Spectroscopic investigation of nitrogen-functionalized carbon materials: Spectroscopic investigation of nitrogen-functionalized carbon
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Wood, Kevin N.↗
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Structure and Function of the Acetylpolyamine Amidohydrolase from the Deep Earth Halophile Marinobacter subterrani
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99 GENERAL AND MISCELLANEOUS↗
Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil
Phosphorus (P) is a scarce nutrient in many tropical ecosystems, yet how soil microbial communities cope with growth-limiting P deficiency at the gene and protein levels remains unknown. Here we report a metagenomic and metaproteomic comparison of microbial communities in P-deficient and P-rich soils in a 17-year fertilization experiment in a tropical forest. The large-scale proteogenomics analyses provided extensive coverage of many microbial functions and taxa in the complex soil communities. A >4-fold increase in the gene abundance of 3-phytase was the strongest response of soil communities to P deficiency. Phytase catalyzes the release of phosphate from phytate, the most recalcitrant P-containing compound in soil organic matter. Genes and proteins for the degradation of P-containing nucleic acids and phospholipids as well as the decomposition of labile carbon and nitrogen were also enhanced in the P-deficient soils. In contrast, microbial communities in the P-rich soils showed increased gene abundances for the degradation of recalcitrant aromatic compounds, the transformation of nitrogenous compounds, and the assimilation of sulfur. Overall, these results demonstrate the adaptive allocation of genes and proteins in soil microbial communities in response to shifting nutrient constraints.
Yao, Qiuming↗
Binary pseudo-random patterned structures for modulation transfer function calibration and resolution characterization of a full-field transmission soft x-ray microscope
We present a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) one-dimensional sequences and two-dimensional arrays as an effective method for spectral characterization in the spatial frequency domain of a broad variety of metrology instrumentation, including interferometric microscopes, scatterometers, phase shifting Fizeau interferometers, scanning and transmission electron microscopes, and at this time, x-ray microscopes. The inherent power spectral density of BPR gratings and arrays, which has a deterministic white-noise-like character, allows a direct determination of the MTF with a uniform sensitivity over the entire spatial frequency range and field of view of an instrument. We demonstrate the MTF calibration and resolution characterization over the full field of a transmission soft x-ray microscope using a BPR multilayer (ML) test sample with 2.8 nm fundamental layer thickness. We show that beyond providing a direct measurement of the microscope’s MTF, tests with the BPRML sample can be used to fine tune the instrument’s focal distance. Our results confirm the universality of the method that makes it applicable to a large variety of metrology instrumentation with spatial wavelength bandwidths from a few nanometers to hundreds of millimeters.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Effect of (Poly)electrolytes on the Interfacial Assembly of Poly(ethylene glycol)-Functionalized Gold Nanoparticles
Abstract not provided
Nayak, Srikanth↗
Resolving Local Configurational Contributions to X-ray and Neutron Radial Distribution Functions Within Solutions of Concentrated Electrolytes – A Case Study of Concentrated NaOH
Extreme conditions of complex materials often lead to a manifold of local environments that challenge characterization and require new advances at the intersection of modern experimental and theoretical techniques. In this contribution, highly caustic and viscous aqueous NaOD solutions were characterized with a combination of X-ray and neutron radial distribution function (RDF) analyses, molecular dynamics simulations and sub-ensemble analysis. The interpretation of the experimental RDFs extends beyond the traditional understanding of atom-pair interactions and to the individual contributions of specific molecular-scale configurations (below 3.5 Å). This integrated approach yields unique insight into the complex and significant breath of ion solvation and pairing structural motifs present, the experimental sensitivity of RDFs to changes in local geometries, and the challenge of experimentally differentiating the ensemble of all superimposed local environments — a feature of increasing importance within the extreme condition of high ionic strength. This study was facilitated by the development of a chemically resistant sample cell for in-situ neutron total scattering measurements of highly caustic materials at elevated temperature and pressure conditions. Advancing these integrated capabilities is critical for ongoing model validation efforts and for extending the predictive capabilities needed for the extremes of chemical composition, aiding a variety of industrial processes that include advanced nuclear waste remediation and metal refining strategies.
Semrouni, David↗
Work Function Modification via Combined Charge-Based Through-Space Interaction and Surface Interaction
Work function modification of electrodes is an important factor to achieve high performance in organic electronics. However, a clear explanation of the origin of work function modification has remained elusive. Here, it is investigated how the work function of electrodes is affected by the charge-based through-space interaction with the well-known surface interaction. The studies reveal that the formation of a surface dipole leads to a work function shift, even when the work function modifying layer and substrate are separated. A work function shift is also demonstrated by electrophoretic deposition of ionic polyelectrolytes while the same polyelectrolytes do not cause any work function shift when they are spin cast. More noteworthy is that a neutral (nonionic) polymer which has no specific surface-interacting functional groups can induce work function shift of its substrate by a charge-based through-space interaction when deposited by electrospraying. These results provide a more comprehensive understanding of work function modification and motivate the design and selection of a wide range of effective work function modifying layers for organic electronics.
36 MATERIALS SCIENCE↗
Lower functional redundancy in “narrow” than “broad” functions in global soil metagenomics
Understanding the relationship between soil microbial taxonomic compositions and functional profiles is essential for predicting ecosystem functions under various environmental disturbances. However, even though microbial communities are sensitive to disturbance, ecosystem functions remain relatively stable, as soil microbes are likely to be functionally redundant. Microbial functional redundancy may be more associated with “broad” functions carried out by a wide range of microbes than with “narrow” functions in which specific microorganisms specialize. Thus, a comprehensive study to evaluate how microbial taxonomic compositions correlate with broad and narrow functional profiles is necessary. Here, we evaluated soil metagenomes worldwide to assess whether functional and taxonomic diversities differ significantly between the five broad and the five narrow functions that we chose. Our results revealed that, compared with the five broad functions, soil microbes capable of performing the five narrow functions were more taxonomically diverse, and thus their functional diversity was more dependent on taxonomic diversity, implying lower levels of functional redundancy in narrow functions. Co-occurrence networks indicated that microorganisms conducting broad functions were positively related, but microbes specializing in narrow functions were interacting mostly negatively. Our study provides strong evidence to support our hypothesis that functional redundancy is significantly different between broad and narrow functions in soil microbes, as the association of functional diversity with taxonomy was greater in the five narrow than in the five broad functions.
54 ENVIRONMENTAL SCIENCES↗
Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory
Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The four-loop six-gluon NMHV ratio function
We use the hexagon function bootstrap to compute the ratio function which characterizes the next-to-maximally-helicity-violating (NMHV) six-point amplitude in planar N=4 super-Yang-Mills theory at four loops. A powerful constraint comes from dual superconformal invariance, in the form of a Q¯ differential equation, which heavily constrains the first derivatives of the transcendental functions entering the ratio function. At four loops, it leaves only a 34-parameter space of functions. Constraints from the collinear limits, and from the multi-Regge limit at the leading-logarithmic (LL) and next-to-leading-logarithmic (NLL) order, suffice to fix these parameters and obtain a unique result. We test the result against multi-Regge predictions at NNLL and N 3 LL, and against predictions from the operator product expansion involving one and two flux-tube excitations; all cross-checks are satisfied. We study the analytical and numerical behavior of the parity-even and parity-odd parts on various lines and surfaces traversing the three-dimensional space of cross ratios. As part of this program, we characterize all irreducible hexagon functions through weight eight in terms of their coproduct. As a result, we also provide representations of the ratio function in particular kinematic regions in terms of multiple polylogarithms.
1/N expansion↗
Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland
Abstract Peatland ecosystems cover only 3% of the world’s land area; however, they store one-third of the global soil carbon (C). Microbial communities are the main drivers of C decomposition in peatlands, yet we have limited knowledge of their structure and function. While the microbial communities in the Northern Hemisphere peatlands are well documented, we have limited understanding of microbial community composition and function in the Southern Hemisphere peatlands, especially in Australia. We investigated the vertical stratification of prokaryote and fungal communities from Wellington Plains peatland in the Australian Alps. Within the peatland complex, bog peat was sampled from the intact peatland and dried peat from the degraded peatland along a vertical soil depth gradient (i.e., acrotelm, mesotelm, and catotelm). We analyzed the prokaryote and fungal community structure, predicted functional profiles of prokaryotes using PICRUSt, and assigned soil fungal guilds using FUNGuild. We found that the structure and function of prokaryotes were vertically stratified in the intact bog. Soil carbon, manganese, nitrogen, lead, and sodium content best explained the prokaryote composition. Prokaryote richness was significantly higher in the intact bog acrotelm compared to degraded bog acrotelm. Fungal composition remained similar across the soil depth gradient; however, there was a considerable increase in saprotroph abundance and decrease in endophyte abundance along the vertical soil depth gradient. The abundance of saprotrophs and plant pathogens was two-fold higher in the degraded bog acrotelm. Soil manganese and nitrogen content, electrical conductivity, and water table level (cm) best explained the fungal composition. Our results demonstrate that both fungal and prokaryote communities are shaped by soil abiotic factors and that peatland degradation reduces microbial richness and alters microbial functions. Thus, current and future changes to the environmental conditions in these peatlands may lead to altered microbial community structures and associated functions which may have implications for broader ecosystem function changes in peatlands.
Environmental Sciences & Ecology↗
Can Kohn–Sham density functional theory predict accurate charge distributions for both single-reference and multi-reference molecules?
Dipole moments are the first moment of electron density and are fundamental quantities that are often available from experiments. An exchange–correlation functional that leads to an accurate representation of the charge distribution of a molecule should accurately predict the dipole moments of the molecule. It is well known that Kohn–Sham density functional theory (DFT) is more accurate for the energetics of single-reference systems than for the energetics of multi-reference ones, but there has been less study of charge distributions. Here, in this work, we benchmark 48 density functionals chosen with various combinations of ingredients, against accurate experimental data for dipole moments of 78 molecules, in particular 55 single-reference molecules and 23 multi-reference ones. We chose both organic and inorganic molecules, and within the category of inorganic molecules there are both main-group and transition-metal-containing molecules, with some of them being multi-reference. As one would expect, the multi-reference molecules are not as well described by single-reference DFT, and the functionals tested in this work do show larger mean unsigned errors (MUEs) for the 23 multi-reference molecules than the single-reference ones. Five of the 78 molecules have relatively large experimental error bars and were therefore not included in calculating the overall MUEs. For the 73 molecules not excluded, we find that three of the hybrid functionals, B97-1, PBE0, and TPSSh (each with less than or equal to 25% Hartree–Fock (HF) exchange), the range-separated hybrid functional, HSE06 (with HF exchange decreasing from 25% to 0 as interelectronic distance increases), and the hybrid functional, PW6B95 (with 28% HF exchange) are the best performing functionals with each yielding an MUE of 0.18 D. Perhaps the most significant finding of this study is that there exists great similarity among the success rate of various functionals in predicting dipole moments. In particular, of 39 functionals designed as general-purpose functionals and that do not have a global value of 100% HF exchange, the average MUE is 0.23 D, with a standard deviation of only 0.04 D. Among gradient approximations, which are especially interesting because of their speed and portability, the best overall performance is by PBE, HCTH/407, OLYP, OreLYP, and GAM, each with MUE of 0.22 D.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Adversarial autoencoder ensemble for fast and probabilistic reconstructions of few-shot photon correlation functions for solid-state quantum emitters
Second-order photon correlation measurements [g (2) (τ) functions] are widely used to classify single-photon emission purity in quantum emitters or to measure the multiexciton quantum yield of emitters that can simultaneously host multiple excitations – such as quantum dots – by evaluating the value of g (2) (τ = 0). Accumulating enough photons to accurately calculate this value is time consuming and could be accelerated by fitting of few-shot photon correlations. Here, we develop an uncertainty-aware, deep adversarial autoencoder ensemble (AAE) that reconstructs noise-free g (2) (τ) functions from noise-dominated, few-shot inputs. The model is trained with simulated g (2) (τ) functions that are facilely generated by Poisson sampling time bins. The AAE reconstructions are performed orders-of-magnitude faster, with reconstruction errors and estimates of g (2) (τ = 0) that are lower in variance and similar in accuracy compared to Maximum likelihood estimation and Levenberg-Marquardt least-squares fitting approaches, for simulated and experimentally measured few-shot g (2) (τ) functions (~100 two-photon events) of InP/ZnS/ZnSe and CdS/CdSe/CdS quantum dots. The deep-ensemble model comprises eight individual autoencoders, allowing for probabilistic reconstructions of noise-free g (2) (τ) functions, and we show that the predicted variance scales inversely with number of shots, with comparable uncertainties to computationally intensive Markov chain Monte Carlo sampling. Furthermore, this work demonstrates the advantage of machine learning models to perform uncertainty-aware, fast, and accurate reconstructions of simple Poisson-distributed photon correlation functions, allowing for on-the-fly reconstructions and accelerated materials characterization of solid-state quantum emitters.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning
Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. Here, this study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.
54 ENVIRONMENTAL SCIENCES↗
Representing plant diversity in land models: An evolutionary approach to make “Functional Types” more functional
Plants are critical mediators of terrestrial mass and energy fluxes, and their structural and functional traits have profound impacts on local and global climate, biogeochemistry, biodiversity, and hydrology. Yet, Earth System Models (ESMs), our most powerful tools for predicting the effects of humans on the coupled biosphere-atmosphere system, simplify the incredible diversity of land plants into a handful of coarse categories of "Plant Functional Types" (PFTs) that often fail to capture ecological dynamics such as biome distributions. The inclusion of more realistic functional diversity is a recognized goal for ESMs, yet there is currently no consistent, widely accepted way to add diversity to models, that is, to determine what new PFTs to add and with what data to constrain their parameters. Here we review approaches to representing plant diversity in ESMs and draw on recent ecological and evolutionary findings to present an evolution-based functional type approach for further disaggregating functional diversity. Specifically, the prevalence of niche conservatism, or the tendency of closely related taxa to retain similar ecological and functional attributes through evolutionary time, reveals that evolutionary relatedness is a powerful framework for summarizing functional similarities and differences among plant types. We advocate that Plant Functional Types based on dominant evolutionary lineages ("Lineage Functional Types") will provide an ecologically defensible, tractable, and scalable framework for representing plant diversity in next-generation ESMs, with the potential to improve parameterization, process representation, and model benchmarking. We highlight how the importance of evolutionary history for plant function can unify the work of disparate fields to improve predictive modeling of the Earth system.
59 BASIC BIOLOGICAL SCIENCES↗
Kinetic corrections from analytic non-Maxwellian distribution functions in magnetized plasmas
In magnetized plasma physics, almost all developed analytic theories assume a Maxwellian distribution function (MDF) and in some cases small deviations are described using the perturbation theory. The deviations with respect to the Maxwellian equilibrium, called kinetic effects, are required to be taken into account especially for fusion reactor plasmas. Generally, because the perturbation theory is not consistent with observed steady-state non-Maxwellians, these kinetic effects are numerically evaluated by very central processing unit (CPU)-expensive codes, avoiding the analytic complexity of velocity phase space integrals. We develop here a new method based on analytic non-Maxwellian distribution functions constructed from non-orthogonal basis sets in order to (i) use as few parameters as possible, (ii) increase the efficiency to model numerical and experimental non-Maxwellians, (iii) help to understand unsolved problems such as diagnostics discrepancies from the physical interpretation of the parameters, and (iv) obtain analytic corrections due to kinetic effects given by a small number of terms and removing the numerical error of the evaluation of velocity phase space integrals. This work does not attempt to derive new physical effects even if it could be possible to discover one from the better understandings of some unsolved problems, but here we focus on the analytic prediction of kinetic corrections from analytic non-Maxwellians. As applications, examples of analytic kinetic corrections are shown for the secondary electron emission, the Langmuir probe characteristic curve, and the entropy. This is done by using three analytic representations of the distribution function: the Kappa distribution function, the bi-modal or a new interpreted non-Maxwellian distribution function (INMDF). The existence of INMDFs is proved by new understandings of the experimental discrepancy of the measured electron temperature between two diagnostics in JET. As main results, it is shown that (i) the empirical formula for the secondary electron emission is not consistent with a MDF due to the presence of super-thermal particles, (ii) the super-thermal particles can replace a diffusion parameter in the Langmuir probe current formula, and (iii) the entropy can explicitly decrease in presence of sources only for the introduced INMDF without violating the second law of thermodynamics. Moreover, the first order entropy of an infinite number of super-thermal tails stays the same as the entropy of a MDF. The latter demystifies the Maxwell's demon by statistically describing non-isolated systems.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Regional Lung Function Profiles of Stage I and III Lung Cancer Patients: An Evaluation for Functional Avoidance Radiation Therapy
Purpose: The development of clinical trials is underway to use 4-dimensional computed tomography (4DCT) ventilation imaging to preferentially spare functional lung in patients undergoing radiation therapy. The purpose of this work was to generate data to aide with clinical trial design by retrospectively characterizing dosimetric and functional profiles for patients with different stages of lung cancer. Methods and Materials: A total of 118 lung cancer patients (36% stage I and 64% stage III) from 2 institutions were used for the study. A 4DCT-ventilation map was calculated using the patient's 4DCT imaging, deformable image registration, and a density-change–based algorithm. To assess each patient's spatial ventilation profile both quantitative and qualitative metrics were developed, including an observer-based defect observation and metrics based on the ventilation in each lung third. For each patient we used the clinical doses to calculate functionally weighted mean lung doses and metrics that assessed the interplay between the spatial location of the dose and high-functioning lung. Results: Both qualitative and quantitative metrics revealed a significant difference in functional profiles between the 2 stage groups (P<.01). We determined that 65% of stage III and 28% of stage I patients had ventilation defects. Average functionally weighted mean lung dose was 19.6 Gy and 5.4 Gy for stage III and I patients, respectively, with both groups containing patients with large spatial overlap between dose and high-function regions. Conclusion: Our 118-patient retrospective study found that 65% of stage III patients have regionally variant ventilation profiles that are suitable for functional avoidance. Our results suggest that regardless of disease stage, it is possible to have unique spatial interplay between dose and high-functional lung, highlighting the importance of evaluating the function of each patient and developing a personalized functional avoidance treatment approach.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Revised M11 Exchange-Correlation Functional for Electronic Excitation Energies and Ground-State Properties
The ability of Kohn-Sham density functional theory (KS-DFT) to accurately predict various types of electronic excitation energies with (necessarily approximate) exchange-correlation functionals faces several challenges. Chief among these is that valence excitations are usually inherently multiconfigurational and therefore best treated by functionals with local exchange, whereas Rydberg and charge transfer excitations are often better treated with nonlocal exchange. The question arises of whether one can optimize a functional such that all three kinds of excitations (valence, Rydberg, and charge transfer – including long-range charge transfer) are treated in a balanced and accurate way. The goal of the present work is to try to answer that question and then to optimize a functional with the best possible balanced behavior. Of the variety of functional types available, we select range-separated hybrid meta functionals because (i) range separation allows the percentage of Hartree–Fock (HF) exchange to change with interelectronic separation, and therefore, one can have 100% HF exchange at large interelectronic separations, which gives good performance for long-range charge-transfer excitations, while the range separation allows one to simultaneously have smaller values of HF exchange at small and intermediate inter-electronic separations, which give good performance for valence and Rydberg excitations and (ii) meta functionals allow one to obtain better accuracy with high HF exchange than is possible with functionals whose local part depends only on spin densities and their gradients. Furthermore, this work starts with the range-separated hybrid meta functional, M11, and re-optimizes it (with stronger smoothness restraints) against electronic excitation energies and ground-state properties to obtain a new functional called revM11 that gives good performance for all three types of electronic excitations and at the same time gives very good predictions across-the-board for ground-state properties.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗