Assessment of the potential energy hypersurfaces in thymine within multiconfigurational theory: CASSCF vs. CASPT2

The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted 1(ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected

Molecular Basis of SARS-CoV-2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches

The emergence in late 2019 of the coronavirus SARS-CoV-2 has resulted in the breakthrough of the COVID-19 pandemic that is presently affecting a growing number of countries. The development of the pandemic has also prompted an unprecedented effort of the scientific community to understand the molecular bases of the virus infection and to propose rational drug design strategies able to alleviate the serious COVID-19 morbidity. In this context, a strong synergy between the structural biophysics and molecular modeling and simulation communities has emerged, resolving at the atomistic level the crucial protein apparatus of the virus and revealing the dynamic aspects of key viral processes. In this Review, we focus on how in silico studies have contributed to the understanding of the SARS-CoV-2 infection mechanism and the proposal of novel and original agents to inhibit the viral key functioning. This Review deals with the SARS-CoV-2 spike protein, including the mode of action that this structural protein uses to entry human cells, as well as with nonstructural viral proteins, focusing the attention on the most studied proteases and also proposing alternative mechanisms involving some of its domains, such as the SARS unique domain. We demonstrate that molecular modeling and simulation represent an effective approach to gather information on key biological processes and thus guide rational molecular design strategies

Quantum chemistry of the excited state: recent trends in methods developments and applications

Advances (2016–2017) in Quantum Chemistry of the Excited State (QCEX) are presented in this book chapter focusing firstly on developments of methodology and excited-state reaction-path computational strategies and secondly on the applications of QCEX to study light–matter interaction in distinct fields of biology, (nano)-technology, medicine and the environment. We highlight in this contribution developments of static and dynamic electron-correlation methods and methodological approaches to determine dynamical properties, recent examples of the roles of conical intersections, novel DNA spectroscopy and photochemistry findings, photo-sensitisation mechanisms in biological structures and the current knowledge on chemi-excitation mechanisms that give rise to light emission (in the chemiluminescence and bioluminescence phenomena)

An Airborne Simulation of the SMAP Data Stream

No abstract availabl

SMOS Measurements Preliminary Validation: Objectives and Approach

European Geosciences Union General Assembly, 2-7 May 2010, Vienna, Austria.-- 2 pagesThe Earth Explorer Soil Moisture and Ocean Salinity (SMOS) mission was successfully launched on November 2nd, 2009, in the framework of the European Space Agency Living Planet programme. It will provide long-awaited remotely-sensed Sea Surface Salinity (SSS) maps over the oceans with a 3-day revisiting time [1]. The SMOS Barcelona Expert Centre (SMOS-BEC) in Barcelona, Spain, will be involved in several activities at different levels of the salinity retrieval processing chain, which are classified according to the objectives/issues being addressed. In particular, those described hereafter refer to the validation of the products and the consolidation/improvement of the salinity retrieval procedure itself [2]. This will be carried out by performing specific comparisons against modelled brightness temperatures (TB) or external salinity data sources. Due to start at the beginning of the Commissioning Phase, the post-launch 6-month checkout and calibration period, these studies will continue through the nominal satellite operation phase. They will support the choice of an optimal data selection strategy in regard to the existing trade-off, for instance the Ascending/Descending tracks selection, the AF-FOV/EAF-FOV (Alias-Free Field Of View/Extended Alias-Free Field Of View) selection, and some possible across-track data filtering. Moreover, they will help in the definition of an optimal processing configuration (separated polarization retrieval versus first Stokes parameter retrieval). Concerning the TB, the approach is to perform inter-comparisons of the TB departures (SMOS TB minus modelled TB, assuming knowledge of auxiliary information and proper TB direct modelling). [...]Peer reviewe

Functional traits determine plant co-occurrence more than environment or evolutionary relatedness in global drylands

Plant–plant interactions are driven by environmental conditions, evolutionary relationships (ER) and the functional traits of the plants involved. However, studies addressing the relative importance of these drivers are rare, but crucial to improve our predictions of the effects of plant–plant interactions on plant communities and of how they respond to differing environmental conditions. To analyze the relative importance of – and interrelationships among – these factors as drivers of plant–plant interactions, we analyzed perennial plant co-occurrence at 106 dryland plant communities established across rainfall gradients in nine countries. We used structural equation modelling to disentangle the relationships between environmental conditions (aridity and soil fertility), functional traits extracted from the literature, and ER, and to assess their relative importance as drivers of the 929 pairwise plant–plant co-occurrence levels measured. Functional traits, specifically facilitated plants’ height and nurse growth form, were of primary importance, and modulated the effect of the environment and ER on plant–plant interactions. Environmental conditions and ER were important mainly for those interactions involving woody and graminoid nurses, respectively. The relative importance of different plant–plant interaction drivers (ER, functional traits, and the environment) varied depending on the region considered, illustrating the difficulty of predicting the outcome of plant–plant interactions at broader spatial scales. In our global-scale study on drylands, plant–plant interactions were more strongly related to functional traits of the species involved than to the environmental variables considered. Thus, moving to a trait-based facilitation/competition approach help to predict that: (1) positive plant–plant interactions are more likely to occur for taller facilitated species in drylands, and (2) plant–plant interactions within woody-dominated ecosystems might be more sensitive to changing environmental conditions than those within grasslands. By providing insights on which species are likely to better perform beneath a given neighbour, our results will also help to succeed in restoration practices involving the use of nurse plants

Photochemistry of oxidized Hg(I) and Hg(II) species suggests missing mercury oxidation in the troposphere

Mercury (Hg), a global contaminant, is emitted mainly in its elemental form Hg0 to the atmosphere where it is oxidized to reactive HgII compounds, which efficiently deposit to surface ecosystems. Therefore, the chemical cycling between the elemental and oxidized Hg forms in the atmosphere determines the scale and geographical pattern of global Hg deposition. Recent advances in the photochemistry of gas-phase oxidized HgI and HgII species postulate their photodissociation back to Hg0 as a crucial step in the atmospheric Hg redox cycle. However, the significance of these photodissociation mechanisms on atmospheric Hg chemistry, lifetime, and surface deposition remains uncertain. Here we implement a comprehensive and quantitative mechanism of the photochemical and thermal atmospheric reactions between Hg0, HgI, and HgII species in a global model and evaluate the results against atmospheric Hg observations. We find that the photochemistry of HgI and HgII leads to insufficient Hg oxidation globally. The combined efficient photoreduction of HgI and HgII to Hg0 competes with thermal oxidation of Hg0, resulting in a large model overestimation of 99% of measured Hg0 and underestimation of 51% of oxidized Hg and ∼66% of HgII wet deposition. This in turn leads to a significant increase in the calculated global atmospheric Hg lifetime of 20 mo, which is unrealistically longer than the 3–6-mo range based on observed atmospheric Hg variability. These results show that the HgI and HgII photoreduction processes largely offset the efficiency of bromine-initiated Hg0 oxidation and reveal missing Hg oxidation processes in the troposphere

Surface indicators are correlated with soil multifunctionality in global drylands

Multiple ecosystem functions need to be considered simultaneously to manage and protect the several ecosystem services that are essential to people and their environments. Despite this, cost effective, tangible, relatively simple and globally relevant methodologies to monitor in situ soil multifunctionality, that is, the provision of multiple ecosystem functions by soils, have not been tested at the global scale. We combined correlation analysis and structural equation modelling to explore whether we could find easily measured, field-based indicators of soil multifunctionality (measured using functions linked to the cycling and storage of soil carbon, nitrogen and phosphorus). To do this, we gathered soil data from 120 dryland ecosystems from five continents. Two soil surface attributes measured in situ (litter incorporation and surface aggregate stability) were the most strongly associated with soil multifunctionality, even after accounting for geographic location and other drivers such as climate, woody cover, soil pH and soil electric conductivity. The positive relationships between surface stability and litter incorporation on soil multifunctionality were greater beneath the canopy of perennial vegetation than in adjacent, open areas devoid of vascular plants. The positive associations between surface aggregate stability and soil functions increased with increasing mean annual temperature. Synthesis and applications. Our findings demonstrate that a reduced suite of easily measured in situ soil surface attributes can be used as potential indicators of soil multifunctionality in drylands world-wide. These attributes, which relate to plant litter (origin, incorporation, cover), and surface stability, are relatively cheap and easy to assess with minimal training, allowing operators to sample many sites across widely varying climatic areas and soil types. The correlations of these variables are comparable to the influence of climate or soil, and would allow cost-effective monitoring of soil multifunctionality under changing land-use and environmental conditions. This would provide important information for evaluating the ecological impacts of land degradation, desertification and climate change in drylands world-wide.Fil: Eldridge, David J.. University of New South Wales; AustraliaFil: Delgado Baquerizo, Manuel. Universidad Rey Juan Carlos; EspañaFil: Quero, José L.. Universidad de Córdoba; EspañaFil: Ochoa, Victoria. Universidad Rey Juan Carlos; España. Universidad de Alicante; EspañaFil: Gozalo, Beatriz. Universidad Rey Juan Carlos; España. Universidad de Alicante; EspañaFil: García Palacios, Pablo. Universidad Rey Juan Carlos; EspañaFil: Escolar, Cristina. Universidad Rey Juan Carlos; EspañaFil: García Gómez, Miguel. Universidad Politécnica de Madrid; EspañaFil: Prina, Aníbal. Universidad Nacional de La Pampa; ArgentinaFil: Bowker, Mathew A.. Northern Arizona University; Estados UnidosFil: Bran, Donaldo Eduardo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Patagonia Norte. Estación Experimental Agropecuaria San Carlos de Bariloche; ArgentinaFil: Castro, Ignacio. Universidad Experimental Simón Rodríguez; VenezuelaFil: Cea, Alex. Universidad de La Serena; ChileFil: Derak, Mchich. No especifíca;Fil: Espinosa, Carlos I.. Universidad Técnica Particular de Loja; EcuadorFil: Florentino, Adriana. Universidad Central de Venezuela; VenezuelaFil: Gaitán, Juan José. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Suelos; Argentina. Universidad Nacional de Luján. Departamento de Tecnología; ArgentinaFil: Gatica, Mario Gabriel. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Departamento de Biología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan. Centro de Investigaciones de la Geosfera y Biosfera. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones de la Geosfera y Biosfera; ArgentinaFil: Gómez González, Susana. Universidad de Cádiz; EspañaFil: Ghiloufi, Wahida. Université de Sfax; TúnezFil: Gutierrez, Julio R.. Universidad de La Serena; ChileFil: Guzman, Elizabeth. Universidad Técnica Particular de Loja; EcuadorFil: Hernández, Rosa M.. Universidad Experimental Simón Rodríguez; VenezuelaFil: Hughes, Frederic M.. Universidade Estadual de Feira de Santana; BrasilFil: Muiño, Walter. Universidad Nacional de La Pampa; ArgentinaFil: Monerris, Jorge. No especifíca;Fil: Ospina, Abelardo. Universidad Central de Venezuela; VenezuelaFil: Ramírez, David A.. International Potato Centre; PerúFil: Ribas Fernandez, Yanina Antonia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan. Centro de Investigaciones de la Geosfera y Biosfera. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones de la Geosfera y Biosfera; ArgentinaFil: Romão, Roberto L.. Universidade Estadual de Feira de Santana; BrasilFil: Torres Díaz, Cristian. Universidad del Bio Bio; ChileFil: Koen, Terrance B.. No especifíca;Fil: Maestre, Fernando T.. Universidad Rey Juan Carlos; España. Universidad de Alicante; Españ

Soil fungal abundance and plant functional traits drive fertile island formation in global drylands

Dryland vegetation is characterized by discrete plant patches that accumulate and capture soil resources under their canopies. These “fertile islands” are major drivers of dryland ecosystem structure and functioning, yet we lack an integrated understanding of the factors controlling their magnitude and variability at the global scale.EEA BarilocheFil: Ochoa-Hueso, Raúl. Universidad Autónoma de Madrid. Department of Ecology; EspañaFil: Eldridge, David J. University of New South Wales. School of Biological, Earth and Environmental Sciences; AustraliaFil: Delgado-Baquerizo, Manuel. University of Colorado. Cooperative Institute for Research in Environmental Sciences; Estados Unidos. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; EspañaFil: Soliveres, Santiago. University of Bern. Institute of Plant Sciences; SuizaFil: Bowker, Matthew A. Northern Arizona University. School of Forestry; Estados UnidosFil: Gross, Nicolás. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; España. Institut Nationale de la Recherche Agronomique; Francia. Université La Rochelle. Centre d’étude biologique de Chizé; FranciaFil: Le Bagousse-Pinguet, Yoann. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; EspañaFil: Quero, José L. Universidad de Córdoba. Escuela Técnica Superior de Ingeniería Agronómica y de Montes. Departamento de Ingeniería Forestal: EspañaFil: García-Gómez, Miguel. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; EspañaFil: Valencia, Enrique. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; EspañaFil: Arredondo, Tulio. Instituto Potosino de Investigación Científica y Tecnológica. División de Ciencias Ambientales; MéxicoFil: Beinticinco, Laura. Universidad Nacional de La Pampa. Facultad de Agronomía; ArgentinaFil: Bran, Donaldo Eduardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; ArgentinaFil: Cea, Alex. Universidad de La Serena. Departamento de Biología; ChileFil: Coaguila, Daniel. Instituto de Ensino Superior de Rio Verde; BrasilFil: Dougill, Andrew J. University of Leeds. School of Earth and Environment; Gran BretañaFil: Espinosa, Carlos I. Universidad Técnica Particular de Loja. Departamento de Ciencias Naturales; EcuadorFil: Gaitan, Juan Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; ArgentinaFil: Guuroh, Reginald T. University of Cologne. Botanical Institute. Range Ecology and Range Management Group; Alemania. CSIR-Forestry Research Institute of Ghana; GhanaFil: Guzmán, Elizabeth. Universidad Técnica Particular de Loja. Departamento de Ciencias Naturales; EcuadorFil: Gutiérrez, Julio R.. Universidad de La Serena. Departamento de Biología; Chile. Centro de Estudios Avanzados en Zonas Áridas (CEAZA); Chile. Instituto de Ecología y Biodiversidad; ChileFil: Hernández, Rosa M. Universidad Experimental Simón Rodríguez. Centro de Agroecología Tropical. Laboratorio de Biogeoquímica; VenezuelaFil: Huber-Sannwald, Elisabeth. Instituto Potosino de Investigación Científica y Tecnológica. División de Ciencias Ambientales; MéxicoFil: Jeffries, Thomas. Western Sydney University. Hawkesbury Institute for the Environment; AustraliaFil: Linstädter, Anja. University of Cologne. Botanical Institute. Range Ecology and Range Management Group; AlemaniaFil: Mau, Rebecca L. Northern Arizona University. Center for Ecosystem Science and Society: Estados UnidosFil: Monerris, Jorge. Université du Québec à Montréal. Pavillon des Sciences Biologiques. Département des Sciences Biologiques; CanadáFil: Prina, Anibal. Universidad Nacional de La Pampa. Facultad de Agronomía; ArgentinaFil: Pucheta, Eduardo. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Departamento de Biología; ArgentinaFil: Stavi, Ilan. Dead Sea and Arava Science Center, IsraelFil: Thomas, Andrew. Aberystwyth University. Department of Geography and Earth Sciences; Gran BretañaFil: Zaady, Eli. Agricultural Research Organization. Gilat Research Center. Natural Resources; IsraelFil: Singh, Brajesh K. Western Sydney University. Hawkesbury Institute for the Environment; Australia. Western Sydney University. Global Centre for Land-Based Innovation; AustraliaFil: Maestre, Fernando T. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; Españ