Mobilization of Pollutant-Degrading Bacteria by Eukaryotic Zoospores

This study was supported by the Spanish Ministry of Science and Innovation (CGL2010-22068-C02-01 and CGL2013- 44554-R), the Andalusian Government (RNM 2337), and the CSIC JAE Program (RS). PvW has funding support from the BBSRC and NERC. Thanks are also given to Sara Hosseini of the Uppsala BioCenter, SLU, Uppsala, Sweden for a useful discussion on oomycete zoospores.Peer reviewedPostprin

Learning a local-variable model of aromatic and conjugated systems

A collection of new approaches to building and training neural networks, collectively referred to as deep learning, are attracting attention in theoretical chemistry. Several groups aim to replace computationally expensive <i>ab initio</i> quantum mechanics calculations with learned estimators. This raises questions about the representability of complex quantum chemical systems with neural networks. Can local-variable models efficiently approximate nonlocal quantum chemical features? Here, we find that convolutional architectures, those that only aggregate information locally, cannot efficiently represent aromaticity and conjugation in large systems. They cannot represent long-range nonlocality known to be important in quantum chemistry. This study uses aromatic and conjugated systems computed from molecule graphs, though reproducing quantum simulations is the ultimate goal. This task, by definition, is both computable and known to be important to chemistry. The failure of convolutional architectures on this focused task calls into question their use in modeling quantum mechanics. To remedy this heretofore unrecognized deficiency, we introduce a new architecture that propagates information back and forth in waves of nonlinear computation. This architecture is still a local-variable model, and it is both computationally and representationally efficient, processing molecules in sublinear time with far fewer parameters than convolutional networks. Wave-like propagation models aromatic and conjugated systems with high accuracy, and even models the impact of small structural changes on large molecules. This new architecture demonstrates that some nonlocal features of quantum chemistry can be efficiently represented in local variable models

On the Electronic Spectroscopy of Closed Shell Cations Derived From Resonance Stabilized Radicals: Insights From Theory and Franck-Condon Analysis

Context. Recent attention has been directed on closed-shell aromatic cations as potential carriers of the diffuse interstellar bands. The spectra of mass-selected, matrix-isolated benzylium, and tropylium cations were recently reported. The visible spectrum of benzylium exhibits a large Franck-Condon (FC) envelope, inconsistent with diffuse interstellar band carriers. Aims. We perform a computational analysis of the experimentally studied benzylium spectrum before extending the methods to a range of larger, closed-shell aromatic cations to determine the potential for this class of systems as diffuse interstellar band carriers. Methods. Density functional theory (DFT), time-dependant ((TD)DFT), and multi-configurational self-consistent field second-order perturbation theory (MRPT2) methods in concert with multidimensional FC analysis is used to model the benzylium spectrum. These methods are extended to larger closed-shell aromatic hydrocarbon cations derived from resonance-stabilized radicals, which are predicted to show strong S0 → Sn transitions in the visible region. The ionization energies of a range of these systems are also calculated by DFT. Results. The simulated benzylium spectrum was found to yield excellent agreement with the experimental spectrum showing an extended progression in a low frequency (510 cm-1) ring distortion mode. The FC progression was found to be significantly quenched in the larger species: 1-indanylium, 1-naphthylmethylium, and fluorenium. Excitation and ionization energies of the closed-shell cations were found to be consistent with diffuse interstellar band carriers, with the former lying in the visible range and the latter straddling the Lyman limit in the 13−14 eV range. Conclusions. Large closed-shell polycyclic aromatic hydrocarbon cations remain viable candidate carriers of the diffuse interstellar bands

Supercritical Pyrolysis of 1-Methylnaphthalene

Fuels used in future high-speed jet aircraft will act as coolants to absorb excess heat produced by the engine, exposing the fuel to elevated temperatures and pressures beyond the fuel’s critical point before entering the combustion environment. Fuels used in this capacity are subject to pyrolysis reactions in the supercritical environment, forming polycyclic aromatic hydrocarbons (PAH) and eventually carbonaceous solids, a disastrous effect for aircraft operation. Thus, it is important to understand how different components of jet fuel will react in the supercritical pyrolysis environment, particularly if their reactions will lead to PAH and/or carbonaceous solids. To better understand these reactions, the model fuel 1-methylnaphthalene, an aromatic component of jet fuel, has been investigated in order to determine the supercritical pyrolysis conditions that form PAH and carbonaceous solids. Experiments have been performed at temperatures ranging from 550 to 650 °C, pressures from 50 to 110 atm, and residence times from 70 to 200 seconds in a supercritical fluid flow reactor. The products have been analyzed by high pressure liquid chromatography (HPLC) with diode-array ultraviolet-visible detection (UV) in series with mass spectrometry (MS), as well as gas chromatography with flame ionization detection and mass spectrometry. Over thirty PAH products have been identified, seventeen of which have never before been reported as products of 1-methylnaphthalene pyrolysis or combustion. A 9-ring PAH product, benzo[cd]phenanthro[1,2,3-lm]perylene, has been identified for the first time as a product of any fuel. The structures of all of the products identified from supercritical 1-methylnaphthalene pyrolysis reveal that in this environment, the two-ring aromatic unit remains intact. Reaction pathways explaining the formation of each product species and yield profiles of the products species at varying temperatures and pressures are presented. All PAH product yields were found to increase with respect to both increasing temperature and pressure, and the largest PAH exhibited dramatic increases in yields at conditions where the onset of solids formation was observed. The conversion of 1-methylnaphthalene conformed to a global first-order kinetic reaction rate, and the pressure-dependent and temperature-dependent parameters of the reaction rate have been calculated with respect to conversion of the reactant

Ediacara biota flourished in oligotrophic and bacterially dominated marine environments across Baltica.

Middle-to-late Ediacaran (575-541 Ma) marine sedimentary rocks record the first appearance of macroscopic, multicellular body fossils, yet little is known about the environments and food sources that sustained this enigmatic fauna. Here, we perform a lipid biomarker and stable isotope (δ15Ntotal and δ13CTOC) investigation of exceptionally immature late Ediacaran strata (&lt;560 Ma) from multiple locations across Baltica. Our results show that the biomarker assemblages encompass an exceptionally wide range of hopane/sterane ratios (1.6-119), which is a broad measure of bacterial/eukaryotic source organism inputs. These include some unusually high hopane/sterane ratios (22-119), particularly during the peak in diversity and abundance of the Ediacara biota. A high contribution of bacteria to the overall low productivity may have bolstered a microbial loop, locally sustaining dissolved organic matter as an important organic nutrient. These oligotrophic, shallow-marine conditions extended over hundreds of kilometers across Baltica and persisted for more than 10 million years