generate and characterize grains formed from gas phase precursors under controlled conditions representative of astrophysical environments [1]. Using COSmIC, it is possible to investigate the evolution of cosmic carbon from the formation of neutral and ionized gas phase hydrocarbons and PAHs [2], to carbon grains [3, 4]. This is achieved by using a discharge nozzle to (1) produce an adiabatic jet expansion and cool down Ar-hydrocarbon/PAH gas mixtures to astrophysically relevant temperature (150 K) before inducing chemistry by generating a plasma discharge in the stream of the expansion. This plasma-induced chemistry results in the formation of complex molecules and solid particles, analogs of cosmic grains. Solid grains are produced in-situ in the plasma expansion, carried by the accelerated gas in the expansion, and collected on substrates placed a few centimeters downstream of the electrodes. The results of a preliminary solid phase ex-situ analysis of cosmic grain analogs produced at low temperature in COSmIC from gas mixtures including molecular precursors of cosmic carbon grains, i.e., such as CH4 and C2H2 found in circumstellar ejecta of late C stars [3] as well as PAHs ubiquitously detected in IR emission bands seen in galactic and extragalactic environments [4] will be discussed. Scanning Electron Microscopy imaging was used to provide insight on the morphology and growth structure of the grains produced in COSmIC, and to investigate how the precursors used to produce the grains affect these parameters [3]. Laser desorption mass spectrometry was used to identify the molecules making up the main structures within the condensed grains [4]. NIR to FIR optical properties are characterized to provide critical information (functional groups, optical constants) to the scientific community, for use in radiative transfer models in particular, and to help decipher and enhance the return data from space observations.

F. Salama↗
DOE OSTI2026

Syngas Production at Si Hybrid Photoelectrodes Modified with Re(I) and Mn(I) Tricarbonyl Phenanthroline Complexes Containing Reactive Aryl Azide Groups

We installed molecular CO 2 reduction (CO 2 R) catalysts directly onto Si (photo)electrodes. The highly reactive M(5-azido-1,10-phenanthroline)(CO) 3 X (where M = Mn or Re, X = Br or Cl) complexes readily bubbled when dissolved in polar organic solvents, in both the presence and absence of an ultraviolet light source. When placed on hydrogen-terminated Si (H-Si) and native silicon oxide (SiOx), similar amounts of the complex were attached to the surface under illumination (367 nm, 50–200 mW/cm 2 ) or in the dark. Surprisingly, these films revealed submonolayer coverages instead of the multilayered structures we expected. DFT analyses support monolayer formation, showing that the triplet-state nitrene of the complex is more energetically favorable than the singlet state. Using controlled-potential electrolysis experiments, we showed that Re- and Mn-containing films on pSi photoelectrodes generated small amounts of CO when exposed to 1 atm of CO 2 and 1 sun illumination. These amounts of CO were an order of magnitude greater than control surfaces, producing 5.59 × 10 –7 mol CO/h for Re(az-phen) and 7.83 × 10 –7 mol CO/h for Mn(az-phen) films. Much of the charge passed at the pSi electrodes was consumed by the competing hydrogen evolution reaction, which we attribute to the low molecular coverage and the presence of native oxide on the electrode surface after attachment. Finally, this work demonstrates the feasibility of reacting azide-containing ligands with Si surfaces. Still, it highlights the need for alternative ligand structures and reaction conditions to form multilayer films.

azides↗
DOE OSTI2022

Structure of the divergent human astrovirus MLB capsid spike

Despite their worldwide prevalence and association with human disease, the molecular bases of human astrovirus (HAstV) infection and evolution remain poorly characterized. Here, we report the structure of the capsid protein spike of the divergent HAstV MLB clade (HAstV MLB). While the structure shares a similar folding topology with that of classical-clade HAstV spikes, it is otherwise strikingly different. We find no evidence of a conserved receptor-binding site between the MLB and classical HAstV spikes, suggesting that MLB and classical HAstVs utilize different receptors for host-cell attachment. We provide evidence for this hypothesis using a novel HAstV infection competition assay. Comparisons of the HAstV MLB spike structure with structures predicted from its sequence reveal poor matches, but template-based predictions were surprisingly accurate relative to machine-learning-based predictions. Our data provide a foundation for understanding the mechanisms of infection by diverse HAstVs and can support structure determination in similarly unstudied systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Modeling laser interactions with aluminum and tantalum targets using a hybrid atomistic-continuum model

A hybrid atomistic-continuum method can model the microstructure evolution of metals subjected to laser irradiation. This method combines classical molecular dynamics (MD) simulations with the two-temperature model (TTM) to account for the laser energy absorption and heat diffusion behavior. Accurate prediction of the temperature evolution in the combined MD-TTM method requires reliable accuracy in electron heat capacity, electron thermal conductivity, and electron–phonon coupling factor across the temperatures generated. This study uses the electronic density of states (DOS) obtained from first-principle calculations. The calculated electron temperature-dependent parameters are used in MD-TTM simulations to study the laser metal interactions in FCC and BCC metals and the phenomenon of laser shock loading and melting. This study uses FCC Al and BCC Ta as model systems to demonstrate this capability. When subjected to short pulsed laser shocks, the dynamic failure behavior predicted using temperature-dependent parameters is compared with the experimentally reported single-crystal and nanocrystalline Al and Ta systems. The MD-TTM simulations also investigate laser ablation and melting behavior of Ta to compare with the ablation threshold reported experimentally. In conclusion, this manuscript demonstrates that integrating the temperature-dependent parameters into MD-TTM simulations leads to the accurate modeling of the laser–metal interaction and allows the prediction of the kinetics of the solid–liquid interface.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Determination of Vibrational Motions Driving Photoinduced Electron Transfer Reactions in Molecular Crystals and Organic Thin Films

The objective of this research is to develop an understanding of how nuclear motions can be used to drive and control photo-induced charge transfer and singlet fission reactions in molecular crystals and thin films. By following the structural evolution of reacting molecules and nanostructures on the timescale of their nuclear motion, we will determine what interplay of nuclear coordinates is most efficient in driving electron transfers, a necessary first step in most photovoltaic and photocatalytic processes. We will identify which nuclear coordinates effectively promote desirable electron transfer processes, or ineffectively dissipate photon energy into unwanted thermal energy, thus guiding the design and implementation of molecular systems tailored for high efficiency processes. Specifically, we aim to identify which nuclear coordinates are responsible for driving electron transfer and singlet fission reactions at different points along the reaction coordinate, particularly in regimes which deviate from Marcus theory predictions. We will do so by investigating systems with electron transfer and singlet fission occurring from non-thermalized states due to strong donor-acceptor electronic coupling. First, we will prove that specific vibrational modes are responsible for charge transfer processes in molecular crystals. Secondly, we will investigate how vibrational coherences and specific nuclear motions can be used to drive high yield singlet fission processes. Finally, we will determine how complex film morphology affects long-range charge transport, a key limiting factor in our ability to make gains in efficiency.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗