Overlay databank unlocks data-driven analyses of biomolecules for all.

Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank-a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due to their intrinsic disorder and complex phase behaviour. While MD simulations have been useful in understanding membrane systems, they require significant computational resources and often suffer from inaccuracies in model parameters. Here, we demonstrate how programmable interface for flexible implementation of data-driven and machine learning applications, and rapid access to simulation data through a graphical user interface, unlock possibilities beyond current MD simulation and experimental studies to understand cellular membranes. The proposed overlay databank concept can be further applied to other biomolecules, as well as in other fields where similar barriers hinder the AI revolution.

Formation of a Single-Crystal Aluminum-Based MOF Nanowire with Graphene Oxide Nanoscrolls as Structure-Directing Agents.

An innovative strategy is proposed to synthesize single-crystal nanowires (NWs) of the Al3+ dicarboxylate MIL-69(Al) MOF by using graphene oxide nanoscrolls as structure-directing agents. MIL-69(Al) NWs with an average diameter of 70±20 nm and lengths up to 2 µm were found to preferentially grow along the [001] crystallographic direction. Advanced characterization methods (electron diffraction, TEM, STEM-HAADF, SEM, XPS) and molecular modeling revealed the mechanism of formation of MIL-69(Al) NWs involving size-confinement and templating effects. The formation of MIL-69(Al) seeds and the self-scroll of GO sheets followed by the anisotropic growth of MIL-69(Al) crystals are mediated by specific GO sheets/MOF interactions. This study delivers an unprecedented approach to control the design of 1D MOF nanostructures and superstructures.

Understanding of the Graphene Oxide/Metal-Organic Framework Interface at the Atomistic Scale.

An atomistic model of the metal-organic framework (MOF) ZIF-8/graphene oxide (GO) interface has been constructed using a combination of density functional theory calculations and force-field-based molecular dynamics simulations. Two microscopic models of GO were constructed integrating basal plane and both basal and edge plane functional groups, called GO-OH and GO-CO2H, respectively. Analysis of the MOF/GO site-to-site interactions, surface coverage, and GO conformation/stiffness and a full characterization of the interfacial region is provided with a special emphasis on the influence of the chemical composition of GO. It was evidenced that the structure of the GO/ZIF-8 composite at the interface is stabilized by a relatively homogeneous set of interactions between the hydrogen atoms of the -NH and -OH terminal functions of ZIF-8 and the oxygen atoms of the epoxy, hydroxyl, and carboxylic groups of GO, leading to an optimal coverage of the MOF surface by GO. Such a scenario implies a significant distortion of the first GO layer brought into contact with the MOF surface, leading to an interfacial region with a relatively small width. This computational exploration strongly suggests that a very good compatibility between these two components would lead, in turn, to the preparation of defect-free ZIF-8/GO films. These predictions are correlated with an experimental effort that consists of successfully prepared homogeneous MOF/GO films that were further characterized by transmission electron microscopy and mechanical testing.