Transport Properties of Liquid Pentaerythritol Tetranitrate (PETN) from Molecular Dynamics Simulations
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36 MATERIALS SCIENCE↗
SEARCH · Engineering Papers
Results for “molecular properties”
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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Thermoelastic properties of bridgmanite using deep-potential molecular dynamics
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Materials Science↗
Structural Properties of Organically Modified Boehmite Nanomaterials from Molecular Simulation
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Greathouse, Jeffery A.↗
Temperature modulates the cell wall mechanical properties of rice coleoptiles by altering the molecular mass of hemicellulosic polysaccharides
The present study was conducted to investigate the mechanism inducing the difference in the cell wall extensibility of rice (Oryza sativa L. cv. Koshihikari) coleoptiles grown under various temperature (10-50 degrees C) conditions. The growth rate and the cell wall extensibility of rice coleoptiles exhibited the maximum value at 30-40 degrees C, and became smaller as the growth temperature rose or dropped from this temperature range. The amounts of cell wall polysaccharides per unit length of coleoptile increased in coleoptiles grown at 40 degrees C, but not at other temperature conditions. On the other hand, the molecular size of hemicellulosic polysaccharides was small at temperatures where the cell wall extensibility was high (30-40 degrees C). The autolytic activities of cell walls obtained from coleoptiles grown at 30 and 40 degrees C were substantially higher than those grown at 10, 20 and 50 degrees C. Furthermore, the activities of (1-->3),(1-->4)-beta-glucanases extracted from coleoptile cell walls showed a similar tendency. When oat (1-->3),(1-->4)-beta-glucans with high molecular mass were incubated with the cell wall enzyme preparations from coleoptiles grown at various temperature conditions, the extensive molecular mass downshifts were brought about only by the cell wall enzymes obtained from coleoptiles grown at 30-40 degrees C. There were close correlations between the cell wall extensibility and the molecular mass of hemicellulosic polysaccharides or the activity of beta -glucanases. These results suggest that the environmental temperature regulates the cell wall extensibility of rice coleoptiles by modifying mainly the molecular mass of hemicellulosic polysaccharides. Modulation of the activity of beta-glucanases under various temperature conditions may be involved in the alteration of the molecular size of hemicellulosic polysaccharides.
Cellulose/chemistry/metabolism↗
Influence of Molecular Simulation Model Accuracy on the Interfacial Properties of an Ionic Liquid: Overview of Recommended Practices
Increasing the energy storage capability of ionic liquid supercapacitors will require better understanding of ion-electrode interactions. We have probed the influence of these interactions on the structure and differential capacitance of of an ionic liquid ([EMIM][BF4]) at an ideal graphite interface as a function of model accuracy. Of note, differential capacitance is determined through newly derived and validated fluctuation formulas. In terms of model accuracy, we test electrostatic techniques, electrode charging techniques, and electrolyte interatomic potentials. For electrostatic summations, we employ high cost, high fidelity techniques as well as less expensive, approximate techniques for summation in slab geometry. For electrode charging, uniform, constant-charge and environmentally responsive, constant-potential conditions are employed. For the ionic liquid, constant charge and atomically polarizable models are employed. We comment on the role of model accuracy on the structure and energetics of the electric double layer as well as on the magnitude and shape of differential capacitance.
simulations↗
Using Advanced Vibrational Molecular Spectroscopy (ATR-Ft/IRS and Synchrotron SR-IMS) to Study an Interaction Between Protein Molecular Structure From Biodegradation Residues and Nutritional Properties of Cool-Climate Adapted Faba Bean Seeds
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99 GENERAL AND MISCELLANEOUS↗
Machine learning molecular dynamics simulations toward exploration of high-temperature properties of nuclear fuel materials: case study of thorium dioxide
Predicting materials properties of nuclear fuel compounds is a challenging task in materials science. Their thermodynamical behaviors around and above the operational temperature are essential for the design of nuclear reactors. However, they are not easy to measure, because the target temperature range is too high to perform various standard experiments safely and accurately. Moreover, theoretical methods such as first-principles calculations also suffer from the computational limitations in calculating thermodynamical properties due to their high calculation-costs and complicated electronic structures stemming from f-orbital occupations of valence electrons in actinide elements. Here, we demonstrate, for the first time, machine-learning molecular-dynamics to theoretically explore high-temperature thermodynamical properties of a nuclear fuel material, thorium dioxide. The target compound satisfies first-principles calculation accuracy because f-electron occupation coincidentally diminishes and the scheme meets sampling sufficiency because it works at the computational cost of classical molecular-dynamics levels. We prepare a set of training data using first-principles molecular dynamics with small number of atoms, which cannot directly evaluate thermodynamical properties but captures essential atomistic dynamics at the high temperature range. Then, we construct a machine-learning molecular-dynamics potential and carry out large-scale molecular-dynamics calculations. Consequently, we successfully access two kinds of thermodynamic phase transitions, namely the melting and the anomalous λ transition induced by large diffusions of oxygen atoms. Furthermore, we quantitatively reproduce various experimental data in the best agreement manner by selecting a density functional scheme known as SCAN. Our results suggest that the present scale-up simulation-scheme using machine-learning techniques opens up a new pathway on theoretical studies of not only nuclear fuel compounds, but also a variety of similar materials that contain both heavy and light elements, like thorium dioxide.
74 ATOMIC AND MOLECULAR PHYSICS↗
A robust clustering algorithm for analysis of composition-dependent organic aerosol thermal desorption measurements
Abstract. One of the challenges of understanding atmospheric organic aerosol (OA) particles stems from its complex composition. Mass spectrometry is commonly used to characterize the compositional variability of OA. Clustering of a mass spectral dataset helps identify components that exhibit similar behavior or have similar properties, facilitating understanding of sources and processes that govern compositional variability. Here, we developed an algorithm for clustering mass spectra, the noise-sorted scanning clustering (NSSC), appropriate for application to thermal desorption measurements of collected OA particles from the Filter Inlet for Gases and AEROsols coupled to a chemical ionization mass spectrometer (FIGAERO-CIMS). NSSC, which extends the common density-based special clustering of applications with noise (DBSCAN) algorithm, provides a robust, reproducible analysis of the FIGAERO temperature-dependent mass spectral data. The NSSC allows for the determination of thermal profiles for compositionally distinct clusters of mass spectra, increasing the accessibility and enhancing the interpretation of FIGAERO data. Applications of NSSC to several laboratory biogenic secondary organic aerosol (BSOA) systems demonstrate the ability of NSSC to distinguish different types of thermal behaviors for the components comprising the particles along with the relative mass contributions and chemical properties (e.g., average molecular formula) of each mass spectral cluster. For each of the systems examined, more than 80 % of the total mass is clustered into 9–13 mass spectral clusters. Comparison of the average thermograms of the mass spectral clusters between systems indicates some commonality in terms of the thermal properties of different BSOA, although with some system-specific behavior. Application of NSSC to sets of experiments in which one experimental parameter, such as the concentration of NO, is varied demonstrates the potential for mass spectral clustering to elucidate the chemical factors that drive changes in the thermal properties of OA particles. Further quantitative interpretation of the thermograms of the mass spectral clusters will allow for a more comprehensive understanding of the thermochemical properties of OA particles.
54 ENVIRONMENTAL SCIENCES↗
Molecular cloud evolution and star formation
The present state of knowledge of the relationship between molecular clouds and young stars is reviewed. The determination of physical parameters from molecular line observations is summarized, and evidence for fragmentation of molecular clouds is discussed. Hierarchical fragmentation is reviewed, minimum fragment scales are derived, and the stability against fragmentation of both spherically and anisotropically collapsing clouds is discussed. Observational evidence for high-velocity flows in clouds is summarized, and the effects of winds from pre-main sequence stars on molecular gas are discussed. The triggering of cloud collapse by enhanced pressure is addressed, as is the formation of dense shells by spherical outflows and their subsequent breakup. A model for low-mass star formation is presented, and constraints on star formation from the initial mass function are examined. The properties of giant molecular clouds and massive star formation are described. The implications of magnetic fields for cloud evolution and star formation are addressed.
Silk, J.↗
A Chemist’s Guide to Solid-State Qubits: Diamond Color Centers as Embedded Vacancy-Centered Molecules
Diamond point defects or color centers are at the crux of solid-state quantum technology applications, from computing to sensing. Modeling molecular qubits has advanced by leaps and bounds mainly due to the advanced quantum mechanical (QM) tools in the arsenal of quantum chemists for modeling (isolated) molecular systems, which should be easily translatable for analogous systems in the solid state. Here, we simulate a series of diamond defects: a carbon vacancy (V C ) and second row substitutions that are adjacent to a V C or D C V C , with D = B, N, and O, to evaluate their magnetic and optical properties. We applied molecular orbital principles, an embedded cluster method, and a multiconfigurational QM theory to computationally characterize the above-mentioned defects for a multitude of spin, charge, and excited states. Our computational approach delivered high-quality QM insights that compare well with experiments. Furthermore, with this framework, we confirm the spin-triplets B C V C – and O C V C 0 to be analogous to N C V C – , with calculated bright transitions that respectively correspond to UV (3.80 eV) and blue (2.65 eV) light absorption and emission lifetimes (τ) of 2.3 and 5.6 ns, which are higher in energy and more short-lived (and thus brighter) than that for N C V C – : green (2.26 eV), τ = 9.5 ns.
Martirez, John Mark P. [Princeton Plasma Physics L↗
Observations of CO isotopic emission and the far-infrared continuum of Centaurus A
Researchers present maps of the CO-12(1=0) line and the 100 micron and 50 micron far-infrared emission of Centaurus A, as well as measurements of the CO-12(2-1), CO-13(1-0), and the C-18O(1-0) lines at selected positions. The observations were taken with the Swedish-ESO Submillimeter Telescope (SEST) and the CPC instrument on board the Infrared Astronomy Satellite (IRAS). The millimeter data show that the bulk molecular material is closely associated with the dust lane and contained in a disk of about 180 seconds diameter and a total molecular mass of about 2 x 10 to the 8th power solar mass. The total molecular mass of the disk and bulge is of the order of 3 x 10 to the 8th power solar mass. The molecular gas in the nucleus is warm with a kinetic temperature of the order of 15 K and a number density of 10 to the 3rd power to 3 x 10 to the 4th power cm(-3). Absorption features in the CO-12 and CO-13 lines against the nuclear continuum emission indicate that the properties of giant molecular clouds are comparable to those of the Galaxy. The far-infrared data show that to a good approximation the dust temperature is constant across the dust lane at a value of about 42 K. The ratio between the far-infrared luminosity and the total molecular mass is 18 solar luminosity/solar mass and close to the mean value obtained for isolated galaxies. A comparison of the CO-12(1-0) and the far-infrared data indicates that a considerable amount of the far-infrared emission is not intimately associated with massive star formation.
Eckart, A.↗
A Wide Latitude CO Survey of Molecular Clouds in the Northern Milky Way
It is now well established that molecular clouds are an important part of the interstellar medium, containing much or most of the dense, cold component of the gas, and producing the massive stars and supernovae responsible for the diffuse, hot component. It would therefore appear essential in formulating a complete picture of the local interstellar medium to have some knowledge of the distribution and properties of nearly molecular clouds. The Goddard-Columbia 1.2 meter telescope was used to carry out a wide latitude, low angular resolution survey of CO along most of the first galactic quadrant and a small part of the second. A plane-of-the-sky map, which resulted from numerically integrating the survey over radial velocity, is presented. The Great Rift and the Aquila Rift molecular clouds of the Milky Way are discussed.
Dame, T. M.↗
Modeling Molecules
The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.
Source record↗
Development of nontoxic heat transport fluids for habitat two-phase thermal control systems
A computational chemistry approach based on pattern recognition techniques is used to correlate molecules thermodynamic and chemical properties with its molecular structure. The potential to develop a suitable two-phase nontoxic heat transport working fluid for the spacecraft habitat environment is discussed. It is concluded that the perfluorocarbons represent a potentially useful class to consider as a source of the working fluids because of their low toxicity, thermal stability, and chemical inertness. The ADAPT software program is considered to be adequate to make structural and property predictions.
Parrish, Clyde F.↗
I ntera C hem : Exploring Excited States in Virtual Reality with Ab Initio Interactive Molecular Dynamics
InteraChem is an ab initio interactive molecular dynamics (AI-IMD) visualizer that leverages recent advances in virtual reality hardware and software, as well as the graphical processing unit (GPU)-accelerated TeraChem electronic structure package, in order to render quantum chemistry in real time. We introduce the exploration of electronically excited states via AI-IMD using the floating occupation molecular orbital-complete active space configuration interaction method. The optimization tools in InteraChem enable identification of excited state minima as well as minimum energy conical intersections for further characterization of excited state chemistry in small- to medium-sized systems. We demonstrate that finite-temperature Hartree–Fock theory is an efficient method to perform ground state AI-IMD. InteraChem allows users to track electronic properties such as molecular orbitals and bond order in real time, resulting in an interactive visualization tool that aids in the interpretation of excited state chemistry data and makes quantum chemistry more accessible for both research and educational purposes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Investigation of pyruvic acid photolysis at the air-liquid interface as a source of aqueous secondary organic aerosols
Pyruvic acid (PA) is a ubiquitous 2-oxocarboxylic acid in the atmosphere. Its photochemical process at the air-liquid (a-l) interface has been suggested as an important source of aqueous secondary organic aerosols. Here, we investigated the photochemical reaction pathways of PA at the a-l interface using synchrotron-based vacuum ultraviolet single-photon ionization mass spectrometry (VUV SPI-MS) coupled with the System for Analysis at the Liquid Vacuum Interface (SALVI) microreactor. Results from mass spectral analysis and the determination of appearance energies (AEs) indicate that photolysis of PA can generate radicals, then they recombine with carboxylic acids and simple molecular oligomers. Furthermore, the preliminary products could form larger oligomers via radical reaction or esterification in the presence of hydroxyl and carboxyl functional groups. Mass spectral comparison shows that most photochemical reactions would complete within 4 h. The expanded photochemistry-driven reaction flowchart of PA is proposed based on the newly discovered products. Our results reveal that the interfacial PA photochemical reactions have different mechanisms from the bulk liquid due to the interfacial properties, such as molecular density, composition, and ion concentration. Our findings show that in situ mass spectral analysis with bright photon ionization is useful to elucidate the contribution of a-l interfacial reactions leading to aqSOA formation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
1000 Soils Pilot Dataset, version 8, May 2025
This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data. A beta visualization tool is available for some data types at https://shinyproxy.emsl.pnnl.gov/app/1000soils. Please submit any suggestions or comments through the 'contact' tab. We are actively working to improve visualizations and value all feedback. Data completed include: Geochemistry, texture, respiration, and enzyme activities FTICR-MS organic matter chemistry Microbial biomass C and N TOC/TDN of water-extractable OM X-ray computed tomography (derived metrics available here, raw data available upon request) Metagenomes; a variety of data formats are available upon request Soil hydraulic properties Data in progress: LC-MS/MS in development, timeline TBD, inquire for status 1000S_processed_BGC_summary.csv contains all available biogeochemical data; microbial biomass C and N; and TOC/TDN of water-extractable OM; and 1000S_Tomography.xslx contains a summary of data generated via X-ray computed tomography. icr_v2_corems2.csv contains FTICR-MS data processed by CoreMS version 2. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates. 1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information. Soil Hydraulics_corrected_02042025.xlsx contains soil hydraulics information. Readme File_v4.xlsx is the readme file. Please contact the MONet project (monet.emsl@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions. The following file and all raw data are available upon request: icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs. For more information, please see: https://www.emsl.pnnl.gov/monet and https://sc-data.emsl.pnnl.gov/monet Acknowledgment: Soil data were provided by the Molecular Observation Network (MONet) at the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), a DOE Office of Science user facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830. The work (proposal: 10.46936/10.25585/60008970) conducted by the U.S. Department of Energy, Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science user facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. The Molecular Observation Network (MONet) database is an open, FAIR, and publicly available compilation of the molecular and microstructural properties of soil. Data in the MONet open science database can be found at https://sc-data.emsl.pnnl.gov/.
biogeochemistry↗