ABSTRACT
The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification.
ABSTRACT
A priori prediction of phase stability of materials is a challenging practice, requiring knowledge of all energetically competing structures at formation conditions. Large materials repositories-housing properties of both experimental and hypothetical compounds-offer a path to prediction through the construction of informatics-based, ab initio phase diagrams. However, limited access to relevant data and software infrastructure has rendered thermodynamic characterizations largely peripheral, despite their continued success in dictating synthesizability. Herein, a new module is presented for autonomous thermodynamic stability analysis, implemented within the open-source, ab initio framework AFLOW. Powered by the AFLUX Search-API, AFLOW-CHULL leverages data of more than 1.8 million compounds characterized in the AFLOW.org repository, and can be employed locally from any UNIX-like computer. The module integrates a range of functionality: the identification of stable phases and equivalent structures, phase coexistence, measures for robust stability, and determination of decomposition reactions. As a proof of concept, thermodynamic characterizations have been performed for more than 1300 binary and ternary systems, enabling the identification of several candidate phases for synthesis based on their relative stability criterion-including 17 promising C15 b-type structures and 2 half-Heuslers. In addition to a full report included herein, an interactive, online web application has been developed showcasing the results of the analysis and is located at aflow.org/aflow-chull .
Subject(s)
Informatics , Software , Thermodynamics , Computer Simulation , Drug Discovery , Materials Science , Models, ChemicalABSTRACT
α-synuclein (aS) is a natively unfolded pre-synaptic protein found in all Parkinson's disease patients as the major component of fibrillar plaques. Metal ions, and especially Cu(II), have been demonstrated to accelerate aggregation of aS into fibrillar plaques, the precursors to Lewy bodies. In this work, copper binding to aS is investigated by a combination of quantum and molecular mechanics simulations. Starting from the experimentally observed attachment site, several optimized structures of Cu-binding geometries are examined. The most energetically favorable attachment results in significant allosteric changes, making aS more susceptible to misfolding. Indeed, an inverse kinematics investigation of the configuration space uncovers a dynamically stable ß-sheet conformation of Cu-aS that serves as a nucleation point for a second ß-strand. Based on these findings, we propose an atomistic mechanism of copper-induced misfolding of aS as an initial event in the formation of Lewy bodies and thus in PD pathogenesis.
