Band gap prediction for large organic crystal structures with machine learning

Machine-learning models are capable of capturing the structure-property relationship from a dataset of computationally demanding ab initio calculations. Over the past two years, the Organic Materials Database (OMDB) has hosted a growing number of calculated electronic properties of previously synthesized organic crystal structures. The complexity of the organic crystals contained within the OMDB, which have on average 82 atoms per unit cell, makes this database a challenging platform for machine learning applications. In this paper, the focus is on predicting the band gap which represents one of the basic properties of a crystalline materials. With this aim, a consistent dataset of 12 500 crystal structures and their corresponding DFT band gap are released, freely available for download at https://omdb.mathub.io/dataset. An ensemble of two state-of-the-art models reach a mean absolute error (MAE) of 0.388 eV, which corresponds to a percentage error of 13% for an average band gap of 3.05 eV. Finally, the trained models are employed to predict the band gap for 260 092 materials contained within the Crystallography Open Database (COD) and made available online so that the predictions can be obtained for any arbitrary crystal structure uploaded by a user.Comment: 10 pages, 6 figure

Online Search Tool for Graphical Patterns in Electronic Band Structures

We present an online graphical pattern search tool for electronic band structure data contained within the Organic Materials Database (OMDB) available at https://omdb.diracmaterials.org/search/pattern. The tool is capable of finding user-specified graphical patterns in the collection of thousands of band structures from high-throughput ab initio calculations in the online regime. Using this tool, it only takes a few seconds to find an arbitrary graphical pattern within the ten electronic bands near the Fermi level for 26,739 organic crystals. The tool can be used to find realizations of functional materials characterized by a specific pattern in their electronic structure, for example, Dirac materials, characterized by a linear crossing of bands; topological insulators, characterized by a "Mexican hat" pattern or an effectively free electron gas, characterized by a parabolic dispersion. The source code of the developed tool is freely available at https://github.com/OrganicMaterialsDatabase/EBS-search and can be transferred to any other electronic band structure database. The approach allows for an automatic online analysis of a large collection of band structures where the amount of data makes its manual inspection impracticable.Comment: 8 pages, 8 figure

Wonderen in de Wieringermeer; groei van beuk, es, esdoorn en eik in fantastisch bos

Hoofdlijnen uit de Staatsbosbeheer studie over de ontwikkeling van loofhout in het Robbenoordbos. Het gehele bos is na de inundatie weer geheel ingeplant in de oorspronkelijke opzet. De studie vermeldt groei, ondergroei, bodemgesteldheid, gemengd bo

Functional analysis of the SRV-1 RNA frameshifting pseudoknot

Simian retrovirus type-1 uses programmed ribosomal frameshifting to control expression of the Gag-Pol polyprotein from overlapping gag and pol open-reading frames. The frameshifting signal consists of a heptanucleotide slippery sequence and a downstream-located 12-base pair pseudoknot. The solution structure of this pseudoknot, previously solved by NMR [Michiels,P.J., Versleijen,A.A., Verlaan,P.W., Pleij,C.W., Hilbers,C.W. and Heus,H.A. (2001) Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting. J. Mol. Biol., 310, 1109–1123] has a classical H-type fold and forms an extended triple helix by interactions between loop 2 and the minor groove of stem 1 involving base–base and base–sugar contacts. A mutational analysis was performed to test the functional importance of the triple helix for −1 frameshifting in vitro. Changing bases in L2 or base pairs in S1 involved in a base triple resulted in a 2- to 5-fold decrease in frameshifting efficiency. Alterations in the length of L2 had adverse effects on frameshifting. The in vitro effects were well reproduced in vivo, although the effect of enlarging L2 was more dramatic in vivo. The putative role of refolding kinetics of frameshifter pseudoknots is discussed. Overall, the data emphasize the role of the triple helix in −1 frameshifting

Materials Informatics for Dark Matter Detection

Dark Matter particles are commonly assumed to be weakly interacting massive particles (WIMPs) with a mass in the GeV to TeV range. However, recent interest has shifted towards lighter WIMPs, which are more difficult to probe experimentally. A detection of sub-GeV WIMPs would require the use of small gap materials in sensors. Using recent estimates of the WIMP mass, we identify the relevant target space towards small gap materials (100-10 meV). Dirac Materials, a class of small- or zero-gap materials, emerge as natural candidates for sensors for Dark Matter detection. We propose the use of informatics tools to rapidly assay materials band structures to search for small gap semiconductors and semimetals, rather than focusing on a few preselected compounds. As a specific example of the proposed strategy, we use the organic materials database (omdb.diracmaterials.org) to identify organic candidates for sensors: the narrow band gap semiconductors BNQ-TTF and DEBTTT with gaps of 40 and 38 meV, and the Dirac-line semimetal (BEDT-TTF)$\cdot$Br which exhibits a tiny gap of $\approx$ 50 meV when spin-orbit coupling is included. We outline a novel and powerful approach to search for dark matter detection sensor materials by means of a rapid assay of materials using informatics tools.Comment: 5 pages, 3 figure

Computational modeling of the structure-function relationship in human placental terminal villi.

Placental oxygen transport takes place at the final branches of the villous tree and is dictated by the relative arrangement of the maternal and fetal circulations. Modeling techniques have failed to accurately assess the structure-function relationship in the terminal villi due to the geometrical complexity. Three-dimensional blood flow and oxygen transport was modeled in four terminal villi reconstructed from confocal image stacks. The blood flow was analyzed along the center lines of capillary segments and the effect of the variability in capillary diameter, tortuosity and branching was investigated. Additionally, a validation study was performed to corroborate the simulation results. The results show how capillary variations impact motion of the fetal blood, and how their bends and dilatations can decelerate the flow by up to 80%. Vortical flow is also demonstrated not to develop in the fetal capillaries. The different geometries are shown to dictate the transport of gases with differences of over 100% in the oxygen flux between samples. Capillary variations are key for efficient oxygen uptake by the fetus; they allow the blood to decelerate where the villous membrane is thinnest allowing for a better oxygenation, but also by reducing the vessel diameter they carry the oxygenated blood away fast. The methodology employed herein could become a platform to simulate complicated in-vivo and in-vitro scenarios of pregnancy complications.The first author gratefully acknowledges the generous support of Centre for Trophoblast Research, University of Cambridge, UK, which funded this work

Probing the plateau-insulator quantum phase transition in the quantum Hall regime

We report quantum Hall experiments on the plateau-insulator transition in a low mobility In_{.53} Ga_{.47} As/InP heterostructure. The data for the longitudinal resistance \rho_{xx} follow an exponential law and we extract a critical exponent \kappa= .55 \pm .05 which is slightly different from the established value \kappa = .42 \pm .04 for the plateau transitions. Upon correction for inhomogeneity effects, which cause the critical conductance \sigma_{xx}^* to depend marginally on temperature, our data indicate that the plateau-plateau and plateau- insulator transitions are in the same universality class.Comment: 4 pages, 4 figures (.eps