Using Gaussian Process Regression to Simulate the Vibrational Raman Spectra of Molecular Crystals

Vibrational properties of molecular crystals are constantly used as structural fingerprints, in order to identify both the chemical nature and the structural arrangement of molecules. The simulation of these properties is typically very costly, especially when dealing with response properties of materials to e.g. electric fields, which require a good description of the perturbed electronic density. In this work, we use Gaussian process regression (GPR) to predict the static polarizability and dielectric susceptibility of molecules and molecular crystals. We combine this framework with ab initio molecular dynamics to predict their anharmonic vibrational Raman spectra. We stress the importance of data representation, symmetry, and locality, by comparing the performance of different flavors of GPR. In particular, we show the advantages of using a recently developed symmetry-adapted version of GPR. As an examplary application, we choose Paracetamol as an isolated molecule and in different crystal forms. We obtain accurate vibrational Raman spectra in all cases with fewer than 1000 training points, and obtain improvements when using a GPR trained on the molecular monomer as a baseline for the crystal GPR models. Finally, we show that our methodology is transferable across polymorphic forms: we can train the model on data for one structure, and still be able to accurately predict the spectrum for a second polymorph. This procedure provides an independent route to access electronic structure properties when performing force-evaluations on empirical force-fields or machine-learned potential energy surfaces

Distribution of inorganic and organic nutrients in the South Pacific Ocean – evidence for long-term accumulation of organic matter in nitrogen-depleted waters

International audienceThe BIOSOPE cruise of the RV Atalante was devoted to study the biogeochemical properties in the South Pacific between the Marquesas Islands (141° W–8° S) and the Chilean upwelling (73° W–34° S). The 8000 km cruise had the opportunity to encounter different trophic situations, and especially strong oligotrophic conditions in the Central South Pacific Gyre (SPG, between 123° W and 101° W). In this isolated region, nitrate was undetectable between surface and 160–180 m, while regenerated nitrogen (nitrite and ammonium) only revealed some traces (-1), even in the subsurface maximum. Integrated nitrate over the photic layer, which reached 165 m, was close to zero. In spite of this severe nitrogen-depletion, phosphate was always present at significant concentrations (˜0.1 µmoles l-1), while silicate maintained at low but classical oceanic levels (˜1 µmoles l-1). In contrast, the Marquesas region (MAR) at west and Chilean upwelling (UPW) at east were characterized by large nutrient contents one hundred to one thousand fold higher than in the SPG. Distribution of surface chlorophyll concentration reflected this gradient of nitrate availability. The lowest value (0.023 nmoles l-1) was measured in the centre of the SPG, where integrated chlorophyll over the photic layer was very weak (˜10 mg m-2), since a great part (up to 50%) of the deep chlorophyll maximum (DCM) was located below the 1% light. But, because of the relative high concentration encountered in the DCM (0.2 µg l-1), chlorophyll a content over the photic layer varied much less (by a factor 2 to 5) than the nitrate content. In contrast to chlorophyll a, integrated content of particulate organic matter (POM) remained more or less constant along the investigated area (500 mmoles m-2, 60 mmoles m-2 and 3.5 mmoles m-2 for particulate organic carbon, particulate organic nitrogen and particulate organic phosphorus, respectively), except in the upwelling where values were two fold higher. Extensive comparison has shown that glass fiber GF/F filters efficiency collected particulate chlorophyll, while a significant fraction of POM (up to 50%) passed trough this filter and was retained by 0.2 µm Teflon membrane. The most striking feature was the large accumulation of dissolved organic matter (DOM) in the SPG relative to surrounding waters, especially dissolved organic carbon (DOC) where concentrations were at levels rarely measured in oceanic waters (>100 µmoles l-1). Due to this large pool of DOM over the whole photic layer of the SPG, integrated values followed an opposite geographical pattern than this of inorganic nutrients with a large accumulation within the centre of the SPG. While suspended particulate matter in the mixed layer had C/N ratio largely conform to Redfield stoichiometry (C/N˜6.6), marked deviations were observed in this excess DOM (C/N˜16 to 23). The existence of C-rich dissolved organic matter is recognized as a feature typical of oligotrophic waters, requiring the over consumption of carbon. Thus, in spite of strong nitrate-depletion leading to low chlorophyll biomass, the closed ecosystem of the SPG can produce a large amount of carbon. The implications of this finding are discussed, the conclusion being that, due to the lack of seasonal vertical mixing and weak lateral advection, the dissolved organic carbon biologically produced can be accumulated and stored in the photic layer for a very long period

Nitrous oxide distribution and its origin in the central and eastern South Pacific Subtropical Gyre

The mechanisms of microbial nitrous oxide (N<sub>2</sub>O) production in the ocean have been the subject of many discussions in recent years. New isotopomeric tools can further refine our knowledge of N<sub>2</sub>O sources in natural environments. This study compares hydrographic, N<sub>2</sub>O concentration, and N<sub>2</sub>O isotopic and isotopomeric data from three stations along a coast-perpendicular transect in the South Pacific Ocean, extending from the center (Sts. GYR and EGY) of the subtropical oligotrophic gyre (~26° S; 114° W) to the upwelling zone (St. UPX) off the central Chilean coast (~34° S). Although AOU/N<sub>2</sub>O and NO<sub>3</sub><sup>−</sup> trends support the idea that most of the N<sub>2</sub>O (mainly from intermediate water (200–600 m)) comes from nitrification, N<sub>2</sub>O isotopomeric composition (intramolecular distribution of <sup>15</sup>N isotopes) expressed as SP (site preference of <sup>15</sup>N) shows low values (10 to 12permil) that could be attributed to the production through of microbial nitrifier denitrification (reduction of nitrite to N<sub>2</sub>O mediated by ammonium oxidizers). The coincidence of this SP signal with high – stability layer, where sinking organic particles can accumulate, suggests that N<sub>2</sub>O could be produced by nitrifier denitrification inside particles. It is postulated that deceleration of particles in the pycnocline can modify the advection - diffusion balance inside particles, allowing the accumulation of nitrite and O<sub>2</sub> depletion suitable for nitrifier denitrication. As lateral advection seems to be relatively insignificant in the gyre, in situ nitrifier denitrification could account for 40–50% of the N<sub>2</sub>O produced in this layer. In contrast, coastal upwelling system is characterized by O<sub>2</sub> deficient condition and some N deficit in a eutrophic system. Here, N<sub>2</sub>O accumulates up to 480% saturation, and isotopic and isotopomer signals show highly complex N<sub>2</sub>O production processes, which presumably reflect both the effect of nitrification and denitrification at low O<sub>2</sub> levels on N<sub>2</sub>O production, but net N<sub>2</sub>O consumption by denitrification was not observed

Periodic formation and propagation of double layers in the expanding chamber of an inductive discharge operating in Ar/SF₆ mixtures

It has previously been shown [Tuszewski et al., Plasma Sources Sci. Technol.12, 396 (2003)] that inductive discharges in electronegative gases are subject to two types of instability: the sourceinstability related to the E to H transition and a transport instability, occurring downstream when an expanding chamber is present. These two types of instability are observed in our “helicon” reactor operated without a static magnetic field in low-pressure Ar∕SF6 mixtures. Temporally and spatially resolved measurements show that, in our experiment, the downstream instability is a periodic formation and propagation of a double layer. The double layer is born at the end of the source tube and propagates slowly to the end of the expansion region with a velocity of 150ms⁻¹

Short-term changes in particulate fluxes measured by drifting sediment traps during end summer oligotrophic regime in the NW Mediterranean Sea

Short-term changes in the flux of particulate matter were determined in the central north western Mediterranean Sea (near DYFAMED site) using drifting sediment traps at 200 m depth in the course of the DYNAPROC 2 cruise (14 September–17 October 2004). In this period of marked water column stratification, POC fluxes varied by an order of magnitude, in the range of 0.03–0.29 mgC m<sup>−2</sup> h<sup>−1</sup> over the month and showed very rapid and high variations. Particulate carbon export represented less than 5% of integrated primary production, suggesting that phytoplankton production was essentially sustained by internal recycling of organic matter and retained within the photic zone. While PON and POP fluxes paralleled one another, the elemental ratios POC/PON and POC/POP, varied widely over short-term periods. Values of these ratios generally higher than the conventional Redfield ratio, together with the very low chlorophyll a flux recorded in the traps (mean 0.017 μg m<sup>−2</sup> h<sup>−1</sup>), and the high phaeopigment and acyl lipid hydrolysis metabolite concentrations of the settling material, indicated that the organic matter reaching 200 m depth was reworked (by grazing, fecal pellets production, degradation) and that algal sinking, dominated by nano- and picoplankton, made a small contribution to the downward flux. Over time, the relative abundance of individual lipid classes in organic matter (OM) changed from glycolipids-dominated to neutral (wax esters, triacylglycerols) and phospholipids-dominated, suggesting ecosystem maturation as well as rapid and continual exchanges between dissolved, suspended and sinking pools. Our most striking result was documenting the rapid change in fluxes of the various measured parameters. In the situation encountered here, with dominant regenerated production, a decrease of fluxes was noticed during windy periods (possibly through reduction of grazing). But fluxes increased as soon as calm conditions settle

Equilibrium model for two low-pressure electronegative plasmas connected by a double layer

Plihon et al. [J. Appl. Phys.98, 023306 (2005)] have recently shown that double layers usually form during the expansion of a low pressure electronegative plasma. These double layers act as permeable internal boundaries between the source (upstream) plasma and the downstream expanding plasma; positive ions flow from upstream to downstream whereas negative ions flow in the opposite direction. So far, the detailed physical mechanisms leading to their formation have not been identified. In this paper, we develop a model for the two plasma equilibria, upstream and downstream, assuming that the double layer exists and couples the two plasmas. At very low pressure, typically 0.5mTorr, the coupling is strong and acts both ways. The negative ions created downstream contributes to the upstream equilibrium as well as the upstream positive ions contribute to the downstream equilibrium. As the pressure increases, the situation becomes asymmetric. The sourceplasma is not affected by the negative ions flowing from downstream, whereas the positive ions coming from the source control the downstream plasma equilibrium, where local ionization is negligible.This work has been supported by the European Space Agency, under Ariadna Study Contract No. ACT-04-3101. One of the authors A.J.L. acknowledges the hospitality of the LPTP, where the collaboration was begun

Collective modes in uniaxial incommensurate-commensurate systems with the real order parameter

The basic Landau model for uniaxial systems of the II class is nonintegrable, and allows for various stable and metastable periodic configurations, beside that representing the uniform (or dimerized) ordering. In the present paper we complete the analysis of this model by performing the second order variational procedure, and formulating the combined Floquet-Bloch approach to the ensuing nonstandard linear eigenvalue problem. This approach enables an analytic derivation of some general conclusions on the stability of particular states, and on the nature of accompanied collective excitations. Furthermore, we calculate numerically the spectra of collective modes for all states participating in the phase diagram, and analyze critical properties of Goldstone modes at all second order and first order transitions between disordered, uniform and periodic states. In particular it is shown that the Goldstone mode softens as the underlying soliton lattice becomes more and more dilute.Comment: 19 pages, 16 figures, REVTeX, to be published in Journal of Physics A: Mathematical and Genera

ClinGen Myeloid Malignancy Variant Curation Expert Panel recommendations for germline RUNX1 variants

Standardized variant curation is essential for clinical care recommendations for patients with inherited disorders. Clinical Genome Resource (ClinGen) variant curation expert panels are developing disease-associated gene specifications using the 2015 American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines to reduce curation discrepancies. The ClinGen Myeloid Malignancy Variant Curation Expert Panel (MM-VCEP) was created collaboratively between the American Society of Hematology and ClinGen to perform gene- and disease-specific modifications for inherited myeloid malignancies. The MM-VCEP began optimizing ACMG/AMP rules for RUNX1 because many germline variants have been described in patients with familial platelet disorder with a predisposition to acute myeloid leukemia, characterized by thrombocytopenia, platelet functional/ultrastructural defects, and a predisposition to hematologic malignancies. The 28 ACMG/AMP codes were tailored for RUNX1 variants by modifying gene/disease specifications, incorporating strength adjustments of existing rules, or both. Key specifications included calculation of minor allele frequency thresholds, formulating a semi-quantitative approach to counting multiple independent variant occurrences, identifying functional domains and mutational hotspots, establishing functional assay thresholds, and characterizing phenotype-specific guidelines. Preliminary rules were tested by using a pilot set of 52 variants; among these, 50 were previously classified as benign/likely benign, pathogenic/likely pathogenic, variant of unknown significance (VUS), or conflicting interpretations (CONF) in ClinVar. The application of RUNX1-specific criteria resulted in a reduction in CONF and VUS variants by 33%, emphasizing the benefit of gene-specific criteria and sharing internal laboratory data.Xi Luo, Simone Feurstein, Shruthi Mohan, Christopher C. Porter, Sarah A. Jackson, Sioban Keel ... et al

Observations of open-ocean deep convection in the northwestern Mediterranean Sea: Seasonal and interannual variability of mixing and deep water masses for the 2007-2013 Period

We present here a unique oceanographic and meteorological data set focus on the deep convection processes. Our results are essentially based on in situ data (mooring, research vessel, glider, and profiling float) collected from a multiplatform and integrated monitoring system (MOOSE: Mediterranean Ocean Observing System on Environment), which monitored continuously the northwestern Mediterranean Sea since 2007, and in particular high‐frequency potential temperature, salinity, and current measurements from the mooring LION located within the convection region. From 2009 to 2013, the mixed layer depth reaches the seabed, at a depth of 2330m, in February. Then, the violent vertical mixing of the whole water column lasts between 9 and 12 days setting up the characteristics of the newly formed deep water. Each deep convection winter formed a new warmer and saltier “vintage” of deep water. These sudden inputs of salt and heat in the deep ocean are responsible for trends in salinity (3.3 ± 0.2 × 10−3/yr) and potential temperature (3.2 ± 0.5 × 10−3 C/yr) observed from 2009 to 2013 for the 600–2300 m layer. For the first time, the overlapping of the three “phases” of deep convection can be observed, with secondary vertical mixing events (2–4 days) after the beginning of the restratification phase, and the restratification/spreading phase still active at the beginning of the following deep convection event