Epistemic metadata for computational engineering information systems

Digitalization is a priority for innovation in the engineering sciences. The digital transformation requires making the knowledge claims from scientific research data machine-actionable, so that they can be integrated and analysed with minimal human intervention. Up until now, the depth of digitalization is often too shallow, with annotations that are only of use to a human reader. In addition, digital infrastructures and their metadata standards are tedious to use: They demand too much effort from researchers, much of which goes into metadata that contribute nothing to an improved reuse of knowledge. These shortcomings are related. Data documentation and annotation are complicated and of little use whenever the metadata that make knowledge reusable are not prioritized. Addressing this gap, we discuss metadata standardization efforts targeted at documenting the knowledge status of data; we refer to such an annotation as epistemic metadata. We propose a schema for epistemic metadata, with a focus on knowledge and reproducibility claims, that is designed to be user-friendly and flexible enough to apply to a spectrum of circumstances and validity assessments. These developments are implemented as part of the PIMS-II ontology. They were conducted in line with requirements procured through a case study on papers and claims from molecular modelling and simulation.Epistemic metadata for computational engineering information systemspublishedVersio

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Molecular Simulation Study of Dielectric Constants of Pure Fluids and Mixtures

The static dielectric constant of fluids is studied with molecular models from the literature. The employed molecular models were developed using only vapor-liquid equilibrium data. No information on the dielectric properties was used, so that the simulation results are predictions. A wide range of different fluids, from slightly to strongly polar, is investigated. Most of the studied models underestimate the dielectric constant, which can be explained by the way the models were developed. For the pure fluids dimethyl ether and acetone, the temperature and pressure dependence of the dielectric constant are also studied. A good agreement with experimental data is found. Additionally, binary mixtures are investigated. Thereby, the validity of several mixing rules for the dielectric constant is assessed

Thermodynamically Rigorous Description of the Open Circuit Voltage of Redox Flow Batteries

Redox flow batteries (RFBs) are considered an outstanding candidate for the integration of renewable energy sources into the existing power grids. A key property of RFBs is the open circuit voltage (OCV) corresponding to the currentless equilibrium state. In the literature, the Nernst equation describing this property is often simplified by neglecting the activity coefficients. In this work, using a thermodynamically rigorous approach, we show that activity coefficients have a significant influence on the OCV of the Iron-Cadmium and All-Vanadium RFBs. Moreover, this influence varies with the state of charge. Therefore, activity coefficients should not be neglected in the Nernst equation. We show that when doing so, the resulting offset in OCV is actually comparable to typical voltage losses occurring during operation. Hence, fitting kinetic parameters to measurement data of voltage losses can lead to ambiguous results if only the idealized OCV, obtained by neglecting the activity coefficients, is used in that evaluation. Therefore, the implementation of a thermodynamically rigorous model has the potential to significantly improve state-of-the-art models for RFBs

Thermodynamically Rigorous Description of the Open Circuit Voltage of Redox Flow Batteries

Redox flow batteries (RFBs) are considered an outstanding candidate for the integration of renewable energy sources into the existing power grids. A key property of RFBs is the open circuit voltage (OCV) corresponding to the currentless equilibrium state. In the literature, the Nernst equation describing this property is often simplified by neglecting the activity coefficients. In this work, using a thermodynamically rigorous approach, we show that activity coefficients have a significant influence on the OCV of the Iron-Cadmium and All-Vanadium RFBs. Moreover, this influence varies with the state of charge. Therefore, activity coefficients should not be neglected in the Nernst equation. We show that when doing so, the resulting offset in OCV is actually comparable to typical voltage losses occurring during operation. Hence, fitting kinetic parameters to measurement data of voltage losses can lead to ambiguous results if only the idealized OCV, obtained by neglecting the activity coefficients, is used in that evaluation. Therefore, the implementation of a thermodynamically rigorous model has the potential to significantly improve state-of-the-art models for RFBs

Relative Permittivity of Dipolar Model Fluids from Molecular Simulation and from the Co-Oriented Fluid Functional Equation for Electrostatic Interactions

The relative permittivity of dipolar fluids is important in many industrial and scientific applications, e.g. whenever electrolytes or electromagnetic fields are present. For non-polarizable model molecules, it is directly linked to the mutual molecular orientation and thereby usually not accessible by equations of state. However, the recently developed Co-Oriented Fluid Functional Equation for Electrostatic interactions (COFFEE) allows for calculating the orientation distribution function of simple polar molecules and thereby establishes a connection between the thermodynamic behavior and the relative permittivity. In this article, we develop an expression to calculate the relative permittivity from the orientation distribution known from COFFEE. Furthermore, we calculate the relative permittivity of simple polar fluids using molecular simulations. We study the original Stockmayer fluid and the shifted Stockmayer fluid, in which the dipole is shifted away from the Lennard-Jones center along the dipole axis. For both fluids, different dipole strengths are investigated. The results from the theoretical expression from COFFEE are compared to the simulation data. Thereby, a possible link between polar equations of state and electric fields or electrolytes is developed

Correction to “Relative Permittivity of Dipolar Model Fluids from Molecular Simulation and from the Co-Oriented Fluid Functional Equation for Electrostatic Interactions”

Correction to “Relative Permittivity of Dipolar Model Fluids from Molecular Simulation and from the Co-Oriented Fluid Functional Equation for Electrostatic Interactions

Correction to “Relative Permittivity of Dipolar Model Fluids from Molecular Simulation and from the Co-Oriented Fluid Functional Equation for Electrostatic Interactions”

The relative permittivity of dipolar fluids is important in many industrial and scientific applications (e.g., whenever electrolytes or electromagnetic fields are present). For nonpolarizable model molecules, it is directly linked to the mutual molecular orientation and therefore is usually not accessible by equations of state. However, the recently developed co-oriented fluid functional equation for electrostatic interactions (COFFEE) allows for calculating the orientation distribution function of simple polar molecules and thereby establishes a connection between the thermodynamic behavior and the relative permittivity. In this article, we develop an expression to calculate the relative permittivity from the orientation distribution known from COFFEE. Furthermore, we calculate the relative permittivity of simple polar fluids using molecular simulations. We study the original Stockmayer fluid and the shifted Stockmayer fluid in which the dipole is shifted away from the Lennard-Jones center along the dipole axis. For both fluids, different dipole strengths are investigated. The results from the theoretical expression from COFFEE are compared to the simulation data. Thereby, a possible link between polar equations of state and electric fields or electrolytes is developed

Relative Permittivity of Stockmayer-Type Model Fluids from MD Simulations and COFFEE

The relative permittivity is a property that depends on the orientation structure of a fluid. Thus, using state-of-the-art equations of state it can be modeled only when using high level techniques, such as nonprimitive models. This is a drawback, especially when electrolytes are present: when using a primitive model, an auxiliary model for the relative permittivity must be introduced. Here, we pursue a different approach to predict the relative permittivity. The recently developed ‘Co-Oriented Fluid Functional Equation for Electrostatic Interactions‘ (COFFEE) framework considers the mutual orientation of molecular dipole moments. It thereby enables a prediction of the relative permittivity when combined with Kirkwood’s theory. To assess these predictions obtained from COFFEE, we present a comprehensive set of molecular simulation data for the relative permittivity of Stockmayer-type model fluids at wide ranges of temperature and density. Continuing a previous work, we extend the range of states considered to the homogeneous vapor, liquid, and supercritical regions. We find that when plotting the relative permittivity as a function of the ratio of density and temperature, all data points for a certain fluid collapse onto a single master curve. To a good approximation, the same holds for experimental data of the relative permittivity of water. By comparing the molecular simulation results with COFFEE, a good overall agreement is observed. Both data sets follow the same qualitative trends. Also reasonable quantitative agreement is found for many state points, the only exception being dense states at low temperatures