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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

PAH101: A GW+BSE Dataset of 101 Polycyclic Aromatic Hydrocarbon (PAH) Molecular Crystals

Abstract The excited-state properties of molecular crystals are important for applications in organic electronic devices. TheGWapproximation and Bethe-Salpeter equation (GW+BSE) is the state-of-the-art method for calculating the excited-state properties of crystalline solids with periodic boundary conditions. We present the PAH101 dataset ofGW+BSE calculations for 101 molecular crystals of polycyclic aromatic hydrocarbons (PAHs) with up to ~500 atoms in the unit cell. To the best of our knowledge, this is the firstGW+BSE dataset for molecular crystals. The data records include theGWquasiparticle band structure, the fundamental band gap, the static dielectric constant, the first singlet exciton energy (optical gap), the first triplet exciton energy, the dielectric function, and optical absorption spectra for light polarized along the three lattice vectors. The dataset can be used to (i) discover materials with desired electronic/optical properties, (ii) identify correlations between DFT andGW+BSE quantities, and (iii) train machine learned models to help in materials discovery efforts.

Science & Technology - Other Topics↗
DOE OSTI2022

PolyDODT: a macrocyclic elastomer with unusual properties

The effect of reaction conditions on the structure of poly(3,6-dioxa-1,8-octanedithiol) (polyDODT) made by Reversible Radical Recombination Polymerization (R3P) using triethylamine (TEA), H 2 O 2 and air was investigated. 800 MHz (1 and 2D) NMR was used to investigate the polymer structures. Sensitivity analysis provided direct evidence for high purity cyclic polyDODT up to M n ~ 100 000 g mol –1 . Here, comparative analysis by High Resolution Multidetector Size Exclusion Chromatography (SEC) using integrated data showed that the cycles had lower viscosity and were more compact (both for R g and R h ) than linear samples of similar molecular weight. However, differential data revealed unusual behavior. While lower molecular weight cyclic polymers eluted later and had lower intrinsic viscosity than their linear counterparts at the same molecular weight, at higher molecular weights the polymers showed strange behavior: both the diffusion coefficient measured by Quasielastic Light Scattering (QELS) and Mark–Houwink–Sakurada plots of intrinsic viscosity for linear and cyclic polyDODT were found to converge. R3P, an aqueous based “green” method is capable of producing polymers at the 10–100 g scale in the lab, which will allow more detailed studies of this new class of biodegradable elastomers so further experimentation can be performed to elucidate the reasons for the unusual findings.

36 MATERIALS SCIENCE↗
DOE OSTI2021

State predictive information bottleneck

We report the ability to make sense of the massive amounts of high-dimensional data generated from molecular dynamics simulations is heavily dependent on the knowledge of a low-dimensional manifold (parameterized by a reaction coordinate or RC) that typically distinguishes between relevant metastable states, and which captures the relevant slow dynamics of interest. Methods based on machine learning and artificial intelligence have been proposed over the years to deal with learning such low-dimensional manifolds, but they are often criticized for a disconnect from more traditional and physically interpretable approaches. To deal with such concerns, in this work we propose a deep learning based state predictive information bottleneck approach to learn the RC from high-dimensional molecular simulation trajectories. We demonstrate analytically and numerically how the RC learnt in this approach is connected to the committor in chemical physics and can be used to accurately identify transition states. A crucial hyperparameter in this approach is the time delay or how far into the future the algorithm should make predictions about. Through careful comparisons for benchmark systems, we demonstrate that this hyperparameter choice gives useful control over how coarse-grained we want the metastable state classification of the system to be. We thus believe that this work represents a step forward in systematic application of deep learning based ideas to molecular simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Laser-induced-fluorescence imaging of a spin-polarized ultracold neutral plasma in a magnetic field

In this work, we report Doppler-sensitive laser-induced-fluorescence (LIF) imaging of an ultracold neutral plasma in a magnetic field. Local values of ion density, hydrodynamic fluid velocity, temperature, and spin polarization are obtained using a fluorescence model based on velocity-resolved rate equations (REs) including the transfer of ions between states due to laser coupling and spontaneous emission. The RE approach captures optical pumping of ions into states that are not driven by the LIF excitation laser, and this is validated with experimental data. Combined molecular-dynamics and quantum-trajectories simulations verify that velocity-changing collisions have a negligible impact on the state population evolution for typical experimental conditions. Relative intensities of Zeeman components of the LIF spectra provide clear evidence that the ions are electron-spin-polarized when created by photoionization of magnetically trapped 88 Sr atoms. This probe opens many possibilities for studying thermal transport and the equilibration of neutral plasmas in overlapping regimes of strong coupling and magnetization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Physical insights into biological memory using phospholipid membranes

Electrical signals may propagate along neuronal membranes in the brain, thus enabling communication between nerve cells. In doing so, lipid bilayers, fundamental scaffolds of all cell membranes, deform and restructure in response to such electrical activity. These changes impact the electromechanical properties of the membrane, which then physically store biological memory. This memory can exist either over a short or long period of time. Traditionally, biological memory is defined by the strengthening or weakening of transmissions between individual neurons. In this report we show that electrical stimulation may also alter the properties of the lipid membrane, thus pointing toward a novel mechanism for memory storage. Furthermore, based on the analysis of existing electrophysiological data, we study molecular mechanisms underlying the long-term potentiation in phospholipid membranes. Finally, we examine possible relationships between the memory capacitive properties of lipid membranes, neuronal learning, and memory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Self-Healing Ceramics and Mechanical Metamaterials

We performed large scale molecular dynamics (MD) simulations and reactive & quantum molecular dynamics simulations to investigate: (1) faceting, grain growth, and crack healing in ceramics; (2) stress-release mechanism and healing in fibers; and (3) mechanical properties of two-dimensional metamaterials. We also designed highly accurate interatomic potentials and forces using artificial neural networks (ANN) and first-principles molecular dynamics simulation data for use in our MD and reactive MD simulations. We demonstrated the efficacy of modeling quantum materials atomistic simulation data using unsupervised deep learning approaches on a quantum computer. These achievements are elaborated in the following sections.

36 MATERIALS SCIENCE↗
DOE OSTI2021

An effective QWBA/UHPLC-MS/tissue punch approach: solving a pharmacokinetic issue via quantitative Met-ID

Methods to provide absolute quantitation of the administered drug and corresponding metabolites in tissue in a spatially resolved manner is a challenging but much needed necessity in pharmaceutical research. Quantitative whole-body autoradiography (QWBA) after a single-dose intravenous (3 mg/kg) and extravascular (30 mg/kg) administrations of an in vitro metabolically stable test compound (structure not reported here) indicated quick tissue distribution and excretion. Good bioavailability and short in vivo half-lives were determined formerly for the same test compound. For closing gaps in the understanding of pharmacokinetic data and in vitro results, radioactive hot spots on whole-body tissue sections had been profiled. Punches from selected tissue regions containing high radioactivity in the tissue sections previously analyzed by QWBA were extracted by a highly organic solvent and analyzed without any consecutive sample preparation step, applying ultra high performance liquid chromatography-mass spectrometry (UHPLC-MS) and off-line radioanalysis to maximize signal levels for metabolite identification and profiling. The analysis revealed that the test compound was metabolized intensively by phase I reactions in vivo and the metabolites formed were excreted in bile and in urine. The predominant metabolites showed abundant signal intensities both by MS and by radioanalysis but the MS signal intensities generally underestimated the real abundances of metabolites relative to the unchanged drug. In this work we illustrate that maximizing the sensitivity of tissue punch radioanalysis and the combination with UHPLC-MS leads to a better insight of pharmacokinetic processes by providing quantitative data with high molecular selectivity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Produced Water DNA Database (PW-DNA): Utilizing KBase to generate an environmental specific curated molecular database

The deep subsurface is estimated to host the majority of Earth’s microbial biomass yet remains one of the most challenging environments to access and study. One common approach to investigate these microbial communities is through the analysis of produced water from subsurface reservoirs, where researchers can assess water and gas chemistry along with molecular (DNA/RNA) sequence data. Advances in high-throughput sequencing have greatly expanded our understanding of these environments and their biotechnological potential. However, further progress requires large-scale, integrative meta-analyses across diverse datasets. To address this need, we developed the Produced Water-DNA (PW-DNA) Database, a curated, publicly available resource that consolidates microbial DNA/RNA sequences, geochemical data, and relevant metadata from in situ hydrocarbon environments such as coal beds, oil reservoirs, and natural gas systems. The PW-DNA database delivers three core benefits to the research community: (1) it improves data sharing by linking environmental microbial datasets with corresponding geochemical parameters, enabling more robust filtering and analysis; (2) it connects with complementary research databases to promote broader dissemination and interoperability; and (3) it supports technological innovation by serving as a resource for identifying microbial trends and exploring genetic potential. While individual studies have highlighted basin-specific microbial communities and functional redundancy in biogeochemical cycling, a comprehensive, system-wide perspective is needed to better understand connectivity and novelty across subsurface ecosystems. By designing the PW-DNA in the KBase platform, we provide a reproducible, visual framework for integrating large-scale genomic and geochemical data, enabling researchers to perform more informed analyses and experimental design. Ultimately, this resource enhances the ability to identify, characterize, and interpret microbial functions across diverse subsurface environments, thereby accelerating discovery in subsurface microbiology and biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Simultaneous Exposure of Cultured Human Lymphoblastic Cells to Simulated Microgravity and Radiation Increases Chromosome Aberrations

During space travel, humans are continuously exposed to two major environmental stresses, microgravity (μG) and space radiation. One of the fundamental questions is whether the two stressors are interactive. For over half a century, many studies were carried out in space, as well as using devices that simulated μG on the ground to investigate gravity effects on cells and organisms, and we have gained insights into how living organisms respond to μG. However, our knowledge on how to assess and manage human health risks in long-term mission to the Moon or Mars is drastically limited. For example, little information is available on how cells respond to simultaneous exposure to space radiation and μG. In this study, we analyzed the frequencies of chromosome aberrations (CA) in cultured human lymphoblastic TK6 cells exposed to X-ray or carbon ion under the simulated μG conditions. A higher frequency of both simple and complex types of CA were observed in cells exposed to radiation and μG simultaneously compared to CA frequency in cells exposed to radiation only. Our study shows that the dose response data on space radiation obtained at the 1G condition could lead to the underestimation of astronauts’ potential risk for health deterioration, including cancer. This study also emphasizes the importance of obtaining data on the molecular and cellular responses to irradiation under μG conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Isolation, Structural Analysis and Biological Activity Assays of Biselisabethoxanes A and B: Two Dissymmetric Bis-Diterpenes from the Southwestern Caribbean Sea Gorgonian Coral Pseudopterogorgia elisabethae

Two novel dissymmetric diterpenoids, biselisabethoxanes A and B (1 and 2), were isolated from the hexane extracts of the gorgonian coral Pseudopterogorgia elisabethae. Biselisabethoxane A (1) represents the first example of a marine-derived C40 dimer made of two distinct diterpene fragments, whereas biselisabethoxane B (2) is a fused heterodimer stemming from coupling of two amphilectane-based fragments. The structures of 1 and 2 were elucidated based on 1D and 2D NMR spectral data analysis. The molecular structure of 1 was subsequently confirmed by X-ray crystallographic analysis. When evaluated for their inhibitory effects in a series of well-established biological activity assays the isolated compounds were shown to moderately inhibit the growth of Mycobacterium tuberculosis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mass accommodation and gas–particle partitioning in secondary organic aerosols: dependence on diffusivity, volatility, particle-phase reactions, and penetration depth

Abstract. Mass accommodation is an essential process for gas–particle partitioning of organic compounds in secondary organic aerosols (SOA). The mass accommodation coefficient is commonly described as the probability of a gas molecule colliding with the surface to enter the particle phase. It is often applied, however, without specifying if and how deep a molecule has to penetrate beneath the surface to be regarded as being incorporated into the condensed phase (adsorption vs. absorption). While this aspect is usually not critical for liquid particles with rapid surface–bulk exchange, it can be important for viscous semi-solid or glassy solid particles to distinguish and resolve the kinetics of accommodation at the surface, transfer across the gas–particle interface, and further transport into the particle bulk. For this purpose, we introduce a novel parameter: an effective mass accommodation coefficient αeff that depends on penetration depth and is a function of surface accommodation coefficient, volatility, bulk diffusivity, and particle-phase reaction rate coefficient. Application of αeff in the traditional Fuchs–Sutugin approximation of mass-transport kinetics at the gas–particle interface yields SOA partitioning results that are consistent with a detailed kinetic multilayer model (kinetic multilayer model of gas–particle interactions in aerosols and clouds, KM-GAP; Shiraiwa et al., 2012) and two-film model solutions (Model for Simulating Aerosol Interactions and Chemistry, MOSAIC; Zaveri et al., 2014) but deviate substantially from earlier modeling approaches not considering the influence of penetration depth and related parameters. For highly viscous or semi-solid particles, we show that the effective mass accommodation coefficient remains similar to the surface accommodation coefficient in the case of low-volatility compounds, whereas it can decrease by several orders of magnitude in the case of semi-volatile compounds. Such effects can explain apparent inconsistencies between earlier studies deriving mass accommodation coefficients from experimental data or from molecular dynamics simulations. Our findings challenge the approach of traditional SOA models using the Fuchs–Sutugin approximation of mass transfer kinetics with a fixed mass accommodation coefficient, regardless of particle phase state and penetration depth. The effective mass accommodation coefficient introduced in this study provides an efficient new way of accounting for the influence of volatility, diffusivity, and particle-phase reactions on SOA partitioning in process models as well as in regional and global air quality models. While kinetic limitations may not be critical for partitioning into liquid SOA particles in the planetary boundary layer (PBL), the effects are likely important for amorphous semi-solid or glassy SOA in the free and upper troposphere (FT–UT) as well as in the PBL at low relative humidity and low temperature.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1972

Excitation of sodium D-line radiation in collisions of sodium atoms with internally excited H2, D2 and N2.

Excitation of D-line radiation in collisions of Na atoms with vibrationally excited N2, H2, and D2 was studied in two modulated crossed-beam experiments. In both experiments, the molecular excitation was provided by heating the molecular beam to temperatures which were assumed to give populations corresponding to the Boltzmann distribution. In the first experiment, a total rate coefficient was measured as a function of molecular beam temperature. The second experiment achieved partial separation of internal vs kinetic energy transfer effects by using a velocity-selected molecular beam. The data from both experiments were used to determine parameters for the dependence of the transfer cross section upon the kinetic energy for a given change in the vibrational quantum number. Results indicate that most of the Na excitation energy comes from internal vibrational energy, with the remainder coming from kinetic energy.

Krause, H. F.↗
NASA NTRS1976

Viking 1: early results

A brief outline of the Viking 1 mission to Mars is followed by descriptions of the Martian landing site and the scientific instrumentation aboard Viking 1 orbiter and lander. Measurements of the Martian atmosphere provided data on its molecular composition, temperature and pressure. The detection of nitrogen in the Martian atmosphere indicates the existence of life. Panoramic photographs of the Martian surface were also obtained and are shown. Preliminary chemical and biological investigations on samples of Martian soil indicated the presence of the elements iron, calcium, silicon, titanium and aluminum as major constituents. Observed biochemical reactions were judged conducive of biological activity.

Source record↗
NASA NTRS1978

Genetic code correlations - Amino acids and their anticodon nucleotides

The data here show direct correlations between both the hydrophobicity and the hydrophilicity of the homocodonic amino acids and their anticodon nucleotides. While the differences between properties of uracil and cytosine derivatives are small, further data show that uracil has an affinity for charged species. Although these data suggest that molecular relationships between amino acids and anticodons were responsible for the origin of the code, it is not clear what the mechanism of the origin might have been.

Weber, A. L.↗
NASA NTRS1982

The NGC 7538 region - The distribution and dynamics of molecules compared with those of HI and H/+/

CO maps and preliminary H2S and H2CO data for the molecular cloud associated with the HII region NGC 7538 are compared with the distributions of ionized and neutral hydrogen. South of the optical HII region is a ridge of high (C-13)O column density with cold, self-absorbed HI gas just beyond it. A dense clump within thy ridge is found adjacent to the HII region in the southeast. The percentage of the hydrogen in atomic form varies from approximately 0.1% in the dense region to approximately 0.8% in the outskirts. The lower-density region of expanding gas seen next to the HII region in the southwest is attributed to the passage of a molecular dissociation wave.

Dickel, H. R.↗
NASA NTRS1982

Thermodynamics of silicon nitridation - Effect of hydrogen

Equilibrium compositions for the nitridization of Si were calculated to detect the effectiveness of H2 in removal of the oxide film and in increasing the concentration of SiO and reducing the proportions of O2. Gibbs free energy for the formation of SiN2O was computed above 1685 K, and at lower temperatures. The thermodynamic properties of SiN2O2 were then considered from 1000-3000 K, taking into account the known thermodynamic data for 39 molecular combinations of the Si, Ni, and O. The gases formed were assumed ideal mixtures with pure phase condensed species. The mole fractions were obtained for a system of SiO2 with each Si particle covered with a thin layer of SiO2 before nitridation, and a system in which the nitriding atmosphere had access to the Si. The presence of H2 was determined to enhance the removal of NiO2 in the first system, decrease the partial pressure of O2, increase the partial pressures of SiO, Si, H2O, NH3, and SiH4, while its effects were negligible in the Si system.

Shaw, N. J.↗
NASA NTRS1983

The disappearance of OH from Comet P/Encke

Photoelectric observations of Comet P/Encke during its 1980 apparition are combined with other published data to relate molecular production rates to the visual lightcurve. In addition to a substantial asymmetry about perihelion which is already well known, there are shorter-term variations in specific molecules which have not been duplicated by models. The most dramatic of these fluctuations is a rapid decrease by more than a factor of 3 in the production of OH at 0.75 AU preperihelion.

Ahearn, M. F.↗