Vibrational spectra and structure of small-ring compounds. XII.
Propylene imine IR and Raman spectra, calculating thermodynamic functions based on rigid rotator harmonic oscillator model
Bush, S. F.↗
SEARCH · Engineering Papers
Results for “model compounds”
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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Production of organic compounds in plasmas - A comparison among electric sparks, laser-induced plasmas, and UV light
In order to ascertain the features of organic compound-production in planetary atmospheres under the effects of plasmas and shocks, various mixtures of N2, CH4, and H2 modeling the atmosphere of Titan were subjected to discrete sparks, laser-induced plasmas, and UV radiation. The experimental results obtained suggest that UV photolysis from the plasma is an important organic compound synthesis process, as confirmed by the photolysis of gas samples that were exposed to the light but not to the shock waves emitted by the sparks. The thermodynamic equilibrium theory is therefore incomplete in the absence of photolysis.
Scattergood, Thomas W.↗
Average Versus High Surface Ozone Levels over the Continental USA: Model Bias, Background Influences, and Interannual Variability
US background ozone (O3) includes O3 produced from anthropogenic O3 precursors emitted outside of the USA, from global methane, and from any natural sources. Using a suite of sensitivity simulations in the GEOS-Chem global chemistry transport model, we estimate the influence from individual background sources versus US anthropogenic sources on total surface O3 over 10 continental US regions from 2004 to 2012. Evaluation with observations reveals model biases of +0-19ppb in seasonal mean maximum daily 8h average (MDA8) O3, highest in summer over the eastern USA. Simulated high-O3 events cluster too late in the season. We link these model biases to excessive regional O3 production (e.g., US anthropogenic, biogenic volatile organic compounds (BVOCs), and soil NOx, emissions), or coincident missing sinks. On the 10 highest observed O3 days during summer (O3_top10obs_JJA), US anthropogenic emissions enhance O3 by 5-11ppb and by less than 2ppb in the eastern versus western USA. The O3 enhancement from BVOC emissions during summer is 1-7 ppb higher on O3_top10obs_JJA days than on average days, while intercontinental pollution is up to 2ppb higher on average versus on O3_top10obs_JJA days. During the summers of 2004-2012, monthly regional mean US background O3 MDA8 levels vary by up to 15ppb from year to year. Observed and simulated summertime total surface O3 levels on O3_top10obs_JJA days decline by 3ppb (averaged over all regions) from 2004-2006 to 2010-2012, reflecting rising US background (+2ppb) and declining US anthropogenic O3 emissions (6ppb) in the model. The model attributes interannual variability in US background O3 on O3_top10obs days to natural sources, not international pollution transport. We find that a 3-year averaging period is not long enough to eliminate interannual variability in background O3 on the highest observed O3 days.
Guo, Jean J.↗
Sensitivity of an atmospheric photochemistry model to chlorine perturbations including consideration of uncertainty propagation
Models of stratospheric photochemistry are generally tested by comparing their predictions for the composition of the present atmosphere with measurements of species concentrations. These models are then used to make predictions of the atmospheric sensitivity to perturbations. Here the problem of the sensitivity of such a model to chlorine perturbations ranging from the present influx of chlorine-containing compounds to several times that influx is addressed. The effects of uncertainties in input parameters, including reaction rate coefficients, cross sections, solar fluxes, and boundary conditions, are evaluated using a Monte Carlo method in which the values of the input parameters are randomly selected. The results are probability distributions for present atmosheric concentrations and for calculated perturbations due to chlorine from fluorocarbons. For more than 300 Monte Carlo runs the calculated ozone perturbation for continued emission of fluorocarbons at today's rates had a mean value of -6.2 percent, with a 1-sigma width of 5.5 percent. Using the same runs but only allowing the cases in which the calculated present atmosphere values of NO, NO2, and ClO at 25 km altitude fell within the range of measurements yielded a mean ozone depletion of -3 percent, with a 1-sigma deviation of 2.2 percent. The model showed a nonlinear behavior as a function of added fluorocarbons. The mean of the Monte Carlo runs was less nonlinear than the model run using mean value of the input parameters.
Stolarski, R. S.↗
Multiple fermion scattering in the weakly coupled spin-chain compound YbAlO 3
The Heisenberg antiferromagnetic spin-1/2 chain, originally introduced almost a century ago, is one of the best studied models in quantum mechanics due to its exact solution, but nevertheless it continues to present new discoveries. Its low-energy physics is described by the Tomonaga-Luttinger liquid of spinless fermions, similar to the conduction electrons in one-dimensional metals. In this work we investigate the Heisenberg spin-chain compound YbAlO3 and show that the weak interchain coupling causes Umklapp scattering between the left- and right-moving fermions and stabilizes an incommensurate spin-density wave order at q = 2k F under finite magnetic fields. These Umklapp processes open a route to multiple coherent scattering of fermions, which results in the formation of satellites at integer multiples of the incommensurate fundamental wavevector Q = nq. Our work provides surprising and profound insight into bandstructure control for emergent fermions in quantum materials, and shows how neutron diffraction can be applied to investigate the phenomenon of coherent multiple scattering in metals through the proxy of quantum magnetic systems.
36 MATERIALS SCIENCE↗
Prediction of Research/Motor Octane Number and Octane Sensitivity Using Artificial Neural Networks
Octane sensitivity (OS), dfined as the research octane number (RON) minus the motor octane number (MON) of a given fuel, has gained interest among researchers due to its apparent ffect on knocking conditions in internal combustion engines. Compounds with a high OS enable higher efficiencies, especially with respect to advanced compression ignition engines. RON/MON must be experimentally tested to determine OS; however, the experimental methods utilized require a substantial amount of time, a significant monetary investment, and specialized equipment. To this end, predictive computational models trained with existing experimental data and molecular properties would allow for the preemptive screening of compounds prior to performing these experiments. The present work proposes two methods for predicting the OS of a given compound: using artficial neural networks (ANNs) trained with quantitative structure-property relationship (QSPR) descriptors to predict RON and MON individually to compute OS from RON/MON predictions (derived octane sensitivity, dOS), and using an ANN trained with QSPR descriptors to directly predict OS. ANNs trained to predict RON and MON achieved test set root-mean-square errors (RMSEs) of 10.499 and 7.551 respectively. dOS calculations were found to have a test set RMSE of 6.432 while predicting OS directly resulted in a test set RMSE of 7.019, showing it is more bene cial to obtain OS from RON/MON predictions than predicting it directly. Furthermore, relationships between individual QSPR descriptors and RON/MON/OS are discussed, highlighting correlations between specfic molecular features and these properties.
09 BIOMASS FUELS↗
Screening a knowledge‐based library of low molecular weight compounds against the proline biosynthetic enzyme 1‐pyrroline‐5‐carboxylate 1 ( PYCR1)
Abstract Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 1 (PYCR1) is the last enzyme of proline biosynthesis and catalyzes the NAD(P)H‐dependent reduction of Δ 1 ‐pyrroline‐5‐carboxylate toL‐proline. High PYCR1 gene expression is observed in many cancers and linked to poor patient outcomes and tumor aggressiveness. The knockdown of thePYCR1gene or the inhibition of PYCR1 enzyme has been shown to inhibit tumorigenesis in cancer cells and animal models of cancer, motivating inhibitor discovery. We screened a library of 71 low molecular weight compounds (average MW of 131 Da) against PYCR1 using an enzyme activity assay. Hit compounds were validated with X‐ray crystallography and kinetic assays to determine affinity parameters. The library was counter‐screened against human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3 and proline dehydrogenase (PRODH) to assess specificity/promiscuity. Twelve PYCR1 and one PRODH inhibitor crystal structures were determined. Three compounds inhibit PYCR1 with competitive inhibition parameter of 100 μM or lower. Among these, (S)‐tetrahydro‐2H‐pyran‐2‐carboxylic acid (70 μM) has higher affinity than the current best tool compoundN‐formyl‐l‐proline, is 30 times more specific for PYCR1 over human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3, and negligibly inhibits PRODH. Structure‐affinity relationships suggest that hydrogen bonding of the heteroatom of this compound is important for binding to PYCR1. The structures of PYCR1 and PRODH complexed with 1‐hydroxyethane‐1‐sulfonate demonstrate that the sulfonate group is a suitable replacement for the carboxylate anchor. This result suggests that the exploration of carboxylic acid isosteres may be a promising strategy for discovering new classes of PYCR1 and PRODH inhibitors. The structure of PYCR1 complexed withl‐pipecolate and NADH supports the hypothesis that PYCR1 has an alternative function in lysine metabolism.
Biochemistry & Molecular Biology↗
Transcriptomics-Based Points of Departure for Daphnia magna Exposed to 18 Per- and Polyfluoroalkyl Substances
Here, per- and polyfluoroalkyl substances (PFAS) represent a large group of contaminants of concern based on their widespread use, environmental persistence, and potential toxicity. Many traditional models for estimating toxicity, bioaccumulation, and other toxicological properties are not well suited for PFAS. Consequently, there is a need to generate hazard information for PFAS in an efficient and cost-effective manner. In the present study, Daphnia magna were exposed to multiple concentrations of 22 different PFAS for 24 h, in 96-well plate format. Following exposure, whole body RNA was extracted and extracts, each representing five exposed individuals, were subjected to RNA sequencing. Following analytical measurements to verify PFAS exposure concentrations, and quality control on processed cDNA libraries for sequencing, concentration-response modeling was applied to the data sets for 18 of the tested compounds, and the concentration at which a concerted molecular response occurred (transcriptomic point of departure; tPOD) was calculated. The tPODs, based on measured concentrations of PFAS, generally ranged from 0.03-0.58 µM (9.9-350 µg/L; interquartile range). In most cases, these concentrations were two orders of magnitude lower than similarly calculated tPODs for human cell lines exposed to PFAS. They were also lower than apical effect concentrations reported for seven PFAS for which some crustacean or invertebrate toxicity data were available, although there were a few exceptions. Despite being lower than most other available hazard benchmarks, Daphnia magna tPODs were, on average, four orders of magnitude greater than the maximum aqueous concentrations of PFAS measured in Great Lakes tributaries. Overall, this high throughput transcriptomics assay with Daphnia magna holds promise as a component of a tiered hazard evaluation strategy employing new approach methodologies.
59 BASIC BIOLOGICAL SCIENCES↗
Origin of replication discovery for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and products
Leveraging predicted origin sequences from a previously characterized groundwater plasmidome, we constructed a barcoded plasmid library to screen for previously unknown origins. Testing this library against a panel of representative bacterial strains led to the identification of 3 previously unknown origins that replicate in gram-negative bacteria not previously associated with these origin sequences. Experimental validation confirmed that a plasmid bearing origin 6911 as the sole origin could replicate with a copy number of 9 (±2) in Pantoea sp. MT58, a fast growing and metal tolerant, environmentally important bacterium. Plasmids based on this new origin were used to express the reporter protein GFP, and non-native metabolite pathways for the natural product indigoidine and the terpenoid compound isoprenol. Functional previously unknown origins of replication in such non-model organisms can expand the toolkit for genetic manipulations of both model and less-studied bacteria.
molecular biology↗
Compound pulse characteristics of a heterogeneous composite scintillator in a gamma-ray field
An important aspect of radiation detection in scintillators is the time dependence of emitted fluorescence, which results in characteristic measured pulse shape. In some materials, a relatively strong dependence of the scintillation pulse shape on stopping power exists, which can provide reliable identification of the incident particle. An alternative method to realize particle identification is by combining materials with different fluorescence lifetimes into heterogeneous structures. Such composite scintillators derive their properties from both the constituent material characteristics and the geometry of the composite structure. In composite scintillators with a high degree of heterogeneous loading, a superposition of fluorescence contributions originating in multiple materials, which is observed as single waveform with an intermediate pulse shape, may affect its ability to reject rays. We measure the time dependence of light output from a scintillator composed of 6 Li-containing glass shards and scintillating polyvinyl toluene and identify events that exhibit such compound behavior when exposed to rays and fast neutrons. We develop a modeling and simulation framework that reproduces the pulse shapes in heterogeneous scintillators and use it study the effect that the weight percentage of 6 Li glass has on rejection. The modeling framework is applied to the experimentally studied scintillator, finding a good agreement. Here, the developed modeling and simulation approach will help optimize the design of heterogeneous scintillators to meet the desired trade-o between neutron capture efficiency and -ray rejection.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Potential Foldamers Based on an ortho- Terphenyl Amino Acid
We describe the synthesis and characterization of a new class of oligomers built from a terphenyl-based amino acid. Here, these oligomeric amides are of interest because the adoption of specific conformations could potentially be driven by the coordinated formation of inter-residue hydrogen bonds and aromatic interactions. Although high-resolution structural data have proven inaccessible, circular dichroism and nuclear magnetic resonance studies suggest that the new oligomers fold concomitantly with discrete self-association in chloroform. Molecular simulations find no sign of folding as a monomer, and in fact suggest that hydrogen bond patterning is anti-cooperative, inhibiting longer helices.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Competing electronic states emerging on polar surfaces
Excess charge on polar surfaces of ionic compounds is commonly described by the two-dimensional electron gas (2DEG) model, a homogeneous distribution of charge, spatially-confined in a few atomic layers. Here, by combining scanning probe microscopy with density functional theory calculations, we show that excess charge on the polar TaO 2 termination of KTaO 3 (001) forms more complex electronic states with different degrees of spatial and electronic localization: charge density waves (CDW) coexist with strongly-localized electron polarons and bipolarons. These surface electronic reconstructions, originating from the combined action of electron-lattice interaction and electronic correlation, are energetically more favorable than the 2DEG solution. They exhibit distinct spectroscopy signals and impact on the surface properties, as manifested by a local suppression of ferroelectric distortions.
36 MATERIALS SCIENCE↗
Generative adversarial networks (GAN) based efficient sampling of chemical composition space for inverse design of inorganic materials
A major challenge in materials design is how to efficiently search the vast chemical design space to find the materials with desired properties. One effective strategy is to develop sampling algorithms that can exploit both explicit chemical knowledge and implicit composition rules embodied in the large materials database. Here, we propose a generative machine learning model (MatGAN) based on a generative adversarial network (GAN) for efficient generation of new hypothetical inorganic materials. Trained with materials from the ICSD database, our GAN model can generate hypothetical materials not existing in the training dataset, reaching a novelty of 92.53% when generating 2 million samples. The percentage of chemically valid (charge-neutral and electronegativity-balanced) samples out of all generated ones reaches 84.5% when generated by our GAN trained with such samples screened from ICSD, even though no such chemical rules are explicitly enforced in our GAN model, indicating its capability to learn implicit chemical composition rules to form compounds. Our algorithm is expected to be used to greatly expand the range of the design space for inverse design and large-scale computational screening of inorganic materials.
36 MATERIALS SCIENCE↗
Stress-tolerant non-conventional microbes enable next-generation chemical biosynthesis
Microbial chemical production is a rapidly growing industry, with much of the growth fueled by advances in synthetic biology. New approaches have enabled rapid strain engineering for the production of various compounds; however, translation to industry is often problematic because native phenotypes of model hosts prevent the design of new low-cost bioprocesses. Here, in this work, we argue for a new approach that leverages the native stress-tolerant phenotypes of non-conventional microbes that directly address design challenges from the outset. Growth at high temperature, high salt and solvent concentrations, and low pH can enable cost savings by reducing the energy required for product separation, bioreactor cooling, and maintaining sterile conditions. These phenotypes have the added benefit of allowing for the use of low-cost sugar and water resources. Non-conventional hosts are needed because these phenotypes are polygenic and thus far have proven difficult to recapitulate in the common hosts Escherichia coli and Saccharomyces cerevisiae.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Secondary organic aerosol formation from evaporated biofuels: comparison to gasoline and correction for vapor wall losses
With an ongoing interest in displacing petroleum-based sources of energy with biofuels, we measure and model the formation and composition of secondary organic aerosol (SOA) from organic compounds present in biofuels.
47 OTHER INSTRUMENTATION↗
Direct prediction of inelastic neutron scattering spectra from the crystal structure*
Abstract Inelastic neutron scattering (INS) is a powerful technique to study vibrational dynamics of materials with several unique advantages. However, analysis and interpretation of INS spectra often require advanced modeling that needs specialized computing resources and relevant expertise. This difficulty is compounded by the limited experimental resources available to perform INS measurements. In this work, we develop a machine-learning based predictive framework which is capable of directly predicting both one-dimensional INS spectra and two-dimensional INS spectra with additional momentum resolution. By integrating symmetry-aware neural networks with autoencoders, and using a large scale synthetic INS database, high-dimensional spectral data are compressed into a latent-space representation, and a high-quality spectra prediction is achieved by using only atomic coordinates as input. Our work offers an efficient approach to predict complex multi-dimensional neutron spectra directly from simple input; it allows for improved efficiency in using the limited INS measurement resources, and sheds light on building structure-property relationships in a variety of on-the-fly experimental data analysis scenarios.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
A Metabolomics Assay to Diagnose Citrus Huanglongbing Disease and to Aid in Assessment of Treatments to Prevent or Cure Infection
Citrus greening disease, or Huanglongbing (HLB), has devastated citrus crops globally in recent years. The causal bacterium, ‘ Candidatus Liberibacter asiaticus’, presents a sampling issue for qPCR diagnostics and results in a high false negative rate. In this work, we compared six metabolomics assays to identify HLB-infected citrus trees from leaf tissue extracted from 30 control and 30 HLB-infected trees. A liquid chromatography-mass spectrometry-based assay was most accurate. A final partial least squares-discriminant analysis (PLS-DA) model was trained and validated on 690 leaf samples with corresponding qPCR measures from three citrus varieties (Rio Red grapefruit, Hamlin sweet orange, and Valencia sweet orange) from orchards in Florida and Texas. Trees were naturally infected with HLB transmitted by the insect vector Diaphorina citri. In a randomized validation set, the assay was 99.9% accurate to classify diseased from nondiseased samples. This model was applied to samples from trees receiving plant defense-inducer compounds or biological treatments to prevent or cure HLB infection. From two trials, HLB-related metabolite abundances and PLS-DA scores were tracked longitudinally and compared with those of control trees. We demonstrate how our assay can assess tree health and the efficacy of HLB treatments and conclude that no trialed treatment was efficacious.
Plant Sciences↗
Reduction of the neutron imaginary potential off the stability line and its possible impact on neutron capture rates
The effect of the isovector imaginary optical potential has been studied experimentally by using the particle-evaporation technique for the 11 B + 48 Ca reaction with a 21.8 MeV 11 B beam. Spectra of neutron, proton, and α particles emitted from the neutron-rich compound nucleus 59 Mn have been measured and analyzed with traditional optical model potentials with their original parametrizations as well as with adjusted isovector imaginary components. It is shown that the isovector component of the imaginary potential is indispensable in the reproduction of proton and α-particle yields from this reaction and even needs to be enhanced compared with the suggestions of the original model parametrizations. Furthermore, this can lead to important consequences for astrophysical reaction-rate calculations.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗