Real-Time Equation-of-Motion CCSD Cumulant Green's Function.

Many-body excitations in X-ray photoemission spectra have been difficult to simulate from first principles. We have recently developed a cumulant-based one-electron Green's function method using the real-time coupled-cluster-singles equation-of-motion approach (RT-EOM-CCS) that provides a general framework for treating these problems. Here we extend this approach to include double excitations in the ground-state energy and in the coupled cluster amplitudes, which have been implemented using subroutines generated by the Tensor Contraction Engine (TCE). As in the case of the singles approximation, RT-EOM-CCSD yields a nonperturbative cumulant form of the Green's function in terms of the time-dependent cluster amplitudes, adding nonlinear corrections to the traditional cumulant forms. The extended approach is applied to the core-hole spectral function for small molecular systems. We find that, when core-optimized basis sets are used, the doubles contributions reduce the mean absolute errors in the core binding energies of the 10e systems from 0.8 to 0.3 eV. They also significantly improve the quasiparticle-satellite gap by reducing its overestimation from about 3-5 to about 0-1 eV in CH4, NH3, and H2O, and also improving the overall shape of the satellite features. Finally, we demonstrate the application of the new implementation to the larger, classical XPS ESCA series of molecules and show that the singles approximation can be paired with a modest basis set to study carbon speciation.

Advanced calculations of X-ray spectroscopies with FEFF10 and Corvus.

The real-space Green's function code FEFF has been extensively developed and used for calculations of X-ray and related spectra, including X-ray absorption (XAS), X-ray emission (XES), inelastic X-ray scattering, and electron energy-loss spectra. The code is particularly useful for the analysis and interpretation of the XAS fine-structure (EXAFS) and the near-edge structure (XANES) in materials throughout the periodic table. Nevertheless, many applications, such as non-equilibrium systems, and the analysis of ultra-fast pump-probe experiments, require extensions of the code including finite-temperature and auxiliary calculations of structure and vibrational properties. To enable these extensions, we have developed in tandem a new version FEFF10 and new FEFF-based workflows for the Corvus workflow manager, which allow users to easily augment the capabilities of FEFF10 via auxiliary codes. This coupling facilitates simplified input and automated calculations of spectra based on advanced theoretical techniques. The approach is illustrated with examples of high-temperature behavior, vibrational properties, many-body excitations in XAS, super-heavy materials, and fits of calculated spectra to experiment.

Equation-of-Motion Coupled-Cluster Cumulant Green's Function for Excited States and X-Ray Spectra.

Green's function methods provide a robust, general framework within many-body theory for treating electron correlation in both excited states and x-ray spectra. Conventional methods using the Dyson equation or the cumulant expansion are typically based on the GW self-energy approximation. In order to extend this approximation in molecular systems, a non-perturbative real-time coupled-cluster cumulant Green's function approach has been introduced, where the cumulant is obtained as the solution to a system of coupled first order, non-linear differential equations. This approach naturally includes non-linear corrections to conventional cumulant Green's function techniques where the cumulant is linear in the GW self-energy. The method yields the spectral function for the core Green's function, which is directly related to the x-ray photoemission spectra (XPS) of molecular systems. The approach also yields very good results for binding energies and satellite excitations. The x-ray absorption spectrum (XAS) is then calculated using a convolution of the core spectral function and an effective, one-body XAS. Here this approach is extended to include the full coupled-cluster-singles (CCS) core Green's function by including the complete form of the non-linear contributions to the cumulant as well as all single, double, and triple cluster excitations in the CC amplitude equations. This approach naturally builds in orthogonality and shake-up effects analogous to those in the Mahan-Noizeres-de Dominicis edge singularity corrections that enhance the XAS near the edge. The method is illustrated for the XPS and XAS of NH3.

Real-Time Coupled-Cluster Approach for the Cumulant Green's Function.

Green's function methods within many-body perturbation theory provide a general framework for treating electronic correlations in excited states and spectra. Here, we develop the cumulant form of the one-electron Green's function using a real-time coupled-cluster equation-of-motion approach, in an extension of our previous study (Rehr J.; et al. J. Chem. Phys. 2020, 152, 174113). The approach yields a nonperturbative expression for the cumulant in terms of the solution to a set of coupled first-order, nonlinear differential equations. The method thereby adds nonlinear corrections to traditional cumulant methods, which are linear in the self-energy. The approach is applied to the core-hole Green's function and is illustrated for a number of small molecular systems. For these systems, we find that the nonlinear contributions yield significant improvements, both for quasiparticle properties such as core-level binding energies and for inelastic losses that correspond to satellites observed in photoemission spectra.

Equation of motion coupled-cluster cumulant approach for intrinsic losses in x-ray spectra.

We present a combined equation of motion coupled-cluster cumulant Green's function approach for calculating and understanding intrinsic inelastic losses in core level x-ray absorption spectra (XAS) and x-ray photoemission spectra. The method is based on a factorization of the transition amplitude in the time domain, which leads to a convolution of an effective one-body absorption spectrum and the core-hole spectral function. The spectral function characterizes intrinsic losses in terms of shake-up excitations and satellites using a cumulant representation of the core-hole Green's function that simplifies the interpretation. The one-body spectrum also includes orthogonality corrections that enhance the XAS at the edge.

Fast fabrication of reusable polyethersulfone microbial biosensors through biocompatible phase separation.

In biosensors fabrication, entrapment in polymeric matrices allows efficient immobilization of the biorecognition elements without compromising their structure and activity. When considering living cells, the biocompatibility of both the matrix and the polymerization procedure are additional critical factors. Bio-polymeric gels (e.g. alginate) are biocompatible and polymerize under mild conditions, but they have poor stability. Most synthetic polymers (e.g. PVA), on the other hand, present improved stability at the expense of complex protocols involving chemical/physical treatments that decrease their biological compatibility. In an attempt to explore new solutions to this problem we have developed a procedure for the immobilization of bacterial cells in polyethersulfone (PES) using phase separation. The technology has been tested successfully in the construction of a bacterial biosensor for toxicity assessment. Biosensors were coated with a 300  µm bacteria-containing PES membrane, using non-solvent induced phase separation (membrane thickness ≈ 300 µm). With this method, up to 2.3 × 106 cells were immobilized in the electrode surface with an entrapment efficiency of 8.2%, without compromising cell integrity or viability. Biosensing was performed electrochemically through ferricyanide respirometry, with metabolically-active entrapped bacteria reducing ferricyanide in the presence of glucose. PES biosensors showed good stability and reusability during dry frozen storage for up to 1 month. The analytical performance of the sensors was assessed carrying out a toxicity assay in which 3,5-dichlorophenol (DCP) was used as a model toxic compound. The biosensor provided a concentration-dependent response to DCP with half-maximal effective concentration (EC50) of 9.2 ppm, well in agreement with reported values. This entrapment methodology is susceptible of mass production and allows easy and repetitive production of robust and sensitive bacterial biosensors.

Corvus: a framework for interfacing scientific software for spectroscopic and materials science applications.

Corvus, a Python-based package designed for managing workflows of physical simulations that utilize multiple scientific software packages, is presented. Corvus can be run as an executable script with an input file and automatically generated or custom workflows, or interactively, in order to build custom workflows with a set of Corvus-specific tools. Several prototypical examples are presented that link density functional, vibrational and X-ray spectroscopy software packages and are of interest to the synchrotron community. These examples highlight the simplification of complex spectroscopy calculations that were previously limited to expert users, and demonstrate the flexibility of the Corvus infrastructure to tackle more general problems in other research areas.

Electro-addressable conductive alginate hydrogel for bacterial trapping and general toxicity determination.

In biosensors development, alginate hydrogels are a first choice for enabling stable biomolecules entrapment in biocompatible membranes obtained under soft physiological conditions. Although widely exploited, most alginate membranes are isolating and poorly repetitive, which limit their application in biosensing. Significant steps forward on improving repeatability and conductivity have been performed, but to date there is no single protocol for controlled deposition of live cells in replicable conductive alginate layers. Here, cell electrotrapping in conductive alginate hydrogels is examined in order to overcome these limitations. Conductive alginate-coated electrodes are obtained after potentiostatic electrodeposition of graphite-doped alginate samples (up to 4% graphite). The presence of graphite reduces electrode passivation and improves the electrochemical response of the sensor, although still significantly lower than that recorded with the naked electrode. Bacterial electrotrapping in the conductive matrix is highly efficient (4.4 × 107 cells per gel) and repetitive (CV < 0.5%), and does not compromise bacterial integrity or activity (cell viability = 56%). Biosensing based on ferricyanide respirometry yielded a four times increase in biosensor response with respect to non-conductive alginate membrane, providing toxicity values completely comparable to those reported. Cell electrotrapping in conductive hydrogels represents a step forward towards in high-sensitive cell-based biosensors development with important influence in environmental analysis, food and beverage industry as well as clinical diagnosis.

Pyrolysis-gas chromatography-isotope ratio mass spectrometry for monitoring natural additives in polylactic acid active food packages.

Compound-specific isotope analysis (CSIA) usually requires preparative steps (pretreatments, extraction, derivatization) to get amenable chromatographic analytes from bulk geological, biological or synthetic materials. Analytical pyrolysis (Py-GC/MS) can help to overcome such sample manipulation. This communication describe the results obtained by hyphenating analytical pyrolysis (Py-GC) with carbon isotope-ratio mass spectrometry (IRMS) for the analysis of a polylactic acid (PLA) a based bio-plastic extruded with variable quantities of a natural plant extract or oregano essential oil. The chemical structural information of pyrolysates was first determined by conventional analytical pyrolysis and the measure of δ13C in specific compounds was done by coupling a pyrolysis unit to a gas chromatograph connected to a continuous flow IRMS unit (Py-GC-C-IRMS). Using this Py-CSIA device it was possible to trace natural additives with depleted δ13C values produced by C3 photosystem vegetation (cymene: -26.7‰±2.52; terpinene: -27.1‰±0.13 and carvacrol: -27.5‰±1.80 from oregano and two unknown structures: -23.3‰±3.32 and -24.4‰±1.70 and butyl valerate: -24.1‰±3.55 from Allium spp.), within the naturally isotopically enriched bio-plastic backbone derived from corn (C4 vegetation) starch (cyclopentanones: -14.2‰±2.11; lactide enantiomers: -9.2‰±1.56 and larger polymeric units: -17.2‰±1.71). This is the first application of Py-CSIA to characterize a bio-plastic and is shown as a promising tool to study such materials, providing not only a fingerprinting, but also valuable information about the origin of the materials, allowing the traceability of additives and minimizing sample preparation.

Quantitative first-principles calculations of valence and core excitation spectra of solid C60.

We present calculated valence and C 1s near-edge excitation spectra of solid C60 and experimental results measured with high-resolution electron energy-loss spectroscopy. The near-edge calculations are carried out using three different methods: solution of the Bethe-Salpeter equation (BSE) as implemented in the OCEAN suite (Obtaining Core Excitations with ab initio methods and the NIST BSE solver), the excited-electron core-hole approach (XCH), and the constrained-occupancy method using the Stockholm-Berlin core-excitation code, StoBe. The three methods give similar results and are in good agreement with experiment, though the BSE results are the most accurate. The BSE formalism is also used to carry out valence level calculations using the NIST Bethe-Salpeter Equation solver (NBSE). Theoretical results include self-energy corrections to the band gap and band widths, lifetime-damping effects, and Debye-Waller effects in the core-excitation case. A comparison of spectral features to those observed experimentally illustrates the sensitivity of certain features to computational details, such as self-energy corrections to the band structure and core-hole screening.

Sperm whale long-range echolocation sounds revealed by ANTARES, a deep-sea neutrino telescope.

Despite dedicated research has been carried out to adequately map the distribution of the sperm whale in the Mediterranean Sea, unlike other regions of the world, the species population status is still presently uncertain. The analysis of two years of continuous acoustic data provided by the ANTARES neutrino telescope revealed the year-round presence of sperm whales in the Ligurian Sea, probably associated with the availability of cephalopods in the region. The presence of the Ligurian Sea sperm whales was demonstrated through the real-time analysis of audio data streamed from a cabled-to-shore deep-sea observatory that allowed the hourly tracking of their long-range echolocation behaviour on the Internet. Interestingly, the same acoustic analysis indicated that the occurrence of surface shipping noise would apparently not condition the foraging behaviour of the sperm whale in the area, since shipping noise was almost always present when sperm whales were acoustically detected. The continuous presence of the sperm whale in the region confirms the ecological value of the Ligurian sea and the importance of ANTARES to help monitoring its ecosystems.

Paper-based chromatic toxicity bioassay by analysis of bacterial ferricyanide reduction.

Water quality assessment requires a continuous and strict analysis of samples to guarantee compliance with established standards. Nowadays, the increasing number of pollutants and their synergistic effects lead to the development general toxicity bioassays capable to analyse water pollution as a whole. Current general toxicity methods, e.g. Microtox(®), rely on long operation protocols, the use of complex and expensive instrumentation and sample pre-treatment, which should be transported to the laboratory for analysis. These requirements delay sample analysis and hence, the response to avoid an environmental catastrophe. In an attempt to solve it, a fast (15 min) and low-cost toxicity bioassay based on the chromatic changes associated to bacterial ferricyanide reduction is here presented. E. coli cells (used as model bacteria) were stably trapped on low-cost paper matrices (cellulose-based paper discs, PDs) and remained viable for long times (1 month at -20 °C). Apart from bacterial carrier, paper matrices also acted as a fluidic element, allowing fluid management without the need of external pumps. Bioassay evaluation was performed using copper as model toxic agent. Chromatic changes associated to bacterial ferricyanide reduction were determined by three different transduction methods, i.e. (i) optical reflectometry (as reference method), (ii) image analysis and (iii) visual inspection. In all cases, bioassay results (in terms of half maximal effective concentrations, EC50) were in agreement with already reported data, confirming the good performance of the bioassay. The validation of the bioassay was performed by analysis of real samples from natural sources, which were analysed and compared with a reference method (i.e. Microtox). Obtained results showed agreement for about 70% of toxic samples and 80% of non-toxic samples, which may validate the use of this simple and quick protocol in the determination of general toxicity. The minimum instrumentation requirements and the simplicity of the bioassay open the possibility of in-situ water toxicity assessment with a fast and low-cost protocol.

Age of onset of recurrent respiratory papillomatosis: a distribution analysis.

OBJECTIVE: Distribution of age of onset of recurrent respiratory papillomatosis (RRP) is generally described to be bimodal, with peaks at approximately 5 years and 30 years. This assumption has never been scientifically confirmed, and authors tend to refer to an article that does not describe distribution. Knowledge of the distribution of age of onset is important for virological and epidemiological comprehension. The objective of this study was to determine the distribution of age of onset of RRP in a large international sample. DESIGN: Cross-sectional distribution analysis. PARTICIPANTS: Laryngologists from 12 European hospitals provided information on date of birth and date of onset of all their RRP patients treated between 1998 and 2012. Centers that exclusively treated either patients with juvenile onset RRP or patients with adult onset RRP, or were less accessible for one of these groups, were excluded to prevent skewness. MAIN OUTCOME MEASURES: A mixture model was implemented to describe distribution of age of onset. The best fitting model was selected using the Bayesian information criterion. RESULTS: Six hundred and thirty-nine patients were included in the analysis. Age of onset was described by a three component mixture distribution with lognormally distributed components. Recurrent respiratory papillomatosis starts at three median ages 7, 35 and 64 years. CONCLUSIONS: Distribution of age of onset of RRP shows three peaks. In addition to the already adopted idea of age peaks at paediatric and adult age, there is an additional peak around the age of 64.

[Runners with back pain: to run or not to run?]. / Coureurs souffrant de maux de dos: courir ou ne pas courir?

We evaluated the perceived impact of physical activity on back pain in runners. Information from 777 runners participating in a half marathon was obtained with a questionnaire about basic data, features of the weekly training and the relationship between running activity and back pain. Half the runners (54.1%) reported a history of back pain. Among them, almost twice as many reported an improvement (49%) than a worsening (27%) of pain with running. No significant associations were found between perceived impact of running on back pain and other factors. In our study favorable effects were much more frequent than unfavorable ones. Further studies are needed to better understand these effects.

Pyrolysis-gas chromatography-isotope ratio mass spectrometry of polyethylene.

Polyethylene is probably the most used plastic material in daily life and its accurate analysis is of importance. In this communication the chemical structure of polyethylenes is studied in detail using conventional analytical pyrolysis (Py-GC/MS), bulk stable isotopic analysis (IRMS) and pyrolysis compound specific stable isotopic analysis (Py-CSIA) to measure stable isotope proportions (δ(13)C, δ(15)N and δD) of polyethylene pyrolysis compounds. Polyethylene pyrolysis yields triplet peaks of n-alkanes, α-alkenes and α,ω-alkanedienes. No differences were found for bulk δ(13)C among different polyethylene types. However, conspicuous differences in δD were evident. It was possible to assign structure δ(13)C and δD values to specific polyethylene pyrolysis products in the range 12-18 carbon chain length. Conspicuous differences were found for the pyrolysis products with unsaturated moieties showing significant higher δD values than saturated chains (alkanes) that were deuterium depleted. In addition, a full isotopic fingerprinting (δ(13)C, δ(15)N and δD) for a dye (o-chloroaniline) contained in a polyethylene is reported. To the best of our knowledge this is the first application Py-CSIA to the study of a synthetic polymer. This hyphenated analytical technique is a promising tool to study synthetic materials, providing not only a fingerprinting, but also allowing the traceability of the polymerization process and the origin of the materials.

Fast and sensitive optical toxicity bioassay based on dual wavelength analysis of bacterial ferricyanide reduction kinetics.

Global urban and industrial growth, with the associated environmental contamination, is promoting the development of rapid and inexpensive general toxicity methods. Current microbial methodologies for general toxicity determination rely on either bioluminescent bacteria and specific medium solution (i.e. Microtox(®)) or low sensitivity and diffusion limited protocols (i.e. amperometric microbial respirometry). In this work, fast and sensitive optical toxicity bioassay based on dual wavelength analysis of bacterial ferricyanide reduction kinetics is presented, using Escherichia coli as a bacterial model. Ferricyanide reduction kinetic analysis (variation of ferricyanide absorption with time), much more sensitive than single absorbance measurements, allowed for direct and fast toxicity determination without pre-incubation steps (assay time=10 min) and minimizing biomass interference. Dual wavelength analysis at 405 (ferricyanide and biomass) and 550 nm (biomass), allowed for ferricyanide monitoring without interference of biomass scattering. On the other hand, refractive index (RI) matching with saccharose reduced bacterial light scattering around 50%, expanding the analytical linear range in the determination of absorbent molecules. With this method, different toxicants such as metals and organic compounds were analyzed with good sensitivities. Half maximal effective concentrations (EC50) obtained after 10 min bioassay, 2.9, 1.0, 0.7 and 18.3 mg L(-1) for copper, zinc, acetic acid and 2-phenylethanol respectively, were in agreement with previously reported values for longer bioassays (around 60 min). This method represents a promising alternative for fast and sensitive water toxicity monitoring, opening the possibility of quick in situ analysis.

Dynamic structural disorder in supported nanoscale catalysts.

We investigate the origin and physical effects of "dynamic structural disorder" (DSD) in supported nano-scale catalysts. DSD refers to the intrinsic fluctuating, inhomogeneous structure of such nano-scale systems. In contrast to bulk materials, nano-scale systems exhibit substantial fluctuations in structure, charge, temperature, and other quantities, as well as large surface effects. The DSD is driven largely by the stochastic librational motion of the center of mass and fluxional bonding at the nanoparticle surface due to thermal coupling with the substrate. Our approach for calculating and understanding DSD is based on a combination of real-time density functional theory/molecular dynamics simulations, transient coupled-oscillator models, and statistical mechanics. This approach treats thermal and dynamic effects over multiple time-scales, and includes bond-stretching and -bending vibrations, and transient tethering to the substrate at longer ps time-scales. Potential effects on the catalytic properties of these clusters are briefly explored. Model calculations of molecule-cluster interactions and molecular dissociation reaction paths are presented in which the reactant molecules are adsorbed on the surface of dynamically sampled clusters. This model suggests that DSD can affect both the prefactors and distribution of energy barriers in reaction rates, and thus can significantly affect catalytic activity at the nano-scale.

Detection of cylindrospermopsin toxin markers in cyanobacterial algal blooms using analytical pyrolysis (Py-GC/MS) and thermally-assisted hydrolysis and methylation (TCh-GC/MS).

The hepatotoxin cylindrospermopsin (CYN) is produced by freshwater cyanobacteria becoming an emerging threat for human health. Methods for the rapid determination of CYN in environmental samples are needed. Conventional analytical pyrolysis (Py-GC/MS) and thermally-assisted hydrolysis and methylation (TCh-GC/MS) were used to study a CYN standard, two Aphanizomenon ovalisporum cultures (CYN+) and one culture of Cylindrospermopsis raciborskii (CYN-). A micro-furnace pyrolyzer was used directly attached to a GC/MS system fitted with a 30 m × 250 µm × 0.25 µm film thickness column (14% cyanopropyl phenyl, 86% dimethyl polysiloxane pahase composition). Oven temperature was held at 50 °C for 1 min and increased to 100 °C at 30 °C min(-1), from 100 °C to 300 °C at 10 °C min(-1), and stabilized at 300 °C for 10 min using helium (1 mL min(-1)) as carrier gas. Pyrolysis at 500 °C yield over 70 compounds with 20 specific for CYN+ samples. Two peaks containing a diagnostic fragment (m/z 194) were found at 25.0 and 28.9 min only in CYN+ samples. Fewer peaks with limited diagnostic value were released after TCh-GC/MS, including breakdown products and TMAH adducts. A compound was detected that may correspond to the CYN molecule (MW 415 Da) thermoevaporation product after the loss of SO3 (MW 80 Da). This TCh-GC/MS peak (m/z 336) together with the fragments obtained by conventional Py-GC/MS (m/z 194) are diagnostic ions with potential use for the direct detection of CYN toxin in environmental samples at last with an estimated 5 ppm detection threshold.

A transferable H2O interaction potential based on a single center multipole expansion: SCME.

A transferable potential energy function for describing the interaction between water molecules is presented. The electrostatic interaction is described rigorously using a multipole expansion. Only one expansion center is used per molecule to avoid the introduction of monopoles. This single center approach turns out to converge and give close agreement with ab initio calculations when carried out up to and including the hexadecapole. Both dipole and quadrupole polarizability are included. All parameters in the electrostatic interaction as well as the dispersion interaction are taken from ab initio calculations or experimental measurements of a single water molecule. The repulsive part of the interaction is parametrized to fit ab initio calculations of small water clusters and experimental measurements of ice Ih. The parametrized potential function was then used to simulate liquid water and the results agree well with experiment, even better than simulations using some of the point charge potentials fitted to liquid water. The evaluation of the new interaction potential for condensed phases is fast because point charges are not present and the interaction can, to a good approximation, be truncated at a finite range.

Safety of intralesional cidofovir in patients with recurrent respiratory papillomatosis: an international retrospective study on 635 RRP patients.

Intralesional use of cidofovir (Vistide(®)) has been one of the mainstays of adjuvant therapy in patients with recurrent respiratory papillomatosis (RRP) since 1998. In 2011, a communication provided by the producer of cidofovir addressed very serious side effects concerning its off-label use. As this was a general warning, it was inconclusive whether this would account for its use in RRP. The aim of this study is to determine whether nephrotoxic, neutropenic, or oncogenic side effects have occurred after intralesional use of cidofovir in patients with RRP. Update of recent developments in RRP, a multicentre questionnaire and a multicentre retrospective chart review. Sixteen hospitals from eleven countries worldwide submitted records of 635 RRP patients, of whom 275 were treated with cidofovir. RRP patients received a median of three intralesional injections (interquartile range 2-6). There were no statistical differences in occurrence of neutropenia or renal dysfunction before and after cidofovir. There was no statistical difference in occurrence of upper airway and tracheal malignancies between the cidofovir and the non-cidofovir group. In this retrospective patient chart review, no clinical evidence was found for more long-term nephrotoxicity, neutropenia or laryngeal malignancies after the administration of intralesional cidofovir in RRP patients.