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At least 37 records · Page 2

Accurate, Uncertainty-Aware Classification of Molecular Chemical Motifs from Multimodal X-ray Absorption Spectroscopy

Accurate classification of molecular chemical motifs from experimental measurement is an important problem in molecular physics, chemistry, and biology. In this work, we present neural network ensemble classifiers for predicting the presence (or lack thereof) of 41 different chemical motifs on small molecules from simulated C, N, and O K-edge X-ray absorption near-edge structure (XANES) spectra. Our classifiers not only achieve class-balanced accuracies of more than 0.95 but also accurately quantify uncertainty. Here, we also show that including multiple XANES modalities improves predictions notably on average, demonstrating a “multimodal advantage” over any single modality. In addition to structure refinement, our approach can be generalized to broad applications with molecular design pipelines.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular attenuation and phase dispersion between 40 and 140-GHz for path models from different altitudes

Radio wave propagation in the 40 to 140 GHz band through the first hundred kilometers of the atmosphere is strongly influenced by the microwave spectrum of oxygen (O2-MS). A unified treatment of molecular attenuation and phase dispersion is formulated. Results of molecular physics are translated into frequency, temperature, pressure, and magnetic field dependencies of a complex refractive index. The intensity distribution of the O2-MS undergoes several changes with increasing altitude. The influence of water vapor is discussed. Examples of computer plots are given as a function of altitude for homogeneous, zenith, and tangential path geometries. Molecular resonances of minor atmospheric gases are discussed briefly.

Liebe, H. J.↗

Better Spectrometers, Beautiful Spectra and Confusion for All

The confluence of enormous improvements in submillimeter receivers and the development of powerful large scale observatories is about to force astrophysics and the sciences that support it to develop novel approaches for interpretation of data. The historical method of observing one or two lines and carefully analyzing them in the context of a simple model is now only applicable for distant objects where only a few lines are strong enough to be observable. Modern observatories collect many GHz of high signal-to-noise spectra in a single observation and in many cases, at sufficiently high spatial resolution to start resolving chemically distinct regions. The observatories planned for the near future and the inevitable upgrades of existing facilities will make large spectral data sets the rule rather than the exception in many areas of molecular astrophysics. The methodology and organization required to fully extract the available information and interpret these beautiful spectra represents a challenge to submillimeter astrophysics similar in magnitude to the last few decades of effort in improving receivers. The quality and abundance of spectra effectively prevents line-by-line analysis from being a time efficient proposition, however, global analysis of complex spectra is a science in its infancy. Spectroscopy at several other wavelengths have developed a number of techniques to analyze complex spectra, which can provide a great deal of guidance to the molecular astrophysics community on how to attack the complex spectrum problem. Ultimately, the challenge is one of organization, similar to building observatories, requiring teams of specialists combining their knowledge of dynamical, structural, chemical and radiative models with detailed knowledge in molecular physics and gas and grain surface chemistry to extract and exploit the enormous information content of complex spectra. This paper presents a spectroscopists view of the necessary elements in a tool for complex spectral analysis.

Spectral Analysis↗

THz Spectroscopy and Spectroscopic Database for Astrophysics

Molecule specific astronomical observations rely on precisely determined laboratory molecular data for interpretation. The Herschel Heterodyne Instrument for Far Infrared, a suite of SOFIA instruments, and ALMA are each well placed to expose the limitations of available molecular physics data and spectral line catalogs. Herschel and SOFIA will observe in high spectral resolution over the entire far infrared range. Accurate data to previously unimagined frequencies including infrared ro-vibrational and ro-torsional bands will be required for interpretation of the observations. Planned ALMA observations with a very small beam will reveal weaker emission features requiring accurate knowledge of higher quantum numbers and additional vibrational states. Historically, laboratory spectroscopy has been at the front of submillimeter technology development, but now astronomical receivers have an enormous capability advantage. Additionally, rotational spectroscopy is a relatively mature field attracting little interest from students and funding agencies. Molecular data base maintenance is tedious and difficult to justify as research. This severely limits funding opportunities even though data bases require the same level of expertise as research. We report the application of some relatively new receiver technology into a simple solid state THz spectrometer that has the performance required to collect the laboratory data required by astronomical observations. Further detail on the lack of preparation for upcoming missions by the JPL spectral line catalog is given.

Pearson, John C.↗

THz Spectroscopy and Spectroscopic Database for Astrophysics

Molecule specific astronomical observations rely on precisely determined laboratory molecular data for interpretation. The Herschel Heterodyne Instrument for Far Infrared, a suite of SOFIA instruments, and ALMA are each well placed to expose the limitations of available molecular physics data and spectral line catalogs. Herschel and SOFIA will observe in high spectral resolution over the entire far infrared range. Accurate data to previously unimagined frequencies including infrared ro-vibrational and ro-torsional bands will be required for interpretation of the observations. Planned ALMA observations with a very small beam will reveal weaker emission features requiring accurate knowledge of higher quantum numbers and additional vibrational states. Historically, laboratory spectroscopy has been at the front of submillimeter technology development, but now astronomical receivers have an enormous capability advantage. Additionally, rotational spectroscopy is a relatively mature field attracting little interest from students and funding agencies. Molecular database maintenance is tedious and difficult to justify as research. This severely limits funding opportunities even though data bases require the same level of expertise as research. We report the application of some relatively new receiver technology into a simple solid state THz spectrometer that has the performance required to collect the laboratory data required by astronomical observations. Further detail on the lack of preparation for upcoming missions by the JPL spectral line catalog is given.

THz spectrometer↗

Physiological Adaptations to Progressive Endurance Exercise Training in Adult and Aged Rats: Insights from the Molecular Transducers of Physical Activity Consortium (MoTrPAC)

While regular physical activity is a cornerstone of health, wellness, and vitality, the impact of endurance exercise training on molecular signaling within and across tissues remains to be delineated. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to characterize molecular networks underlying the adaptive response to exercise. Here, we describe the endurance exercise training studies undertaken by the Preclinical Animal Sites Studies component of MoTrPAC, in which we sought to develop and implement a standardized endurance exercise protocol in a large cohort of rats. To this end, Adult (6-mo) and Aged (18-mo) female (n = 151) and male (n = 143) Fischer 344 rats were subjected to progressive treadmill training (5 d/wk, ~70%–75% VO 2 max) for 1, 2, 4, or 8 wk; sedentary rats were studied as the control group. A total of 18 solid tissues, as well as blood, plasma, and feces, were collected to establish a publicly accessible biorepository and for extensive omics-based analyses by MoTrPAC. Treadmill training was highly effective, with robust improvements in skeletal muscle citrate synthase activity in as little as 1–2 wk and improvements in maximum run speed and maximal oxygen uptake by 4–8 wk. For body mass and composition, notable age- and sex-dependent responses were observed. This work in mature, treadmill-trained rats represents the most comprehensive and publicly accessible tissue biorepository, to date, and provides an unprecedented resource for studying temporal-, sex-, and age-specific responses to endurance exercise training in a preclinical rat model.

60 APPLIED LIFE SCIENCES↗

Measuring Electronic Structure of Multiply Charged Anions to Understand their Chemistry: A Case Study on Gaseous Polyhedral closo-Borate Dianions

Research on multiply charged anions (MCAs) in the gas phase has been intensively performed during the last decades, mainly to understand fundamental molecular physics phenomena, e.g., intramolecular Coulomb repulsion and existence of the repulsive Coulomb barrier. However, the relevance of these investigations with respect to understanding MCAs’ chemistry appears often vague. Here, we discuss how insights on the electronic structure obtained from negative ion photoelectron spectroscopy (NIPES) combined with theoretical calculations and collision induced dissociation can provide fundamental understanding on the intrinsic chemical reactivity of MCAs and their fragments. This is exemplified on our studies on polyhedral closo-borate dianions [BnXn]2- (n = 6, 10, 11, 12; X = H, F-I, CN) and their fragment ions. For example, the rational design of closo-borate dianions with specific electronic properties is described, which leads to generating highly reactive fragments. Depending on the dianionic precursor, these fragments are either tuned to bind noble gases effectively or to activate small molecules like CO and N2. The intrinsic electronic properties of closo-borate dianions are further compared to their electrochemistry in solutions, revealing solvent effects on the redox potentials. Neutral host molecules such as cyclodextrins are found to bind strongly to [BnXn]2-, and gas phase NIPES provides insights on the intrinsic host-guest interactions. Finally, outlooks including the direct NIPES of molecular fragment ions which cannot be generated in the condensed phase and their utilization in preparative mass spectrometry are discussed. J.W is grateful to the Volkswagen foundation for a Freigeist Fellowship. X. B. W acknowledges support from the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, the Division of Chemical Sciences, Geosciences and Biosciences. We are grateful to our colleagues who support our work on gas phase ion chemistry for many years. In particular we acknowledge the members of our groups, the Asmis group (Leipzig), Laskin Group (West Lafayette), the Jenne group (Wuppertal), the Finze group (Würzburg), the Grabowsky group (Bern), and the Sun group (Shanghai). We are grateful to Edoardo Apra for the many theoretical investigations on closo-borate anions. JW acknowledges support of Harald Knorke and Markus Rohdenburg with the preparation of graphical material, and XBW thanks Qinqin Yuan for the help in organizing references.

Warneke, Jonas↗

A Study on Recycled Polymers Recovered from Multilayer Plastic Packaging Films by Solvent–Targeted Recovery and Precipitation (STRAP)

Multilayer plastic film use increased in multiple packaging applications due to its versatility and overall increased performance over monolayer structures. However, the performance gains from multiple layers also make recycling difficult because they contain multiple polymers that can be immiscible and burdensome to traditional mechanical recycling operations. A possible solution is the solvent-targeted recovery and precipitation (STRAP) process, but the effect on the retrieved polymer is still unknown. Here, the STRAP process is applied to two different multilayer films and samples of recovered polymers are evaluated for physical, molecular, and thermal properties. Changes in the molecular weight are not significant, but differences in thermal properties are reported along with the coprecipitation of different polymers. Solvent retention in the polymer matrix from STRAP reduced the glass transition temperature of samples, but enhanced drying recovered it. Heavy metals, such as Cd, Cr, and Pb are not detected, indicating regulatory compliance for different applications.

36 MATERIALS SCIENCE↗

Assessment of Different Application Grades of Post-Consumer Recycled (PCR) Polyolefins from Material Recovery Facilities (MRFs) in the United States

The recycling of plastics has been gaining traction in the following years as many companies, organizations, and governments are pushing toward a more circular economy. However, plastic recycling rates are still small compared to those of plastic production, especially for polyolefins, such as high-density polyethylene (HDPE) and polypropylene (PP). With the goal of finding applications for recycled plastic resin, recyclers can face some challenges associated with the heterogeneity in the polymer properties of plastic waste streams, which could hinder the full potential of recycling due to the lack of a consistent feedstock. Here, this study assessed how an additional sorting step of recycled HDPE and PP streams, separating them into two categories based on the previous application, impacts the recycled polymer properties, such as physical, molecular, and thermal. It was demonstrated that manually separating HDPE articles previously processed by extrusion blow molding (EBM) or injection molding (IM) and PP articles by thermoforming (TF) or IM could yield recycled resins with more consistent properties, considering the significant differences between them. This highlights that an additional sorting step would allow recyclers to target more premium or currently unattainable plastic processing applications with postconsumer recycled (PCR) resins, which could significantly promote an increase in plastic recycling rates. Nevertheless, the development of new technologies is needed to automate this extra sorting step, as with the increase in scale manual sortation could not be feasible and cost-effective, reducing the attractiveness of using PCR resins in comparison to virgin ones.

36 MATERIALS SCIENCE↗

Deep learning-based quasi-continuum theory for structure of confined fluids

Predicting the structural properties of water and simple fluids confined in nanometer scale pores and channels is essential in, for example, energy storage and biomolecular systems. Classical continuum theories fail to accurately capture the interfacial structure of fluids. In this work, we develop a deep learning-based quasi-continuum theory (DL-QT) to predict the concentration and potential profiles of a Lennard-Jones (LJ) fluid and water confined in a nanochannel. The deep learning model is built based on a convolutional encoder–decoder network (CED) and is applied for high-dimensional surrogate modeling to relate the fluid properties to the fluid–fluid potential. The CED model is then combined with the interatomic potential-based continuum theory to determine the concentration profiles of a confined LJ fluid and confined water. Further, we show that the DL-QT model exhibits robust predictive performance for a confined LJ fluid under various thermodynamic states and for water confined in a nanochannel of different widths. The DL-QT model seamlessly connects molecular physics at the nanoscale with continuum theory by using a deep learning model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Materials research at Stanford University

Research activity related to the science of materials is described. The following areas are included: elastic and thermal properties of composite materials, acoustic waves and devices, amorphous materials, crystal structure, synthesis of metal-metal bonds, interactions of solids with solutions, electrochemistry, fatigue damage, superconductivity and molecular physics and phase transition kinetics.

Source record↗

Circumstellar grain formation

Dust formation around cool giant and supergiant stars is examined in terms of grain formulation. Optical properties of small clusters, molecular physics of cluster nucleation and growth, circumstellar mass flows, and their application to alpha Ori are discussed.

Draine, B. T.↗

Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise

Exercise provides a robust physiological stimulus that evokes cross-talk between a wide range of tissues via hormonal, cellular and molecular signals that when repeated regularly over time (i.e., training) improves physiological capacity, benefits numerous organ systems and decreases the risk for premature mortality. In spite of its fundamental importance, a gap remains in identifying the detailed molecular signals and responses to exercise and its benefits for health and disease prevention. To further knowledge in this emerging area, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to generate a molecular map of the effects of acute and chronic exercise. MoTrPAC investigators are conducting preclinical and clinical studies to better understand the systemic effects of exercise across multiple tissues. The preclinical studies were performed on more than 700 rats with the analysis of twenty or more organs per rat. The clinical study involves a large cohort of ~2600 individuals with a range of ages and fitness levels (untrained, trained, highly trained) who will be evaluated physiologically and by molecular probing of blood, muscle and adipose tissues before and after acute and chronic endurance or resistance exercise. Multi-omic analyses (genomics, epigenomics, transcriptomics, proteomics and metabolomics/lipidomics) will be performed followed by state-of-the-art bioinformatics to create a molecular map of exercise. This mapping project will provide a public database that is expected to enhance our understanding of the health benefits of physical activity in many organ systems and potentially provide insight into mitigating diseases through activity.

Sanford, James A.↗

Warm neutral halos around molecular clouds. VI - Physical and chemical modeling

A combined physical and chemical modeling of the halos around molecular clouds is presented, with special emphasis on the H-to-H2 transition. On the basis of H I 21 cm observations, it is shown that the halos are extended. A physical model is employed in conjunction with a chemistry code to provide a self-consistent description of the gas. The radiative transfer code provides a check with H I, CO, and OH observations. It is concluded that the warm neutral halos are not gravitationally bound to the underlying molecular clouds and are isobaric. It is inferred from the observed extent of the H I envelopes and the large observed abundance of OH in them that the generally accepted rate for H2 information on grains is too large by a factor of two to three.

Andersson, B.-G.↗

Spatial variation of the physical conditions of molecular gas in galaxies

Multi-line studies of CO-12, CO-13, C-18O, HCN, and HCO(+) at 3 mm, 1.3 mm, and 0.8 mm using the Institute for Radio Astronomy in the Millimeter range (IRAM) 30 m telescope, with the IRAM superconductor insulator superconductor (SIS) receivers and the Max Planck Institute for External Physics (MPE) 350 GHz SIS receiver, show that the densities and temperatures of molecular gas in external galaxies change significantly with position. CO-12 measures the densities and temperature of diffuse interclump molecular gas, but not the bulk of the molecular gas. Simple one-component models, with or without external heating, cannot account for the weakness of the CO-12 J = 3 to 2 line relative to J = 2 to 1 and J = 1 to 0. CO-12 does not trace the bulk of the molecular gas, and optical depth effects obviate a straightforward interpretation of CO-12 data. Instead, researchers turned to the optically thin CO isotopes and other molecular species. Isotopic CO lines measure the bulk of the molecular gas, and HCN and HCO(+) pick out denser regions. Researchers find a warm ridge of gas in IC 342 (Eckart et al. 1989), denser gas in the starburst nucleus of IC 342, and a possible hot-spot in NGC 2903. In IC 342, NGC 2146, and NGC 6764, the CO-13 J = 2 to 1 line is subthermally populated, implying gas densities less than or equal to 10(exp 4) cm(-3).

Jackson, James M.↗

Correlation of physical properties with molecular structure for some dicyclic hydrocarbons having high thermal-energy release per unit volume -- 2-alkylbiphenyl and the two isomeric 2-alkylbicyclohexyl series

Three homologous series of related dicyclic hydrocarbons are presented for comparison on the basis of their physical properties, which include net heat of combustion, density, melting point, boiling point, and kinematic viscosity. The three series investigated include the 2-n-alkylbiphenyl, 2-n-alkylbicyclohexyl (high boiling), and 2-n-alkylbiphenyls (low boiling) series through c sub 16, in addition to three branched-chain (isopropyl, sec-butyl, and isobutyl) 2-alkylbiphenyls and their corresponding 2-alkylbicyclohexyls. The physical properties of the low-boiling and high-boiling isomers of 2-sec-butylbicyclohexyl and 2-isobutylbicyclohexyl are reported herein for the first time.

Goodman, Irving A↗

Comprehensive models of diffuse interstellar clouds - Physical conditions and molecular abundances

The limitations of steady state models of interstellar clouds are explored by means of comparison with observational data corresponding to clouds in front of Zeta Per, Zeta Oph, Chi Oph, and Omicron Per. The improved cloud models were constructed to reproduce the observed H and H2(J) column densities for several lines of sight. The main difference from previous models is the treatment of self-shielding in the H2 lines. Other improvements over previous models are discussed as well.

Van Dishoeck, E. F.↗