Machine Learning with bond information for local structure optimizations in surface science

Local optimization of adsorption systems inherently involves different scales: within the substrate, within the molecule, and between molecule and substrate. In this work, we show how the explicit modeling of the different character of the bonds in these systems improves the performance of machine learning methods for optimization. We introduce an anisotropic kernel in the Gaussian process regression framework that guides the search for the local minimum, and we show its overall good performance across different types of atomic systems. The method shows a speed-up of up to a factor two compared with the fastest standard optimization methods on adsorption systems. Additionally, we show that a limited memory approach is not only beneficial in terms of overall computational resources, but can result in a further reduction of energy and force calculations

Hyperspectral Imaging for the Detection of Bitter Almonds in Sweet Almond Batches

A common fraud in the sweet almond industry is the presence of bitter almonds in commercial batches. The presence of bitter almonds not only causes unpleasant flavours but also problems in the commercialisation and toxicity for consumers. Hyperspectral Imaging (HSI) has been proved to be suitable for the rapid and non-destructive quality evaluation in foods as it integrates the spectral and spatial dimensions. Thus, we aimed to study the feasibility of using an HSI system to identify single bitter almond kernels in commercial sweet almond batches. For this purpose, sweet and bitter almond batches, as well as different mixtures, were analysed in bulk using an HSI system which works in the spectral range 946.6–1648.0 nm. Qualitative models were developed using Partial Least Squares-Discriminant Analysis (PLS-DA) to differentiate between sweet and bitter almonds, obtaining a classification success of over the 99%. Furthermore, data reduction, as a function of the most relevant wavelengths (VIP scores), was applied to evaluate its performance. Then, the pixel-by-pixel validation of the mixtures was carried out, identifying correctly between 61–85% of the adulterations, depending on the group of mixtures and the cultivar analysed. The results confirm that HSI, without VIP scores data reduction, can be considered a promising approach for classifying the bitterness of almonds analysed in bulk, enabling identifying individual bitter almonds inside sweet almond batches. However, a more complex mathematical analysis is necessary before its implementation in the processing lines

Strong substrate mediation of attractive lateral interactions of CO on Cu(110)

Funding: Scottish Funding Council (through EaStCHEM and SRD-Grant HR07003), EPSRC (PhD studentship for JAGT, EP/M506631/1), Royal Society Industry Fellowship (PBW).The mechanism of chemical reactions between adsorbed species is defined by the combined effects of the adsorbate–substrate potential landscape and lateral interactions. Such lateral interactions are therefore integral to catalytic processes, but their study is often complicated by “substrate mediation”, the regulation of a two-body potential between adsorbed particles by the surface itself. Substrate mediation can influence the sign and magnitude of lateral interactions. There are notable exceptions of ordered structures forming at low coverage, indicative of short-range attractive forces where repulsive forces are expected to dominate, suggesting a strong substrate-mediated contribution. To explore further the origins of such interactions, we have investigated the adsorption of CO on Cu(110) using a combination of low-temperature microscopy and first-principles calculations. Our studies reveal that lateral adsorbate interactions, which are constrained by the metal surface, regulate the bonding between the adsorbate and substrate. Anisotropic CO–CO coupling is seen to arise from a perfect balance between the intermolecular accumulation of charge that acts as a glue (chemical coupling) at sufficiently large distances to avoid repulsive effects (dipole–dipole coupling and Pauli’s repulsion between electron clouds).PostprintPostprintPeer reviewe

IAA : Información y actualidad astronómica (15)

Sumario : INVESTIGACIÓN. Aerosoles atmosféricos: sus efectos en el clima de las atmósferas del sistema solar.-- El gas molecular en las galaxias.-- VENTANA ABIERTA. Todo un privilegio.-- CHARLAS CON...Vicent Martínez.-- ACTUALIDAD CIENTÍFICA. Un sistema planetario joven en torno a Beta Pictores.-- Una nueva visita a Canis Major .-- ACTIVIDADES IAA.-- AGENDA.Esta revista se publica con la ayuda de la Accion Especial DIF 2001-4284-E del Programa Nacional de Difusión de la Ciencia y la Tecnología, del Ministerio de Ciencia y Tecnología.N

Calculating the frequencies and intensities of strongly anharmonic modes of adsorbates on surfaces : a low-cost but accurate computational approach

Funding: Scottish Funding Council (through EaStCHEM and SRD-Grant HR07003) and from EPSRC (PhD studentship for JAGT, EP/M506631/1).We present a new method for calculating the frequencies and intensities of the vibrational modes of adsorbates on surfaces. Our method is based on density functional perturbation theory (DFPT) and provides accurate estimates of the vibrational intensities even when the vibrations are strongly anharmonic. Furthermore, it does so at a negligible additional computation cost compared to conventional DFPT calculation. We illustrate our method by calculating the vibrational spectra of three example systems — ethylidyne on Rh(111), benzene on Rh(111) coadsorbed with CO, and terephthalic acid (TPA) on Cu(100) — and comparing them to experimental measurements performed using High-Resolution Electron Energy Loss Spectroscopy (HREELS). We find excellent agreement between our predictions and the experimentally measured frequencies and intensities in all three cases.PostprintPostprintPeer reviewe

Benzene adsorption on Rh(111) : a new perspective on intermolecular interactions and molecular ordering

The authors acknowledge financial support from the Scottish Funding Council (through EaStCHEM and SRD-Grant HR07003) and from EPSRC (PhD studentships for JAGT − EP/M506631/1, and MJT − EP/K503162/1).The adsorption of benzene on the Rh(111) substrate was investigated through scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations. Experiments were carried out at various surface coverages, with the amount of benzene adsorbed determined to influence the molecular adsorption site, the intermolecular interactions, and the interaction between the molecule and the substrate. At a sub-monolayer coverage of the surface, the molecules are disordered and kept apart by a strong inter-adsorbate repulsion, with a preference for the molecule to adsorb on a three-fold hcp hollow site. At high coverage, the preferred adsorption site becomes the two-fold symmetric bridge site, whether as part of the two dense ordered structures that form at high coverage ((2√3×3)rect or (√19×√19)R23.4°) or as part of the disordered array of benzene molecules, which are arranged in formations which resemble the “building blocks” of the ordered overlayers. Despite the adsorption energy for benzene within both dense structures being similar, the (√19×√19)R23.4° overlayer is only observed if the substrate is annealed to 363 K during or after deposition, indicating that the formation of the (√19×√19)R23.4° ordering is inhibited by an activation barrier at lower temperatures and can only be overcome by increasing the temperature of the Rh(111) support.PostprintPeer reviewe

Un viaje al Cosmos en 52 semanas

230 p.Este libro se plantea como una serie de artículos que dibujan un recorrido por el Universo, desde lo más cercano a lo más distante. Constituye una herramienta útil y actualizada para los interesados en la astronomía, y combina el conocimiento básico con los resultados científicos más novedosos. La astrofísica constituye una ciencia viva y en permanente avance por ello nos encontramos con un Plutón que ya no es considerado planeta; con nuevos datos sobre la posible presencia de agua en Marte; con géiseres en Encelado, un pequeño satélite de Saturno que se creía geológicamente inactivo; con una miríada de nuevos planetas girando alrededor de otras estrellas; con, quizá, un nuevo tipo de agujero negro y fascinantes resultados sobre las explosiones cortas de rayos gamma, uno de los eventos más energéticos del Universo y, hasta hace poco, también uno de los más desconocidos; con la mision COROT, y otras, como BepiColombo, que ya se encuentran en su fase de desarrollo instrumental.Peer reviewe

TGFβ Governs the Pleiotropic Activity of NDRG1 in Triple-Negative Breast Cancer Progression

In triple-negative breast cancer (TNBC), the pleiotropic NDRG1 (N-Myc downstream regulated gene 1) promotes progression and worse survival, yet contradictory results were documented, and the mechanisms remain unknown. Phosphorylation and localization could drive NDRG1 pleiotropy, nonetheless, their role in TNBC progression and clinical outcome was not investigated. We found enhanced p-NDRG1 (Thr346) by TGFβ1 and explored whether it drives NDRG1 pleiotropy and TNBC progression. In tissue microarrays of 81 TNBC patients, we identified that staining and localization of NDRG1 and p-NDRG1 (Thr346) are biomarkers and risk factors associated with shorter overall survival. We found that TGFβ1 leads NDRG1, downstream of GSK3β, and upstream of NF-κB, to differentially regulate migration, invasion, epithelial-mesenchymal transition, tumor initiation, and maintenance of different populations of cancer stem cells (CSCs), depending on the progression stage of tumor cells, and the combination of TGFβ and GSK3β inhibitors impaired CSCs. The present study revealed the striking importance to assess both total NDRG1 and p-NDRG1 (Thr346) positiveness and subcellular localization to evaluate patient prognosis and their stratification. NDRG1 pleiotropy is driven by TGFβ to differentially promote metastasis and/or maintenance of CSCs at different stages of tumor progression, which could be abrogated by the inhibition of TGFβ and GSK3β.Instituto de Salud Carlos III European Commission PI15/00336 PI19/01533 CP14/00197 CP19/00029 PIE16/00045Ministry of Science and Innovation, Spain (MICINN)Instituto de Salud Carlos IIISpanish Government RTI2018.101309B-C22Chair "Doctors Galera-Requena in cancer stem cell research" CMC-CTS963European Regional Development Fund (European Union)Ministerio de Universidades FPU19/04450Junta de Andalucia RH-0139-2020Sistema Nacional de Garantia Juvenil (Fondo Social Europeo) 8064Junta de Andalucia, Consejeria de Transformacion Economica, Industria, Conocimiento y Universidades DOC_01686Fundacion Cientifica Asociacion Espanola Contra el Cancer, Junta Provincial de Jaen (AECC) PRDJA19001BLA

Mechanical and electromagnetic design of the vacuum vessel of the SMART tokamak

The SMall Aspect Ratio Tokamak (SMART) is a new spherical device that is currently being designed at the University of Seville. SMART is a compact machine with a plasma major radius (R) greater than 0.4 m, plasma minor radius (a) greater than 0.2 m, an aspect ratio (A) over than 1.7 and an elongation (k) of more than 2. It will be equipped with 4 poloidal field coils, 4 divertor field coils, 12 toroidal field coils and a central solenoid. The heating system comprises of a Neutral Beam Injector (NBI) of 600 kW and an Electron Cyclotron Resonance Heating (ECRH) of 6 kW for pre-ionization. SMART has been designed for a plasma current (I) of 500 kA, a toroidal magnetic field (B) of 1 T and a pulse length of 500 ms preserving the compactness of the machine. The free boundary equilibrium solver code FIESTA [1] coupled to the linear time independent, rigid plasma model RZIP [2] has been used to calculate the target equilibria taking into account the physics goals, the required plasma parameters, vacuum vessel structures and power supply requirements. We present here the final design of the SMART vacuum vessel together with the Finite Element Model (FEM) analysis carried out to ensure that the tokamak vessel provides high quality vacuum and plasma performance withstanding the electromagnetic j×B loads caused by the interaction between the eddy currents induced in the vessel itself and the surrounding magnetic fields. A parametric model has been set up for the topological optimization of the vessel where the thickness of the wall has been locally adapted to the expected forces. An overview of the new machine is presented here.This work received funding from the Fondo Europeo de Desarollo Regional (FEDER) by the European Commission under grant agreement numbers IE17-5670 and US-15570. This work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014-2018 and 2019-2020 under grant agreement No 633053. The views and opinions expressed herein do not necessarily reflect those of the European Commission