Kohn-Sham decomposition in real-time time-dependent density-functional theory: An efficient tool for analyzing plasmonic excitations

The real-time-propagation formulation of time-dependent density-functional theory (RT-TDDFT) is an efficient method for modeling the optical response of molecules and nanoparticles. Compared to the widely adopted linear-response TDDFT approaches based on, e.g., the Casida equations, RT-TDDFT appears, however, lacking efficient analysis methods. This applies in particular to a decomposition of the response in the basis of the underlying single-electron states. In this work, we overcome this limitation by developing an analysis method for obtaining the Kohn-Sham electron-hole decomposition in RT-TDDFT. We demonstrate the equivalence between the developed method and the Casida approach by a benchmark on small benzene derivatives. Then, we use the method for analyzing the plasmonic response of icosahedral silver nanoparticles up to Ag$_{561}$. Based on the analysis, we conclude that in small nanoparticles individual single-electron transitions can split the plasmon into multiple resonances due to strong single-electron-plasmon coupling whereas in larger nanoparticles a distinct plasmon resonance is formed.Comment: 11 pages, 3 figure

icet - A Python library for constructing and sampling alloy cluster expansions

Alloy cluster expansions (CEs) provide an accurate and computationally efficient mapping of the potential energy surface of multi-component systems that enables comprehensive sampling of the many-dimensional configuration space. Here, we introduce \textsc{icet}, a flexible, extensible, and computationally efficient software package for the construction and sampling of CEs. \textsc{icet} is largely written in Python for easy integration in comprehensive workflows, including first-principles calculations for the generation of reference data and machine learning libraries for training and validation. The package enables training using a variety of linear regression algorithms with and without regularization, Bayesian regression, feature selection, and cross-validation. It also provides complementary functionality for structure enumeration and mapping as well as data management and analysis. Potential applications are illustrated by two examples, including the computation of the phase diagram of a prototypical metallic alloy and the analysis of chemical ordering in an inorganic semiconductor.Comment: 10 page

A systems view of risk factors for knee osteoarthritis reveals insights into the pathogenesis of the disease.

Early detection of osteoarthritis (OA) remains a critical yet unsolved multifaceted problem. To address the multifaceted nature of OA a systems model was developed to consolidate a number of observations on the biological, mechanical and structural components of OA and identify features common to the primary risk factors for OA (aging, obesity and joint trauma) that are present prior to the development of clinical OA. This analysis supports a unified view of the pathogenesis of OA such that the risk for developing OA emerges when one of the components of the disease (e.g., mechanical) becomes abnormal, and it is the interaction with the other components (e.g., biological and/or structural) that influences the ultimate convergence to cartilage breakdown and progression to clinical OA. The model, applied in a stimulus-response format, demonstrated that a mechanical stimulus at baseline can enhance the sensitivity of a biomarker to predict cartilage thinning in a 5 year follow-up in patients with knee OA. The systems approach provides new insight into the pathogenesis of the disease and offers the basis for developing multidisciplinary studies to address early detection and treatment at a stage in the disease where disease modification has the greatest potential for a successful outcome

Revealing the free energy landscape of halide perovskites: Metastability and transition characters in CsPbBr3_3 and MAPbI3_3

Halide perovskites have emerged as a promising class of materials for photovoltaic applications. A challenge in these applications is how to prevent the crystal structure from degradation to photovoltaically inactive phases, which requires an understanding of the free energy landscape of these materials. Here, we uncover the free energy landscape of two prototypical halide perovskites, CsPbBr$_3$ and MAPbI$_3$ via atomic scale simulations using umbrella sampling and machine-learned potentials. For CsPbBr$_3$ we find very small free energy differences and barriers close to the transition temperatures for both the tetragonal-to-cubic and the orthorhombic-to-tetragonal transition. For MAPbI$_3$, however, the situation is more intricate. In particular the orthorhombic-to-tetragonal transition exhibits a large free energy barrier and there are several competing tetragonal phases. Using large-scale molecular dynamics simulations we explore the character of these transition and observe latent heat and a discrete change in structural parameters for the tetragonal-to-cubic phase transition in both CsPbBr$_3$ and MAPbI$_3$ indicating first-order transitions. We find that in MAPbI$_3$ the orthorhombic phase has an extended metastability range and furthermore identify a second metastable tetragonal phase. Finally, we compile a phase diagram for MAPbI$_3$ that includes potential metastable phases.Comment: 9 pages, 5 figure

Measuring Air Quality for Advocacy in Africa (MA3): Feasibility and Practicality of Longitudinal Ambient PM2.5 Measurement Using Low-Cost Sensors.

Ambient air pollution in urban cities in sub-Saharan Africa (SSA) is an important public health problem with models and limited monitoring data indicating high concentrations of pollutants such as fine particulate matter (PM2.5). On most global air quality index maps, however, information about ambient pollution from SSA is scarce. We evaluated the feasibility and practicality of longitudinal measurements of ambient PM2.5 using low-cost air quality sensors (Purple Air-II-SD) across thirteen locations in seven countries in SSA. Devices were used to gather data over a 30-day period with the aim of assessing the efficiency of its data recovery rate and identifying challenges experienced by users in each location. The median data recovery rate was 94% (range: 72% to 100%). The mean 24 h concentration measured across all sites was 38 µg/m3 with the highest PM2.5 period average concentration of 91 µg/m3 measured in Kampala, Uganda and lowest concentrations of 15 µg/m3 measured in Faraja, The Gambia. Kampala in Uganda and Nnewi in Nigeria recorded the longest periods with concentrations >250µg/m3. Power outages, SD memory card issues, internet connectivity problems and device safety concerns were important challenges experienced when using Purple Air-II-SD sensors. Despite some operational challenges, this study demonstrated that it is reasonably practicable and feasible to establish a network of low-cost devices to provide data on local PM2.5 concentrations in SSA countries. Such data are crucially needed to raise public, societal and policymaker awareness about air pollution across SSA