A Fuzzy Classification Framework to Identify Equivalent Atoms in Complex Materials and Molecules

The nature of an atom in a bonded structure -- such as in molecules, in nanoparticles or solids, at surfaces or interfaces -- depends on its local atomic environment. In atomic-scale modeling and simulation, identifying groups of atoms with equivalent environments is a frequent task, to gain an understanding of the material function, to interpret experimental results or to simply restrict demanding first-principles calculations. While routine, this task can often be challenging for complex molecules or non-ideal materials with breaks of symmetries or long-range order. To automatize this task, we here present a general machine-learning framework to identify groups of (nearly) equivalent atoms. The initial classification rests on the representation of the local atomic environment through a high-dimensional smooth overlap of atomic positions (SOAP) vector. Recognizing that not least thermal vibrations may lead to deviations from ideal positions, we then achieve a fuzzy classification by mean-shift clustering within a low-dimensional embedded representation of the SOAP points as obtained through multidimensional scaling. The performance of this classification framework is demonstrated for simple aromatic molecules and crystalline Pd surface examples.Comment: Accepted manuscript in Journal of Chemical Physics. Repositories of the package (DECAF): DOI:10.17617/3.U7VKBM or https://gitlab.mpcdf.mpg.de/klai/deca

Chest CT Findings and SARS-CoV-2 Infection in Trauma Patients-Is There a Prediction towards Higher Complication Rates?

BACKGROUND Polytrauma patients with SARS-CoV-2 infections may be associated with an increased complication rate. The main goal of this study was to analyze the clinical course of trauma patients with COVID infection and a positive CT finding. METHODS This was a retrospective in-hospital study. Polytrauma patients diagnosed with SARS-CoV-2 infections were included in our analysis. The outcome parameters were pulmonary complication during admission, pulmonary embolism, pleural effusion, pneumonia, mortality, length of stay and readmission < 30 days. RESULTS 48 patients were included in the study. Trauma patients in the age-adjusted matched-pair analysis with typical changes in SARS-CoV-2 infection in CT findings showed significantly more pulmonary complications in general and significantly more cases of pneumonia (complications: 56% vs. 11%, p = 0.046; pneumonia 44% vs. 0%, p = 0.023). In addition, the clinical course of polytrauma patients with SARS-CoV-2 infection showed a high rate of pulmonary complications in the inpatient course (53%). CONCLUSION The results of our study show that the changes in the CT findings of trauma patients with SARS-CoV-2 infection are a good indicator of further inpatient outcomes. Similarly, polytrauma patients with a SARS-CoV-2 infection and positive CT findings are shown to have increased risk for pulmonary complications

Interface between graphene and liquid Cu from molecular dynamics simulations

Controllable synthesis of defect-free graphene is crucial for applications since the properties of graphene are highly sensitive to any deviations from the crystalline lattice. We focus here on the emerging use of liquid Cu catalysts, which has high potential for fast and efficient industrial-scale production of high-quality graphene. The interface between graphene and liquid Cu is studied using force field and ab initio molecular dynamics, revealing a complete or partial embedding of finite-sized flakes. By analyzing flakes of different sizes we find that the size-dependence of the embedding can be rationalized based on the energy cost of embedding versus bending the graphene flake. The embedding itself is driven by the formation of covalent bonds between the under-coordinated edge C atoms and the liquid Cu surface, which is accompanied by a significant charge transfer. In contrast, the central flake atoms are located around or slightly above 3 {\AA} from the liquid Cu surface and exhibit weak vdW-bonding and much lower charge transfer. The structural and electronic properties of the embedded state revealed in our work provides the atomic-scale information needed to develop effective models to explain the special growth observed in experiments where various interesting phenomena such as flake self-assembly and rotational alignment, high growth speeds and low defect densities in the final graphene product have been observed.Comment: This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in J. Chem. Phys. 153, 074702 (2020) and may be found at https://doi.org/10.1063/5.002012

IrO2 Surface Complexions Identified Through Machine Learning and Surface Investigations

A Gaussian Approximation Potential (GAP) was trained using density-functional theory data to enable a global geometry optimization of low-index rutile IrO2 facets through simulated annealing. Ab initio thermodynamics identifies (101) and (111) (1x1)-terminations competitive with (110) in reducing environments. Experiments on single crystals find that (101) facets dominate, and exhibit the theoretically predicted (1x1) periodicity and X-ray photoelectron spectroscopy (XPS) core level shifts. The obtained structures are analogous to the complexions discussed in the context of ceramic battery materials.Comment: 13 pages 2 figure

Safety and differences between direct oral anticoagulants and vitamin K antagonists in the risk of post-traumatic intrathoracic bleeding after rib fractures in elderly patients

Closed chest traumas are frequent consequences of falls in the elderly. The presence of concomitant oral anticoagulant therapy can increase the risk of post-traumatic bleeding even in cases of trauma with non-severe dynamics. There is limited information about the differences between vitamin K antagonists and direct oral anticoagulants in the risk of post-traumatic bleeding. To assess differences in the risk of developing intra-thoracic hemorrhages after chest trauma with at least one rib fracture caused by an accidental fall in patients over 75 years of age taking oral anticoagulant therapy. This study involved data from four emergency departments over two years. All patients on oral anticoagulant therapy and over 75 years of age who reported a closed thoracic trauma with at least one rib fracture were retrospectively evaluated. Patients were divided into two study groups according their anticoagulant therapy. Of the 342 patients included in the study, 38.9% (133/342) were treated with direct oral anticoagulants and 61.1% (209/342) were treated with vitamin K antagonist. A total of 7% (24/342) of patients presented intrathoracic bleeding, while 5% (17/342) required surgery or died as a result for the trauma. Posttraumatic intrathoracic bleeding occurred in 4.5% (6/133) of patients receiving direct oral anticoagulants and 8.6% (18/209) of patients receiving vitamin K antagonist. Logistic regression analysis, revealed no difference in the risk of intrathoracic haemorrhages between the two studied groups. Direct oral anticoagulants therapy presents a risk of post-traumatic intrathoracic haemorrhage comparable to that of vitamin K antagonist therapy

Characterization of Novel Antimalarial Compound ACT-451840: Preclinical Assessment of Activity and Dose-Efficacy Modeling.

BACKGROUND: Artemisinin resistance observed in Southeast Asia threatens the continued use of artemisinin-based combination therapy in endemic countries. Additionally, the diversity of chemical mode of action in the global portfolio of marketed antimalarials is extremely limited. Addressing the urgent need for the development of new antimalarials, a chemical class of potent antimalarial compounds with a novel mode of action was recently identified. Herein, the preclinical characterization of one of these compounds, ACT-451840, conducted in partnership with academic and industrial groups is presented. METHOD AND FINDINGS: The properties of ACT-451840 are described, including its spectrum of activities against multiple life cycle stages of the human malaria parasite Plasmodium falciparum (asexual and sexual) and Plasmodium vivax (asexual) as well as oral in vivo efficacies in two murine malaria models that permit infection with the human and the rodent parasites P. falciparum and Plasmodium berghei, respectively. In vitro, ACT-451840 showed a 50% inhibition concentration of 0.4 nM (standard deviation [SD]: ± 0.0 nM) against the drug-sensitive P. falciparum NF54 strain. The 90% effective doses in the in vivo efficacy models were 3.7 mg/kg against P. falciparum (95% confidence interval: 3.3-4.9 mg/kg) and 13 mg/kg against P. berghei (95% confidence interval: 11-16 mg/kg). ACT-451840 potently prevented male gamete formation from the gametocyte stage with a 50% inhibition concentration of 5.89 nM (SD: ± 1.80 nM) and dose-dependently blocked oocyst development in the mosquito with a 50% inhibitory concentration of 30 nM (range: 23-39). The compound's preclinical safety profile is presented and is in line with the published results of the first-in-man study in healthy male participants, in whom ACT-451840 was well tolerated. Pharmacokinetic/pharmacodynamic (PK/PD) modeling was applied using efficacy in the murine models (defined either as antimalarial activity or as survival) in relation to area under the concentration versus time curve (AUC), maximum observed plasma concentration (Cmax), and time above a threshold concentration. The determination of the dose-efficacy relationship of ACT-451840 under curative conditions in rodent malaria models allowed prediction of the human efficacious exposure. CONCLUSION: The dual activity of ACT-451840 against asexual and sexual stages of P. falciparum and the activity on P. vivax have the potential to meet the specific profile of a target compound that could replace the fast-acting artemisinin component and harbor additional gametocytocidal activity and, thereby, transmission-blocking properties. The fast parasite reduction ratio (PRR) and gametocytocidal effect of ACT-451840 were recently also confirmed in a clinical proof-of-concept (POC) study

Benefits from using mixed precision computations in the ELPA-AEO and ESSEX-II eigensolver projects

We first briefly report on the status and recent achievements of the ELPA-AEO (Eigenvalue Solvers for Petaflop Applications - Algorithmic Extensions and Optimizations) and ESSEX II (Equipping Sparse Solvers for Exascale) projects. In both collaboratory efforts, scientists from the application areas, mathematicians, and computer scientists work together to develop and make available efficient highly parallel methods for the solution of eigenvalue problems. Then we focus on a topic addressed in both projects, the use of mixed precision computations to enhance efficiency. We give a more detailed description of our approaches for benefiting from either lower or higher precision in three selected contexts and of the results thus obtained

Search for exotic resonances decaying into WZ/ZZ in pp collisions at √s=7 TeV

Journal of High Energy Physics 2013.2 (2013): 036 reproduced by permission of Scuola Internazionale Superiore di Studi Avanzati (SISSA)Artículo escrito por un elevado número de autores, solo se referencian el que aparece en primer lugar, el nombre del grupo de colaboración, si le hubiere, y los autores pertenecientes a la UAMA search for new exotic particles decaying to the VZ final state is performed, where V is either a W or a Z boson decaying into two overlapping jets and the Z decays into a pair of electrons, muons or neutrinos. The analysis uses a data sample of pp collisions corresponding to an integrated luminosity of 5 fb-1 collected by the CMS experiment at the LHC at √s=7 TeV in 2011. No significant excess is observed in the mass distribution of the VZ candidates compared with the background expectation from standard model processes. Model-dependent upper limits at the 95% confidence level are set on the product of the cross section times the branching fraction of hypothetical particles decaying to the VZ final state as a function of mass. Sequential standard model W′ bosons with masses between 700 and 940 GeV are excluded. In the Randall-Sundrum model for graviton resonances with a coupling parameter of 0.05, masses between 750 and 880 GeV are also exclude