Design and Implementation of the UniProt Website

The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The "www.uniprot.org":http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access

How Robust are Modern Graph Neural Network Potentials in Long and Hot Molecular Dynamics Simulations?

Graph neural networks (GNNs) have emerged as a powerful machine learning approach for the prediction of molecular properties. In particular, recently proposed advanced GNN models promise quantum chemical accuracy at a fraction of the computational cost. While the capabilities of such advanced GNNs have been extensively demonstrated on benchmark datasets, there have been few applications in real atomistic simulations. Here, we therefore put the robustness of GNN interatomic potentials to the test, using the recently proposed GemNet architecture as a testbed. Models are trained on the QM7-x database of organic molecules and used to perform extensive MD simulations. We find that low test set errors are not sufficient for obtaining stable dynamics and that severe pathologies sometimes only become apparent after hundreds of ps of dynamics. Nonetheless, highly stable and transferable GemNet potentials can be obtained with sufficiently large training sets

Pi Charge Distribution from Molecular Topology and Pi Orbital Electronegativity

The automatic and computer-aided prediction of reactivity by means of a few basic atomic parameters is achieved. Considering that only the topology of a molecule is required for the computation it is evident that PEOE (partial equalization of orbital electronegativity) and SD-POE (sigma dependent POE) models proposed by the authors together establish a valid alternative to the presently available, time consuming quantum mechanical procedures. Furthermore, this approach gives a new insight into the interaction between a and it electrons which seems worthy of further investigation. In addition, we have revived the concept of orbital electronegativity, especially in the case of the Jt electrons for which no calculation based on POE (pi orbital electronegativy) has, up to now, ever been performed

A model sensitivity study of the impact of clouds on satellite detection and retrieval of volcanic ash

Volcanic ash is commonly observed by infrared detectors on board Earth-orbiting satellites. In the presence of ice and/or liquid-water clouds, the detected volcanic ash signature may be altered. In this paper the sensitivity of detection and retrieval of volcanic ash to the presence of ice and liquid-water clouds was quantified by simulating synthetic equivalents to satellite infrared images with a 3-D radiative transfer model. The sensitivity study was made for the two recent eruptions of Eyjafjallajokull (2010) and Grimsvotn (2011) using realistic water and ice clouds and volcanic ash clouds. The water and ice clouds were taken from European Centre for Medium-RangeWeather Forecast (ECMWF) analysis data and the volcanic ash cloud fields from simulations by the Lagrangian particle dispersion model FLEXPART. The radiative transfer simulations were made both with and without ice and liquid-water clouds for the geometry and channels of the Spinning Enhanced Visible and Infrared Imager (SEVIRI). The synthetic SEVIRI images were used as input to standard reverse absorption ash detection and retrieval methods. Ice and liquid-water clouds were on average found to reduce the number of detected ash-affected pixels by 6-12 %. However, the effect was highly variable and for individual scenes up to 40% of pixels with mass loading > 0 : 2 gm 2 could not be detected due to the presence of water and ice clouds. For coincident pixels, i. e. pixels where ash was both present in the FLEXPART (hereafter referred to as "Flexpart") simulation and detected by the algorithm, the presence of clouds overall increased the retrieved mean mass loading for the Eyjafjallajokull (2010) eruption by about 13 %,while for the Grimsvotn (2011) eruption ash-mass loadings the effect was a 4% decrease of the retrieved ash-mass loading. However, larger differences were seen between scenes (standard deviations of +/- 30 and +/- 20% for Eyjafjallajokull and Grimsvotn, respectively) and even larger ones within scenes. The impact of ice and liquid-water clouds on the detection and retrieval of volcanic ash, implies that to fully appreciate the location and amount of ash, hyperspectral and spectral band measurements by satellite instruments should be combined with ash dispersion modelling

Editors\u27 Choice—Understanding Chemical Stability Issues between Different Solid Electrolytes in All-Solid-State Batteries

Sulfide-based solid electrolytes (SE) are quite attractive for application in all-solid-state batteries (ASSB) due to their high ionic conductivities and low grain boundary resistance. However, limited chemical and electrochemical stability demands for protection on both cathode and anode side. One promising concept to prevent unwanted reactions and simultaneously improve interfacial contacting at the anode side consists in applying a thin polymer film as interlayer between Li metal and the SE. In the present study, we investigated the combination of polyethylene oxide (PEO) based polymer films with the sulfide-based SE Li10SnP2S12 (LSPS). We analyzed their compatibility using both electrochemical and chemical techniques. A steady increase in the cell resistance during calendar aging indicated decomposition reactions at the interfaces. By means of X-ray photoelectron spectroscopy and further analytical methods, the formation of polysulfides, P–[S]n–P like bridged PS43− units and sulfite, SO32−, was demonstrated. We critically discuss potential reasons and propose a plausible mechanism for the degradation of LSPS with PEO. The main objective of this paper is to highlight the importance of understanding interfaces in ASSBs not only from an electrochemical perspective, but also from a chemical point of view

What is the benefit of ceilometers for aerosol remote sensing? An answer from EARLINET

With the establishment of ceilometer networks by national weather services, a discussion commenced to which extent these simple backscatter lidars can be used for aerosol research. Though primarily designed for the detection of clouds it was shown that at least observations of the vertical structure of the boundary layer might be possible. However, an assessment of the potential of ceilometers for the quantitative retrieval of aerosol properties is still missing. In this paper we discuss different retrieval methods to derive the aerosol backscatter coefficient beta(p),with special focus on the calibration of the ceilometers. Different options based on forward and backward integration methods are compared with respect to their accuracy and applicability. It is shown that advanced lidar systems such as those being operated in the framework of the European Aerosol Research Lidar Network (EARLINET) are excellent tools for the calibration, and thus beta(p) retrievals based on forward integration can readily be implemented and used for real-time applications. Furthermore, we discuss uncertainties introduced by incomplete overlap, the unknown lidar ratio, and water vapor absorption. The latter is relevant for the very large number of ceilometers operating in the spectral range around lambda = 905-910 nm. The accuracy of the retrieved beta(p) mainly depends on the accuracy of the calibration and the long-term stability of the ceilometer. Under favorable conditions, a relative error of beta(p) on the order of 10% seems feasible. In the case of water vapor absorption, corrections assuming a realistic water vapor distribution and laser spectrum are indispensable;otherwise errors on the order of 20% could occur. From case studies it is shown that ceilometers can be used for the reliable detection of elevated aerosol layers below 5 km, and can contribute to the validation of chemistry transport models, e. g.,the height of the boundary layer. However, the exploitation of ceilometer measurements is still in its infancy, so more studies are urgently needed to consolidate the present state of knowledge, which is based on a limited number of case studies